From 998c053741415ca06a8b1b5d9f034553214d0fb1 Mon Sep 17 00:00:00 2001
From: "piotr.gawron" <piotr.gawron@uni-new>
Date: Tue, 20 Sep 2016 15:27:14 +0200
Subject: [PATCH] new lines issue

---
 .../applicationContext-annotation.xml         |   90 +-
 .../annotation/AllAnnotationTests.java        |   36 +-
 .../annotation/AnnotationTestFunctions.java   |  594 +-
 .../src/test/resources/log4j.properties       |   44 +-
 .../resources/test-applicationContext.xml     |   34 +-
 .../common/EventStorageLoggerAppender.java    |  280 +-
 .../common/HttpConnectionMethodType.java      |   40 +-
 .../java/lcsb/mapviewer/common/MimeType.java  |  172 +-
 .../lcsb/mapviewer/common/ObjectUtils.java    |  104 +-
 .../main/java/lcsb/mapviewer/common/Pair.java |  166 +-
 .../mapviewer/common/SystemClipboard.java     |  126 +-
 .../lcsb/mapviewer/common/TextFileUtils.java  |  112 +-
 .../java/lcsb/mapviewer/common/XmlParser.java |  714 +-
 .../lcsb/mapviewer/common/AllCommonTests.java |   54 +-
 .../EventStorageLoggerAppenderTest.java       |  116 +-
 .../common/HttpConnectionMethodTypeTest.java  |   58 +-
 .../lcsb/mapviewer/common/MimeTypeTest.java   |   64 +-
 .../mapviewer/common/ObjectUtilsTest.java     |  116 +-
 .../java/lcsb/mapviewer/common/PairTest.java  |  140 +-
 .../mapviewer/common/SystemClipboardTest.java |  196 +-
 .../mapviewer/common/TextFileUtilsTest.java   |  152 +-
 .../lcsb/mapviewer/common/XmlParserTest.java  |  948 +-
 .../java/lcsb/mapviewer/run/BellExport.java   |  280 +-
 .../lcsb/mapviewer/run/ConsoleConverter.java  |  934 +-
 .../lcsb/mapviewer/run/PdMapAnnotations.java  |  164 +-
 .../mapviewer/run/ReactomeComparison.java     |  810 +-
 .../lcsb/mapviewer/run/ReactomeExport.java    | 1232 +--
 .../lcsb/mapviewer/run/VibineSnippet.java     |  232 +-
 .../mapviewer/run/PdMapAnnotationsTest.java   |   80 +-
 .../layouts/PD substantia nigra.txt           | 8682 ++++++++---------
 .../pd_full/PD_151217_2/layouts/ageing.txt    |  830 +-
 .../layouts/PD substantia nigra.txt           | 8682 ++++++++---------
 .../pd_full/PD_160714_2/layouts/ageing.txt    |  830 +-
 .../src/test/resources/log4j.properties       |   42 +-
 .../testFiles/annotation/invalid_rdf.xml      |    2 +-
 .../testFiles/annotation/invalid_rdf2.xml     |   18 +-
 .../testFiles/annotation/invalid_rdf3.xml     |   18 +-
 .../testFiles/annotation/invalid_rdf4.xml     |   16 +-
 .../testFiles/invalid/antisense_rna.xml       |   30 +-
 .../testFiles/invalid/antisense_rna2.xml      |   30 +-
 .../testFiles/invalid/antisense_rna3.xml      |   28 +-
 .../testFiles/invalid/antisense_rna4.xml      |   32 +-
 .../invalid/antisense_rna_collection.xml      |    4 +-
 .../testFiles/invalid/block_diagrams.xml      |    6 +-
 .../testFiles/invalid/compartment.xml         |    8 +-
 .../testFiles/invalid/compartment2.xml        |   16 +-
 .../testFiles/invalid/compartment3.xml        |   16 +-
 .../testFiles/invalid/compartment_alias.xml   |   14 +-
 .../testFiles/invalid/compartment_alias2.xml  |   16 +-
 .../testFiles/invalid/compartment_alias3.xml  |   16 +-
 .../invalid/compartment_alias_collection.xml  |   54 +-
 .../invalid/complex_alias_collection.xml      |  132 +-
 .../testFiles/invalid/gene_collection.xml     |    4 +-
 .../testFiles/invalid/group_collection.xml    |    8 +-
 .../testFiles/invalid/group_collection2.xml   |    6 +-
 .../testFiles/invalid/group_collection3.xml   |   10 +-
 .../invalid/included_species_collection.xml   |  104 +-
 .../invalid/included_species_collection2.xml  |   90 +-
 .../invalid/included_species_collection3.xml  |   90 +-
 .../invalid/included_species_collection4.xml  |   28 +-
 .../invalid/included_species_collection5.xml  |    4 +-
 .../invalid/included_species_collection6.xml  |   26 +-
 .../invalid/invalid_complex_alias.xml         |   42 +-
 .../invalid/invalid_complex_alias2.xml        |    6 +-
 .../invalid/invalid_complex_alias3.xml        |   42 +-
 .../invalid/invalid_complex_alias4.xml        |   42 +-
 .../invalid/invalid_complex_alias5.xml        |   42 +-
 .../testFiles/invalid/invalid_gene_1.xml      |    4 +-
 .../testFiles/invalid/invalid_gene_2.xml      |   10 +-
 .../invalid/invalid_modification_residue.xml  |    6 +-
 .../invalid/invalid_sbml_protein.xml          |    2 +-
 .../invalid/invalid_sbml_protein10.xml        |   20 +-
 .../invalid/invalid_sbml_protein11.xml        |   20 +-
 .../invalid/invalid_sbml_protein12.xml        |   20 +-
 .../invalid/invalid_sbml_protein13.xml        |   22 +-
 .../invalid/invalid_sbml_protein14.xml        |   24 +-
 .../invalid/invalid_sbml_protein2.xml         |    4 +-
 .../invalid/invalid_sbml_protein3.xml         |    8 +-
 .../invalid/invalid_sbml_protein4.xml         |    6 +-
 .../invalid/invalid_sbml_protein5.xml         |   12 +-
 .../invalid/invalid_sbml_protein6.xml         |   10 +-
 .../invalid/invalid_sbml_protein7.xml         |   20 +-
 .../invalid/invalid_sbml_protein8.xml         |   18 +-
 .../invalid/invalid_sbml_protein9.xml         |   20 +-
 .../testFiles/invalid/layer.xml               |   70 +-
 .../testFiles/invalid/layer2.xml              |   68 +-
 .../testFiles/invalid/layer3.xml              |   70 +-
 .../testFiles/invalid/layer4.xml              |   70 +-
 .../testFiles/invalid/layer5.xml              |   70 +-
 .../testFiles/invalid/layer_collection.xml    |   72 +-
 .../testFiles/invalid/layer_line.xml          |   10 +-
 .../testFiles/invalid/layer_oval.xml          |   12 +-
 .../testFiles/invalid/layer_square.xml        |   12 +-
 .../testFiles/invalid/layer_text.xml          |   18 +-
 .../testFiles/invalid/listOfCompartments.xml  |   22 +-
 .../invalid/list_of_species_alias.xml         | 1106 +--
 .../invalid/list_of_species_alias2.xml        | 1108 +--
 .../testFiles/invalid/protein.xml             |   30 +-
 .../testFiles/invalid/protein2.xml            |   32 +-
 .../testFiles/invalid/protein3.xml            |   32 +-
 .../testFiles/invalid/protein4.xml            |   34 +-
 .../testFiles/invalid/protein5.xml            |   34 +-
 .../testFiles/invalid/protein6.xml            |   34 +-
 .../testFiles/invalid/protein_collection.xml  |    4 +-
 .../testFiles/invalid/rna.xml                 |   10 +-
 .../testFiles/invalid/rna2.xml                |   10 +-
 .../testFiles/invalid/rna3.xml                |   12 +-
 .../testFiles/invalid/rna_collection.xml      |    8 +-
 .../testFiles/invalid/sbml_collection.xml     |  202 +-
 .../testFiles/invalid/species_alias.xml       |   36 +-
 .../testFiles/invalid/species_alias2.xml      |   38 +-
 .../testFiles/invalid/species_alias3.xml      |   36 +-
 .../testFiles/invalid/species_alias4.xml      |   36 +-
 .../testFiles/invalid/species_alias5.xml      |   36 +-
 .../testFiles/invalid/species_alias6.xml      |   36 +-
 .../invalid/species_alias_collection.xml      |  158 +-
 .../xmlNodeTestExamples/block_diagrams.xml    |   30 +-
 .../cd_complex_alias_with_empty_state.xml     |   42 +-
 .../testFiles/xmlNodeTestExamples/notes.xml   |   20 +-
 .../testFiles/xmlNodeTestExamples/notes2.xml  |   46 +-
 .../testFiles/xmlNodeTestExamples/notes3.xml  |   22 +-
 .../testFiles/xmlNodeTestExamples/notes4.xml  |   22 +-
 .../testFiles/xmlNodeTestExamples/notes5.xml  |   84 +-
 .../notes_invalid_charge.xml                  |   22 +-
 .../xmlNodeTestExamples/sbml_gene.xml         |  144 +-
 .../xmlNodeTestExamples/sbml_ion.xml          |  246 +-
 .../xmlNodeTestExamples/sbml_protein.xml      |  124 +-
 .../xmlNodeTestExamples/sbml_rna.xml          |  154 +-
 .../xmlNodeTestExamples/species_alias.xml     |   36 +-
 .../species_alias_with_font.xml               |   38 +-
 .../species_alias_without_state.xml           |   36 +-
 .../converter/ComplexZipConverter.java        |  842 +-
 .../lcsb/mapviewer/converter/IConverter.java  |  164 +-
 .../lcsb/mapviewer/converter/AllTests.java    |   26 +-
 .../converter/ComplexZipConverterTest.java    | 1220 +--
 converter/tmp/test.png                        |  Bin 0 -> 10796 bytes
 .../mapviewer/commands/ColorModelCommand.java |  712 +-
 .../commands/CommandExecutionException.java   |  110 +-
 .../lcsb/mapviewer/commands/CopyCommand.java  |  952 +-
 .../commands/CreateHierarchyCommand.java      | 1094 +--
 .../commands/ColorModelCommandTest.java       |  682 +-
 .../commands/CommandTestFunctions.java        |  168 +-
 .../mapviewer/commands/CopyCommandTest.java   |  688 +-
 .../commands/CreateHierarchyCommandTest.java  |  570 +-
 .../java/lcsb/mapviewer/model/Project.java    |  736 +-
 .../lcsb/mapviewer/model/ProjectStatus.java   |  220 +-
 .../test/java/lcsb/mapviewer/AllTests.java    |   32 +-
 .../lcsb/mapviewer/ModelTestFunctions.java    |   64 +-
 .../lcsb/mapviewer/model/AllModelTests.java   |   48 +-
 .../mapviewer/model/ProjectStatusTest.java    |   60 +-
 .../lcsb/mapviewer/model/ProjectTest.java     |  260 +-
 151 files changed, 20810 insertions(+), 20810 deletions(-)
 create mode 100644 converter/tmp/test.png

diff --git a/annotation/src/main/resources/applicationContext-annotation.xml b/annotation/src/main/resources/applicationContext-annotation.xml
index 98f2dfa11b..8d26b7a2b6 100644
--- a/annotation/src/main/resources/applicationContext-annotation.xml
+++ b/annotation/src/main/resources/applicationContext-annotation.xml
@@ -1,46 +1,46 @@
-<beans xmlns="http://www.springframework.org/schema/beans"
-	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xmlns:tx="http://www.springframework.org/schema/tx"
-	xmlns:context="http://www.springframework.org/schema/context"
-	xsi:schemaLocation="http://www.springframework.org/schema/beans
-		http://www.springframework.org/schema/beans/spring-beans-4.0.xsd
-		http://www.springframework.org/schema/tx 
-		http://www.springframework.org/schema/tx/spring-tx-4.0.xsd
-		http://www.springframework.org/schema/context
-		http://www.springframework.org/schema/context/spring-context.xsd">
-
-	
-	<!-- Annotation services -->
-	
-	<!-- Annotators -->
-	<bean id="BiocompendiumAnnotator" class="lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator"/>
-	<bean id="ChebiAnnotator" class="lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator"/>
-	<bean id="EnsemblAnnotator" class="lcsb.mapviewer.annotation.services.annotators.EnsemblAnnotator"/>
-	<bean id="EntrezAnnotator" class="lcsb.mapviewer.annotation.services.annotators.EntrezAnnotator"/>
-	<bean id="GoAnnotator" class="lcsb.mapviewer.annotation.services.annotators.GoAnnotator"/>
-	<bean id="HgncAnnotator" class="lcsb.mapviewer.annotation.services.annotators.HgncAnnotator"/>
-	<bean id="ReconAnnotator" class="lcsb.mapviewer.annotation.services.annotators.ReconAnnotator"/>
-	<bean id="UniprotAnnotator" class="lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator"/>
-	
-	<bean id="ChEMBLParser" class="lcsb.mapviewer.annotation.services.ChEMBLParser"/>
-	<bean id="ChemicalParser" class="lcsb.mapviewer.annotation.services.ChemicalParser"/>
-	<bean id="DrugbankHTMLParser" class="lcsb.mapviewer.annotation.services.DrugbankHTMLParser"/>
-	<bean id="MiriamConnector" class="lcsb.mapviewer.annotation.services.MiriamConnector"/>
-	<bean id="ModelAnnotator" class="lcsb.mapviewer.annotation.services.ModelAnnotator"/>
-	<bean id="MeSHParser" class="lcsb.mapviewer.annotation.services.MeSHParser"/>
-	<bean id="PubmedParser" class="lcsb.mapviewer.annotation.services.PubmedParser"/>
-	<bean id="TaxonomyBackend" class="lcsb.mapviewer.annotation.services.TaxonomyBackend"/>
-	<bean id="MiRNAParser" class="lcsb.mapviewer.annotation.services.MiRNAParser"/>
-
-	<!-- Reference Genome services -->
-
-	<bean id="UcscReferenceGenomeConnector" class="lcsb.mapviewer.annotation.services.genome.UcscReferenceGenomeConnector"/>
-	
-	<!-- Cache services -->
-	
-	<bean id="GeneralCache" class="lcsb.mapviewer.annotation.cache.GeneralCache"/>
-	<bean id="PermanentDatabaseLevelCache" class="lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache"/>
-	<bean id="BigFileCache" class="lcsb.mapviewer.annotation.cache.BigFileCache"/>
-	
-
+<beans xmlns="http://www.springframework.org/schema/beans"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xmlns:tx="http://www.springframework.org/schema/tx"
+	xmlns:context="http://www.springframework.org/schema/context"
+	xsi:schemaLocation="http://www.springframework.org/schema/beans
+		http://www.springframework.org/schema/beans/spring-beans-4.0.xsd
+		http://www.springframework.org/schema/tx 
+		http://www.springframework.org/schema/tx/spring-tx-4.0.xsd
+		http://www.springframework.org/schema/context
+		http://www.springframework.org/schema/context/spring-context.xsd">
+
+	
+	<!-- Annotation services -->
+	
+	<!-- Annotators -->
+	<bean id="BiocompendiumAnnotator" class="lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator"/>
+	<bean id="ChebiAnnotator" class="lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator"/>
+	<bean id="EnsemblAnnotator" class="lcsb.mapviewer.annotation.services.annotators.EnsemblAnnotator"/>
+	<bean id="EntrezAnnotator" class="lcsb.mapviewer.annotation.services.annotators.EntrezAnnotator"/>
+	<bean id="GoAnnotator" class="lcsb.mapviewer.annotation.services.annotators.GoAnnotator"/>
+	<bean id="HgncAnnotator" class="lcsb.mapviewer.annotation.services.annotators.HgncAnnotator"/>
+	<bean id="ReconAnnotator" class="lcsb.mapviewer.annotation.services.annotators.ReconAnnotator"/>
+	<bean id="UniprotAnnotator" class="lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator"/>
+	
+	<bean id="ChEMBLParser" class="lcsb.mapviewer.annotation.services.ChEMBLParser"/>
+	<bean id="ChemicalParser" class="lcsb.mapviewer.annotation.services.ChemicalParser"/>
+	<bean id="DrugbankHTMLParser" class="lcsb.mapviewer.annotation.services.DrugbankHTMLParser"/>
+	<bean id="MiriamConnector" class="lcsb.mapviewer.annotation.services.MiriamConnector"/>
+	<bean id="ModelAnnotator" class="lcsb.mapviewer.annotation.services.ModelAnnotator"/>
+	<bean id="MeSHParser" class="lcsb.mapviewer.annotation.services.MeSHParser"/>
+	<bean id="PubmedParser" class="lcsb.mapviewer.annotation.services.PubmedParser"/>
+	<bean id="TaxonomyBackend" class="lcsb.mapviewer.annotation.services.TaxonomyBackend"/>
+	<bean id="MiRNAParser" class="lcsb.mapviewer.annotation.services.MiRNAParser"/>
+
+	<!-- Reference Genome services -->
+
+	<bean id="UcscReferenceGenomeConnector" class="lcsb.mapviewer.annotation.services.genome.UcscReferenceGenomeConnector"/>
+	
+	<!-- Cache services -->
+	
+	<bean id="GeneralCache" class="lcsb.mapviewer.annotation.cache.GeneralCache"/>
+	<bean id="PermanentDatabaseLevelCache" class="lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache"/>
+	<bean id="BigFileCache" class="lcsb.mapviewer.annotation.cache.BigFileCache"/>
+	
+
 </beans>
\ No newline at end of file
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java
index 4a05c389f6..f14e65dd4e 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java
@@ -1,18 +1,18 @@
-package lcsb.mapviewer.annotation;
-
-import lcsb.mapviewer.annotation.cache.AllCacheTests;
-import lcsb.mapviewer.annotation.data.AllDataTests;
-import lcsb.mapviewer.annotation.services.AllServicesTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllCacheTests.class, //
-		AllDataTests.class, //
-		AllServicesTests.class, //
-})
-
-public class AllAnnotationTests {
-}
+package lcsb.mapviewer.annotation;
+
+import lcsb.mapviewer.annotation.cache.AllCacheTests;
+import lcsb.mapviewer.annotation.data.AllDataTests;
+import lcsb.mapviewer.annotation.services.AllServicesTests;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllCacheTests.class, //
+		AllDataTests.class, //
+		AllServicesTests.class, //
+})
+
+public class AllAnnotationTests {
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
index 829ed417ed..2064bb9443 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
@@ -1,297 +1,297 @@
-package lcsb.mapviewer.annotation;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.io.UnsupportedEncodingException;
-import java.net.HttpURLConnection;
-import java.net.URL;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.test.annotation.Rollback;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.test.context.junit4.AbstractTransactionalJUnit4SpringContextTests;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.transaction.annotation.Transactional;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
-
-@Transactional(value = "txManager")
-@Rollback(false)
-@ContextConfiguration(locations = { //
-		"/applicationContext-annotation.xml", //
-		"/applicationContext-persist.xml", //
-		"/test-applicationContext.xml", //
-})
-@RunWith(SpringJUnit4ClassRunner.class)
-public abstract class AnnotationTestFunctions extends AbstractTransactionalJUnit4SpringContextTests {
-
-	@Autowired
-	protected PermanentDatabaseLevelCacheInterface cache;
-
-	@Autowired
-	protected CacheTypeDao												 cacheTypeDao;
-
-	@Autowired
-	protected DbUtils															 dbUtils;
-
-	private Logger																 logger	= Logger.getLogger(AnnotationTestFunctions.class);
-
-	private EventStorageLoggerAppender						 appender;
-
-	@Before
-	public final void _setUp() throws Exception {
-		Logger.getRootLogger().removeAppender(appender);
-		appender = new EventStorageLoggerAppender(false);
-		Logger.getRootLogger().addAppender(appender);
-	}
-
-	@After
-	public final void _tearDown() throws Exception {
-		Logger.getRootLogger().removeAppender(appender);
-	}
-
-	protected List<LoggingEvent> getWarnings() {
-		return appender.getWarnings();
-	}
-
-	protected List<LoggingEvent> getErrors() {
-		return appender.getErrors();
-	}
-
-	protected List<LoggingEvent> getFatals() {
-		return appender.getFatals();
-	}
-
-	protected String readFile(String file) throws IOException {
-		StringBuilder stringBuilder = new StringBuilder();
-		BufferedReader reader = new BufferedReader(new FileReader(file));
-		try {
-			String line = null;
-			String ls = System.getProperty("line.separator");
-
-			while ((line = reader.readLine()) != null) {
-				stringBuilder.append(line);
-				stringBuilder.append(ls);
-			}
-		} finally {
-			reader.close();
-		}
-
-		return stringBuilder.toString();
-	}
-
-	protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
-		InputSource is = new InputSource();
-		is.setCharacterStream(new StringReader(text));
-		return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
-	}
-
-	protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
-		File file = new File(fileName);
-		InputStream inputStream = new FileInputStream(file);
-		Reader reader = null;
-		try {
-			reader = new InputStreamReader(inputStream, "UTF-8");
-			InputSource is = new InputSource(reader);
-
-			Document result = getXmlDocumentFromInputSource(is);
-			inputStream.close();
-			return result;
-		} catch (UnsupportedEncodingException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-		return null;
-	}
-
-	protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
-		DocumentBuilder db;
-		try {
-			db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
-		} catch (ParserConfigurationException e) {
-			throw new InvalidXmlSchemaException("Problem with xml parser");
-		}
-		Document doc = null;
-		try {
-			doc = db.parse(stream);
-		} catch (SAXException e) {
-			logger.error(e);
-		} catch (IOException e) {
-			logger.error(e);
-		}
-		return doc;
-	}
-
-	private static Map<String, Model> models = new HashMap<String, Model>();
-
-	protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
-		if (!fromCache) {
-			logger.debug("File without cache: " + fileName);
-			return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
-		}
-		Model result = AnnotationTestFunctions.models.get(fileName);
-		if (result == null) {
-			logger.debug("File to cache: " + fileName);
-
-			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
-			AnnotationTestFunctions.models.put(fileName, result);
-		}
-		return result;
-	}
-
-	protected String createTmpFileName() {
-		try {
-			File f = File.createTempFile("prefix", ".txt");
-			String filename = f.getName();
-			f.delete();
-			return filename;
-		} catch (IOException e) {
-			e.printStackTrace();
-			return null;
-		}
-	}
-
-	protected String nodeToString(Node node) {
-		return nodeToString(node, false);
-	}
-
-	protected String nodeToString(Node node, boolean includeHeadNode) {
-		if (node == null)
-			return null;
-		StringWriter sw = new StringWriter();
-		try {
-			Transformer t = TransformerFactory.newInstance().newTransformer();
-			t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
-			t.setOutputProperty(OutputKeys.INDENT, "yes");
-			t.setOutputProperty(OutputKeys.METHOD, "xml");
-
-			NodeList list = node.getChildNodes();
-			for (int i = 0; i < list.getLength(); i++) {
-				Node element = list.item(i);
-				t.transform(new DOMSource(element), new StreamResult(sw));
-			}
-		} catch (TransformerException te) {
-			logger.debug("nodeToString Transformer Exception");
-		}
-		if (includeHeadNode) {
-			return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
-		}
-		return sw.toString();
-	}
-
-	protected boolean equalFiles(String fileA, String fileB) throws IOException {
-		int BLOCK_SIZE = 65536;
-		FileInputStream inputStreamA = new FileInputStream(fileA);
-		FileInputStream inputStreamB = new FileInputStream(fileB);
-		// vary BLOCK_SIZE to suit yourself.
-		// it should probably a factor or multiple of the size of a disk
-		// sector/cluster.
-		// Note that your max heap size may need to be adjused
-		// if you have a very big block size or lots of these comparators.
-
-		// assume inputStreamA and inputStreamB are streams from your two files.
-		byte[] streamABlock = new byte[BLOCK_SIZE];
-		byte[] streamBBlock = new byte[BLOCK_SIZE];
-		boolean match = true;
-		int bytesReadA = 0;
-		int bytesReadB = 0;
-		do {
-			bytesReadA = inputStreamA.read(streamABlock);
-			bytesReadB = inputStreamB.read(streamBBlock);
-			match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
-		} while (match && (bytesReadA > -1));
-		inputStreamA.close();
-		inputStreamB.close();
-		return match;
-	}
-
-	public File createTempDirectory() throws IOException {
-		final File temp;
-
-		temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
-
-		if (!(temp.delete())) {
-			throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
-		}
-
-		if (!(temp.mkdir())) {
-			throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
-		}
-
-		return (temp);
-	}
-
-	protected String getWebpage(String accessUrl) throws IOException {
-		String inputLine;
-		IOException exception = null;
-		for (int i = 0; i < 3; i++) {
-			try {
-				StringBuilder tmp = new StringBuilder();
-				URL url = new URL(accessUrl);
-				HttpURLConnection urlConn = (HttpURLConnection) url.openConnection();
-				urlConn.setRequestMethod("GET");
-				urlConn.connect();
-				BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
-				while ((inputLine = in.readLine()) != null) {
-					tmp.append(inputLine);
-				}
-				in.close();
-				return tmp.toString();
-			} catch (IOException e) {
-				exception = e;
-			}
-		}
-		throw exception;
-	}
-
-	protected void waitForRefreshCacheQueueToEmpty() throws InterruptedException {
-		while (cache.refreshIsBusy()) {
-			logger.debug(
-					"Waiting for refresh queue to empty. " + cache.getRefreshPendingQueueSize() + " pending. " + cache.getRefreshExecutingTasksSize()
-							+ " tasks are executed.");
-			Thread.sleep(300);
-		}
-	}
-
-}
+package lcsb.mapviewer.annotation;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.io.UnsupportedEncodingException;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.AbstractTransactionalJUnit4SpringContextTests;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.transaction.annotation.Transactional;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
+
+@Transactional(value = "txManager")
+@Rollback(false)
+@ContextConfiguration(locations = { //
+		"/applicationContext-annotation.xml", //
+		"/applicationContext-persist.xml", //
+		"/test-applicationContext.xml", //
+})
+@RunWith(SpringJUnit4ClassRunner.class)
+public abstract class AnnotationTestFunctions extends AbstractTransactionalJUnit4SpringContextTests {
+
+	@Autowired
+	protected PermanentDatabaseLevelCacheInterface cache;
+
+	@Autowired
+	protected CacheTypeDao												 cacheTypeDao;
+
+	@Autowired
+	protected DbUtils															 dbUtils;
+
+	private Logger																 logger	= Logger.getLogger(AnnotationTestFunctions.class);
+
+	private EventStorageLoggerAppender						 appender;
+
+	@Before
+	public final void _setUp() throws Exception {
+		Logger.getRootLogger().removeAppender(appender);
+		appender = new EventStorageLoggerAppender(false);
+		Logger.getRootLogger().addAppender(appender);
+	}
+
+	@After
+	public final void _tearDown() throws Exception {
+		Logger.getRootLogger().removeAppender(appender);
+	}
+
+	protected List<LoggingEvent> getWarnings() {
+		return appender.getWarnings();
+	}
+
+	protected List<LoggingEvent> getErrors() {
+		return appender.getErrors();
+	}
+
+	protected List<LoggingEvent> getFatals() {
+		return appender.getFatals();
+	}
+
+	protected String readFile(String file) throws IOException {
+		StringBuilder stringBuilder = new StringBuilder();
+		BufferedReader reader = new BufferedReader(new FileReader(file));
+		try {
+			String line = null;
+			String ls = System.getProperty("line.separator");
+
+			while ((line = reader.readLine()) != null) {
+				stringBuilder.append(line);
+				stringBuilder.append(ls);
+			}
+		} finally {
+			reader.close();
+		}
+
+		return stringBuilder.toString();
+	}
+
+	protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
+		InputSource is = new InputSource();
+		is.setCharacterStream(new StringReader(text));
+		return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
+	}
+
+	protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
+		File file = new File(fileName);
+		InputStream inputStream = new FileInputStream(file);
+		Reader reader = null;
+		try {
+			reader = new InputStreamReader(inputStream, "UTF-8");
+			InputSource is = new InputSource(reader);
+
+			Document result = getXmlDocumentFromInputSource(is);
+			inputStream.close();
+			return result;
+		} catch (UnsupportedEncodingException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return null;
+	}
+
+	protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
+		DocumentBuilder db;
+		try {
+			db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+		} catch (ParserConfigurationException e) {
+			throw new InvalidXmlSchemaException("Problem with xml parser");
+		}
+		Document doc = null;
+		try {
+			doc = db.parse(stream);
+		} catch (SAXException e) {
+			logger.error(e);
+		} catch (IOException e) {
+			logger.error(e);
+		}
+		return doc;
+	}
+
+	private static Map<String, Model> models = new HashMap<String, Model>();
+
+	protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
+		if (!fromCache) {
+			logger.debug("File without cache: " + fileName);
+			return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
+		}
+		Model result = AnnotationTestFunctions.models.get(fileName);
+		if (result == null) {
+			logger.debug("File to cache: " + fileName);
+
+			CellDesignerXmlParser parser = new CellDesignerXmlParser();
+			result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
+			AnnotationTestFunctions.models.put(fileName, result);
+		}
+		return result;
+	}
+
+	protected String createTmpFileName() {
+		try {
+			File f = File.createTempFile("prefix", ".txt");
+			String filename = f.getName();
+			f.delete();
+			return filename;
+		} catch (IOException e) {
+			e.printStackTrace();
+			return null;
+		}
+	}
+
+	protected String nodeToString(Node node) {
+		return nodeToString(node, false);
+	}
+
+	protected String nodeToString(Node node, boolean includeHeadNode) {
+		if (node == null)
+			return null;
+		StringWriter sw = new StringWriter();
+		try {
+			Transformer t = TransformerFactory.newInstance().newTransformer();
+			t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+			t.setOutputProperty(OutputKeys.INDENT, "yes");
+			t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+			NodeList list = node.getChildNodes();
+			for (int i = 0; i < list.getLength(); i++) {
+				Node element = list.item(i);
+				t.transform(new DOMSource(element), new StreamResult(sw));
+			}
+		} catch (TransformerException te) {
+			logger.debug("nodeToString Transformer Exception");
+		}
+		if (includeHeadNode) {
+			return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+		}
+		return sw.toString();
+	}
+
+	protected boolean equalFiles(String fileA, String fileB) throws IOException {
+		int BLOCK_SIZE = 65536;
+		FileInputStream inputStreamA = new FileInputStream(fileA);
+		FileInputStream inputStreamB = new FileInputStream(fileB);
+		// vary BLOCK_SIZE to suit yourself.
+		// it should probably a factor or multiple of the size of a disk
+		// sector/cluster.
+		// Note that your max heap size may need to be adjused
+		// if you have a very big block size or lots of these comparators.
+
+		// assume inputStreamA and inputStreamB are streams from your two files.
+		byte[] streamABlock = new byte[BLOCK_SIZE];
+		byte[] streamBBlock = new byte[BLOCK_SIZE];
+		boolean match = true;
+		int bytesReadA = 0;
+		int bytesReadB = 0;
+		do {
+			bytesReadA = inputStreamA.read(streamABlock);
+			bytesReadB = inputStreamB.read(streamBBlock);
+			match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
+		} while (match && (bytesReadA > -1));
+		inputStreamA.close();
+		inputStreamB.close();
+		return match;
+	}
+
+	public File createTempDirectory() throws IOException {
+		final File temp;
+
+		temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
+
+		if (!(temp.delete())) {
+			throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
+		}
+
+		if (!(temp.mkdir())) {
+			throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
+		}
+
+		return (temp);
+	}
+
+	protected String getWebpage(String accessUrl) throws IOException {
+		String inputLine;
+		IOException exception = null;
+		for (int i = 0; i < 3; i++) {
+			try {
+				StringBuilder tmp = new StringBuilder();
+				URL url = new URL(accessUrl);
+				HttpURLConnection urlConn = (HttpURLConnection) url.openConnection();
+				urlConn.setRequestMethod("GET");
+				urlConn.connect();
+				BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
+
+				while ((inputLine = in.readLine()) != null) {
+					tmp.append(inputLine);
+				}
+				in.close();
+				return tmp.toString();
+			} catch (IOException e) {
+				exception = e;
+			}
+		}
+		throw exception;
+	}
+
+	protected void waitForRefreshCacheQueueToEmpty() throws InterruptedException {
+		while (cache.refreshIsBusy()) {
+			logger.debug(
+					"Waiting for refresh queue to empty. " + cache.getRefreshPendingQueueSize() + " pending. " + cache.getRefreshExecutingTasksSize()
+							+ " tasks are executed.");
+			Thread.sleep(300);
+		}
+	}
+
+}
diff --git a/annotation/src/test/resources/log4j.properties b/annotation/src/test/resources/log4j.properties
index e550f09e60..473855faa6 100644
--- a/annotation/src/test/resources/log4j.properties
+++ b/annotation/src/test/resources/log4j.properties
@@ -1,23 +1,23 @@
-#Set root logger 's level and its appender to an appender called CONSOLE which is defined below.
-log4j.rootLogger=info, CONSOLE
-
-#Set the behavior of the CONSOLE appender 
-log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
-log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
-log4j.appender.CONSOLE.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
-#log4j.appender.CONSOLE.layout.ConversionPattern=%m%n
-
-
-#Set the behavior of the FILE appender 
-log4j.appender.R=org.apache.log4j.FileAppender
-log4j.appender.R.File=${catalina.home}/logs/MapViewer.log
-log4j.appender.R.layout=org.apache.log4j.PatternLayout
-log4j.appender.R.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
-
-
-log4j.logger.org.springframework=warn
-log4j.logger.org.hibernate=warn
-log4j.logger.lcsb=debug
-log4j.logger.lcsb.mapviewer.persist.DbUtils=info
-log4j.logger.lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache=info
+#Set root logger 's level and its appender to an appender called CONSOLE which is defined below.
+log4j.rootLogger=info, CONSOLE
+
+#Set the behavior of the CONSOLE appender 
+log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
+log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
+log4j.appender.CONSOLE.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
+#log4j.appender.CONSOLE.layout.ConversionPattern=%m%n
+
+
+#Set the behavior of the FILE appender 
+log4j.appender.R=org.apache.log4j.FileAppender
+log4j.appender.R.File=${catalina.home}/logs/MapViewer.log
+log4j.appender.R.layout=org.apache.log4j.PatternLayout
+log4j.appender.R.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
+
+
+log4j.logger.org.springframework=warn
+log4j.logger.org.hibernate=warn
+log4j.logger.lcsb=debug
+log4j.logger.lcsb.mapviewer.persist.DbUtils=info
+log4j.logger.lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache=info
 log4j.logger.lcsb.mapviewer.annotation.cache.CachableInterface=info
\ No newline at end of file
diff --git a/annotation/src/test/resources/test-applicationContext.xml b/annotation/src/test/resources/test-applicationContext.xml
index cf221aca42..47dc97e5d9 100644
--- a/annotation/src/test/resources/test-applicationContext.xml
+++ b/annotation/src/test/resources/test-applicationContext.xml
@@ -1,17 +1,17 @@
-<beans xmlns="http://www.springframework.org/schema/beans"
-	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xmlns:tx="http://www.springframework.org/schema/tx"
-	xmlns:context="http://www.springframework.org/schema/context"
-	xsi:schemaLocation="http://www.springframework.org/schema/beans
-		http://www.springframework.org/schema/beans/spring-beans-4.0.xsd
-		http://www.springframework.org/schema/tx 
-		http://www.springframework.org/schema/tx/spring-tx-4.0.xsd
-		http://www.springframework.org/schema/context 
-		http://www.springframework.org/schema/context/spring-context-4.0.xsd">
-
-	<!-- Testing Password Encoder used for hashing passwords -->
-	<bean id="PasswordEncoder" class="org.springframework.security.crypto.password.NoOpPasswordEncoder"/>
-
-	<bean id="MockCacheInterface" class="lcsb.mapviewer.annotation.cache.MockCacheInterface"/>
-
-</beans>
+<beans xmlns="http://www.springframework.org/schema/beans"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xmlns:tx="http://www.springframework.org/schema/tx"
+	xmlns:context="http://www.springframework.org/schema/context"
+	xsi:schemaLocation="http://www.springframework.org/schema/beans
+		http://www.springframework.org/schema/beans/spring-beans-4.0.xsd
+		http://www.springframework.org/schema/tx 
+		http://www.springframework.org/schema/tx/spring-tx-4.0.xsd
+		http://www.springframework.org/schema/context 
+		http://www.springframework.org/schema/context/spring-context-4.0.xsd">
+
+	<!-- Testing Password Encoder used for hashing passwords -->
+	<bean id="PasswordEncoder" class="org.springframework.security.crypto.password.NoOpPasswordEncoder"/>
+
+	<bean id="MockCacheInterface" class="lcsb.mapviewer.annotation.cache.MockCacheInterface"/>
+
+</beans>
diff --git a/commons/src/main/java/lcsb/mapviewer/common/EventStorageLoggerAppender.java b/commons/src/main/java/lcsb/mapviewer/common/EventStorageLoggerAppender.java
index 705c545a5d..402e0437f5 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/EventStorageLoggerAppender.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/EventStorageLoggerAppender.java
@@ -1,140 +1,140 @@
-package lcsb.mapviewer.common;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Appender;
-import org.apache.log4j.AppenderSkeleton;
-import org.apache.log4j.Level;
-import org.apache.log4j.lf5.LogLevel;
-import org.apache.log4j.spi.LoggingEvent;
-
-/**
- * Custom log4j {@link Appender}. This class is used to store logs in the
- * memory. Such logs should be stored for short period of time. Only logs for
- * the {@link Thread} that created the object will be stored.
- * 
- * @author Piotr Gawron
- *
- */
-public class EventStorageLoggerAppender extends AppenderSkeleton {
-
-	/**
-	 * List of {@link LogLevel#DEBUG} logs.
-	 */
-	private List<LoggingEvent> debugEvents					= new ArrayList<>();
-
-	/**
-	 * List of {@link LogLevel#INFO} logs.
-	 */
-	private List<LoggingEvent> infoEvents						= new ArrayList<>();
-
-	/**
-	 * List of {@link LogLevel#WARN} logs.
-	 */
-	private List<LoggingEvent> warnEvents						= new ArrayList<>();
-
-	/**
-	 * List of {@link LogLevel#ERROR} logs.
-	 */
-	private List<LoggingEvent> errorEvents					= new ArrayList<>();
-
-	/**
-	 * List of {@link LogLevel#FATAL} logs.
-	 */
-	private List<LoggingEvent> fatalEvents					= new ArrayList<>();
-
-	/**
-	 * List of logs with unknown log level.
-	 */
-	private List<LoggingEvent> otherEvents					= new ArrayList<>();
-
-	/**
-	 * Identifier of {@link Thread} that created this object.
-	 */
-	private long							 threadId;
-
-	/**
-	 * Flag that describe if we log only entries for current thread (
-	 * <code>true</code>) or for all threads (<code>false</code>).
-	 */
-	private boolean						 currentThreadLogOnly	= true;
-
-	/**
-	 * Default constructor.
-	 */
-	public EventStorageLoggerAppender() {
-		this(true);
-	}
-
-	/**
-	 * Default constructor.
-	 * 
-	 * @param currentThreadLogOnly
-	 *          if <code>true</code> logs should be taken only from thread that
-	 *          created object, if <code>false</code> all logs will be stored
-	 */
-	public EventStorageLoggerAppender(boolean currentThreadLogOnly) {
-		this.threadId = Thread.currentThread().getId();
-		this.currentThreadLogOnly = currentThreadLogOnly;
-	}
-
-	@Override
-	protected void append(LoggingEvent event) {
-
-		// store information for all thread only if it is flagged by
-		// currentThreadLogOnly, if not only logs from current thread should be
-		// stored
-		if (!currentThreadLogOnly || threadId == Thread.currentThread().getId()) {
-			if (event.getLevel().equals(Level.DEBUG)) {
-				debugEvents.add(event);
-			} else if (event.getLevel().equals(Level.INFO)) {
-				infoEvents.add(event);
-			} else if (event.getLevel().equals(Level.WARN)) {
-				warnEvents.add(event);
-			} else if (event.getLevel().equals(Level.ERROR)) {
-				errorEvents.add(event);
-			} else if (event.getLevel().equals(Level.FATAL)) {
-				fatalEvents.add(event);
-			} else {
-				otherEvents.add(event);
-			}
-		}
-	}
-
-	@Override
-	public void close() {
-	}
-
-	@Override
-	public boolean requiresLayout() {
-		return false;
-	}
-
-	/**
-	 * Returns list of warning logs.
-	 * 
-	 * @return list of warning logs
-	 */
-	public List<LoggingEvent> getWarnings() {
-		return warnEvents;
-	}
-
-	/**
-	 * Returns list of error logs.
-	 * 
-	 * @return list of error logs
-	 */
-	public List<LoggingEvent> getErrors() {
-		return errorEvents;
-	}
-
-	/**
-	 * Returns list of fatal logs.
-	 * 
-	 * @return list of fatal logs
-	 */
-	public List<LoggingEvent> getFatals() {
-		return fatalEvents;
-	}
-}
+package lcsb.mapviewer.common;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Appender;
+import org.apache.log4j.AppenderSkeleton;
+import org.apache.log4j.Level;
+import org.apache.log4j.lf5.LogLevel;
+import org.apache.log4j.spi.LoggingEvent;
+
+/**
+ * Custom log4j {@link Appender}. This class is used to store logs in the
+ * memory. Such logs should be stored for short period of time. Only logs for
+ * the {@link Thread} that created the object will be stored.
+ * 
+ * @author Piotr Gawron
+ *
+ */
+public class EventStorageLoggerAppender extends AppenderSkeleton {
+
+	/**
+	 * List of {@link LogLevel#DEBUG} logs.
+	 */
+	private List<LoggingEvent> debugEvents					= new ArrayList<>();
+
+	/**
+	 * List of {@link LogLevel#INFO} logs.
+	 */
+	private List<LoggingEvent> infoEvents						= new ArrayList<>();
+
+	/**
+	 * List of {@link LogLevel#WARN} logs.
+	 */
+	private List<LoggingEvent> warnEvents						= new ArrayList<>();
+
+	/**
+	 * List of {@link LogLevel#ERROR} logs.
+	 */
+	private List<LoggingEvent> errorEvents					= new ArrayList<>();
+
+	/**
+	 * List of {@link LogLevel#FATAL} logs.
+	 */
+	private List<LoggingEvent> fatalEvents					= new ArrayList<>();
+
+	/**
+	 * List of logs with unknown log level.
+	 */
+	private List<LoggingEvent> otherEvents					= new ArrayList<>();
+
+	/**
+	 * Identifier of {@link Thread} that created this object.
+	 */
+	private long							 threadId;
+
+	/**
+	 * Flag that describe if we log only entries for current thread (
+	 * <code>true</code>) or for all threads (<code>false</code>).
+	 */
+	private boolean						 currentThreadLogOnly	= true;
+
+	/**
+	 * Default constructor.
+	 */
+	public EventStorageLoggerAppender() {
+		this(true);
+	}
+
+	/**
+	 * Default constructor.
+	 * 
+	 * @param currentThreadLogOnly
+	 *          if <code>true</code> logs should be taken only from thread that
+	 *          created object, if <code>false</code> all logs will be stored
+	 */
+	public EventStorageLoggerAppender(boolean currentThreadLogOnly) {
+		this.threadId = Thread.currentThread().getId();
+		this.currentThreadLogOnly = currentThreadLogOnly;
+	}
+
+	@Override
+	protected void append(LoggingEvent event) {
+
+		// store information for all thread only if it is flagged by
+		// currentThreadLogOnly, if not only logs from current thread should be
+		// stored
+		if (!currentThreadLogOnly || threadId == Thread.currentThread().getId()) {
+			if (event.getLevel().equals(Level.DEBUG)) {
+				debugEvents.add(event);
+			} else if (event.getLevel().equals(Level.INFO)) {
+				infoEvents.add(event);
+			} else if (event.getLevel().equals(Level.WARN)) {
+				warnEvents.add(event);
+			} else if (event.getLevel().equals(Level.ERROR)) {
+				errorEvents.add(event);
+			} else if (event.getLevel().equals(Level.FATAL)) {
+				fatalEvents.add(event);
+			} else {
+				otherEvents.add(event);
+			}
+		}
+	}
+
+	@Override
+	public void close() {
+	}
+
+	@Override
+	public boolean requiresLayout() {
+		return false;
+	}
+
+	/**
+	 * Returns list of warning logs.
+	 * 
+	 * @return list of warning logs
+	 */
+	public List<LoggingEvent> getWarnings() {
+		return warnEvents;
+	}
+
+	/**
+	 * Returns list of error logs.
+	 * 
+	 * @return list of error logs
+	 */
+	public List<LoggingEvent> getErrors() {
+		return errorEvents;
+	}
+
+	/**
+	 * Returns list of fatal logs.
+	 * 
+	 * @return list of fatal logs
+	 */
+	public List<LoggingEvent> getFatals() {
+		return fatalEvents;
+	}
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java b/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java
index 78ed3bbf2c..8d5f0c4322 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java
@@ -1,20 +1,20 @@
-package lcsb.mapviewer.common;
-
-/**
- * Defines type of http connection method.
- * 
- * @author Piotr Gawron
- * 
- */
-public enum HttpConnectionMethodType {
-	
-	/**
-	 * GET method.
-	 */
-	GET, //
-	
-	/**
-	 * POST method.
-	 */
-	POST;
-}
+package lcsb.mapviewer.common;
+
+/**
+ * Defines type of http connection method.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public enum HttpConnectionMethodType {
+	
+	/**
+	 * GET method.
+	 */
+	GET, //
+	
+	/**
+	 * POST method.
+	 */
+	POST;
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/MimeType.java b/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
index c52311b48e..54c7c29e1b 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
@@ -1,86 +1,86 @@
-package lcsb.mapviewer.common;
-
-/**
- * Mime content types of data used in the system. If there is publically
- * available class with all posible types then we should use it, but I couldn't
- * quickly find it. For the full list see <a
- * href="http://www.iana.org/assignments/media-types/media-types.xhtml">IANA
- * MIME media types list</a>
- * 
- * @author Piotr Gawron
- * 
- */
-public enum MimeType {
-	/**
-	 * SBML type of file.
-	 */
-	SBML("application/sbml+xml"), //
-
-	/**
-	 * Standard text file.
-	 */
-	TEXT("text/plain"), //
-
-	/**
-	 * Standard XML file.
-	 */
-	XML("application/xml"),
-
-	/**
-	 * <a href="http://www.w3.org/TR/SVG11/mimereg.html">SVG</a> file type.
-	 */
-	SVG("image/svg+xml"),
-
-	/**
-	 * JPG image file type.
-	 */
-	JPG("image/jpeg"),
-
-	/**
-	 * PNG image file type.
-	 */
-	PNG("image/png"),
-
-	/**
-	 * PDF files (see <a href="http://www.rfc-editor.org/rfc/rfc3778.txt"> RFC
-	 * 3778, The application/pdf Media Type</a>).
-	 */
-	PDF("application/pdf"), //
-
-	/**
-	 * CSS files.
-	 */
-	CSS("text/css"), //
-
-	/**
-	 * Javascript files.
-	 */
-	JS("text/javascript"), 
-	
-	/**
-	 * Zip files.
-	 */
-	ZIP("application/zip"); //
-
-	/**
-	 * String representation of the MIME content.
-	 */
-	private String textRepresentation;
-
-	/**
-	 * Default constructor with string definition.
-	 * 
-	 * @param textRepresentation
-	 *          text representation for MIME type
-	 */
-	MimeType(String textRepresentation) {
-		this.textRepresentation = textRepresentation;
-	}
-
-	/**
-	 * @return the textRepresentation
-	 */
-	public String getTextRepresentation() {
-		return textRepresentation;
-	}
-}
+package lcsb.mapviewer.common;
+
+/**
+ * Mime content types of data used in the system. If there is publically
+ * available class with all posible types then we should use it, but I couldn't
+ * quickly find it. For the full list see <a
+ * href="http://www.iana.org/assignments/media-types/media-types.xhtml">IANA
+ * MIME media types list</a>
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public enum MimeType {
+	/**
+	 * SBML type of file.
+	 */
+	SBML("application/sbml+xml"), //
+
+	/**
+	 * Standard text file.
+	 */
+	TEXT("text/plain"), //
+
+	/**
+	 * Standard XML file.
+	 */
+	XML("application/xml"),
+
+	/**
+	 * <a href="http://www.w3.org/TR/SVG11/mimereg.html">SVG</a> file type.
+	 */
+	SVG("image/svg+xml"),
+
+	/**
+	 * JPG image file type.
+	 */
+	JPG("image/jpeg"),
+
+	/**
+	 * PNG image file type.
+	 */
+	PNG("image/png"),
+
+	/**
+	 * PDF files (see <a href="http://www.rfc-editor.org/rfc/rfc3778.txt"> RFC
+	 * 3778, The application/pdf Media Type</a>).
+	 */
+	PDF("application/pdf"), //
+
+	/**
+	 * CSS files.
+	 */
+	CSS("text/css"), //
+
+	/**
+	 * Javascript files.
+	 */
+	JS("text/javascript"), 
+	
+	/**
+	 * Zip files.
+	 */
+	ZIP("application/zip"); //
+
+	/**
+	 * String representation of the MIME content.
+	 */
+	private String textRepresentation;
+
+	/**
+	 * Default constructor with string definition.
+	 * 
+	 * @param textRepresentation
+	 *          text representation for MIME type
+	 */
+	MimeType(String textRepresentation) {
+		this.textRepresentation = textRepresentation;
+	}
+
+	/**
+	 * @return the textRepresentation
+	 */
+	public String getTextRepresentation() {
+		return textRepresentation;
+	}
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java b/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java
index b5fd056b5e..145a9790da 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java
@@ -1,52 +1,52 @@
-package lcsb.mapviewer.common;
-
-import java.lang.reflect.Method;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-/**
- * Util class that performs primitive operations on the object.
- * 
- * @author Piotr Gawron
- * 
- */
-public final class ObjectUtils {
-
-	/**
-	 * Default constructor. Prevents instatiation.
-	 */
-	private ObjectUtils() {
-	}
-
-	/**
-	 * Returns object identifier. It assumes that object contains getId method
-	 * that returns Integer.
-	 * 
-	 * @param object
-	 *          object for which identifier is looked for
-	 * @return object identifier
-	 */
-	public static Integer getIdOfObject(Object object) {
-		Integer id = (Integer) getParamByGetter(object, "getId");
-		return id;
-	}
-
-	/**
-	 * Returns object param using string getter function.
-	 * 
-	 * @param object
-	 *          object from which parameter will be taken
-	 * @param getterName
-	 *          string with name of the getter function
-	 * @return object field
-	 */
-	public static Object getParamByGetter(Object object, String getterName) {
-		try {
-			Method method = object.getClass().getMethod(getterName);
-			Object result = method.invoke(object);
-			return result;
-		} catch (Exception e) {
-			throw new InvalidArgumentException(e.getMessage());
-		}
-	}
-}
+package lcsb.mapviewer.common;
+
+import java.lang.reflect.Method;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+/**
+ * Util class that performs primitive operations on the object.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public final class ObjectUtils {
+
+	/**
+	 * Default constructor. Prevents instatiation.
+	 */
+	private ObjectUtils() {
+	}
+
+	/**
+	 * Returns object identifier. It assumes that object contains getId method
+	 * that returns Integer.
+	 * 
+	 * @param object
+	 *          object for which identifier is looked for
+	 * @return object identifier
+	 */
+	public static Integer getIdOfObject(Object object) {
+		Integer id = (Integer) getParamByGetter(object, "getId");
+		return id;
+	}
+
+	/**
+	 * Returns object param using string getter function.
+	 * 
+	 * @param object
+	 *          object from which parameter will be taken
+	 * @param getterName
+	 *          string with name of the getter function
+	 * @return object field
+	 */
+	public static Object getParamByGetter(Object object, String getterName) {
+		try {
+			Method method = object.getClass().getMethod(getterName);
+			Object result = method.invoke(object);
+			return result;
+		} catch (Exception e) {
+			throw new InvalidArgumentException(e.getMessage());
+		}
+	}
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/Pair.java b/commons/src/main/java/lcsb/mapviewer/common/Pair.java
index 32fb0263a8..8d8573c0c4 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/Pair.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/Pair.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.common;
-
-import java.io.Serializable;
-
-/**
- * Represents pair of two objects. It's immutable as long as param classes are
- * immutable.
- * 
- * @author Piotr Gawron
- * 
- * @param <L>
- *          class type of the first object
- * @param <R>
- *          class type of the second object
- */
-public class Pair<L, R> implements Serializable {
-
-	/**
-	 * 
-	 */
-	private static final long	serialVersionUID = 1L;
-
-	/**
-	 * First object.
-	 */
-	private final L						left;
-
-	/**
-	 * Second object.
-	 */
-	private final R						right;
-
-	/**
-	 * Default constructor.
-	 * 
-	 * @param left
-	 *          {@link #left}
-	 * @param right
-	 *          {@link #right}
-	 */
-	public Pair(L left, R right) {
-		this.left = left;
-		this.right = right;
-	}
-
-	/**
-	 * 
-	 * @return {@link #left}
-	 */
-	public L getLeft() {
-		return left;
-	}
-
-	/**
-	 * 
-	 * @return {@link #right}
-	 */
-	public R getRight() {
-		return right;
-	}
-
-	@Override
-	public int hashCode() {
-		return left.hashCode() ^ right.hashCode();
-	}
-
-	@Override
-	public boolean equals(Object o) {
-		if (o == null) {
-			return false;
-		}
-		if (!(o instanceof Pair)) {
-			return false;
-		}
-		Pair<?, ?> pairo = (Pair<?, ?>) o;
-		return this.left.equals(pairo.getLeft()) && this.right.equals(pairo.getRight());
-	}
-
-	@Override
-	public String toString() {
-		return "Pair: " + getLeft().toString() + ", " + getRight().toString();
-	}
-
+package lcsb.mapviewer.common;
+
+import java.io.Serializable;
+
+/**
+ * Represents pair of two objects. It's immutable as long as param classes are
+ * immutable.
+ * 
+ * @author Piotr Gawron
+ * 
+ * @param <L>
+ *          class type of the first object
+ * @param <R>
+ *          class type of the second object
+ */
+public class Pair<L, R> implements Serializable {
+
+	/**
+	 * 
+	 */
+	private static final long	serialVersionUID = 1L;
+
+	/**
+	 * First object.
+	 */
+	private final L						left;
+
+	/**
+	 * Second object.
+	 */
+	private final R						right;
+
+	/**
+	 * Default constructor.
+	 * 
+	 * @param left
+	 *          {@link #left}
+	 * @param right
+	 *          {@link #right}
+	 */
+	public Pair(L left, R right) {
+		this.left = left;
+		this.right = right;
+	}
+
+	/**
+	 * 
+	 * @return {@link #left}
+	 */
+	public L getLeft() {
+		return left;
+	}
+
+	/**
+	 * 
+	 * @return {@link #right}
+	 */
+	public R getRight() {
+		return right;
+	}
+
+	@Override
+	public int hashCode() {
+		return left.hashCode() ^ right.hashCode();
+	}
+
+	@Override
+	public boolean equals(Object o) {
+		if (o == null) {
+			return false;
+		}
+		if (!(o instanceof Pair)) {
+			return false;
+		}
+		Pair<?, ?> pairo = (Pair<?, ?>) o;
+		return this.left.equals(pairo.getLeft()) && this.right.equals(pairo.getRight());
+	}
+
+	@Override
+	public String toString() {
+		return "Pair: " + getLeft().toString() + ", " + getRight().toString();
+	}
+
 }
\ No newline at end of file
diff --git a/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java b/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java
index f69c4c2cb6..16585aa4ef 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java
@@ -1,63 +1,63 @@
-package lcsb.mapviewer.common;
-
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.ClipboardOwner;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class allowing access to system clipboard.
- * 
- * @author Piotr Gawron
- * 
- */
-public class SystemClipboard implements ClipboardOwner {
-	/**
-	 * Default class logger.
-	 */
-	private final Logger logger = Logger.getLogger(SystemClipboard.class);
-
-	@Override
-	public void lostOwnership(Clipboard clipboard, Transferable contents) {
-	}
-
-	/**
-	 * Place a String on the clipboard, and make this class the owner of the
-	 * Clipboard's contents.
-	 * 
-	 * @param aString
-	 *          what we want to put into clipboard
-	 */
-	public void setClipboardContents(String aString) {
-		StringSelection stringSelection = new StringSelection(aString);
-		Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
-		clipboard.setContents(stringSelection, this);
-	}
-
-	/**
-	 * Get the String residing on the clipboard.
-	 * 
-	 * @return any text found on the Clipboard; if none found, return an empty
-	 *         String.
-	 */
-	public String getClipboardContents() {
-		String result = null;
-		Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
-		// odd: the Object param of getContents is not currently used
-		Transferable contents = clipboard.getContents(null);
-		boolean hasTransferableText = contents.isDataFlavorSupported(DataFlavor.stringFlavor);
-		if (hasTransferableText) {
-			try {
-				result = (String) contents.getTransferData(DataFlavor.stringFlavor);
-			} catch (Exception ex) {
-				logger.error(ex, ex);
-			}
-		}
-		return result;
-	}
-
-}
+package lcsb.mapviewer.common;
+
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.ClipboardOwner;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class allowing access to system clipboard.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public class SystemClipboard implements ClipboardOwner {
+	/**
+	 * Default class logger.
+	 */
+	private final Logger logger = Logger.getLogger(SystemClipboard.class);
+
+	@Override
+	public void lostOwnership(Clipboard clipboard, Transferable contents) {
+	}
+
+	/**
+	 * Place a String on the clipboard, and make this class the owner of the
+	 * Clipboard's contents.
+	 * 
+	 * @param aString
+	 *          what we want to put into clipboard
+	 */
+	public void setClipboardContents(String aString) {
+		StringSelection stringSelection = new StringSelection(aString);
+		Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+		clipboard.setContents(stringSelection, this);
+	}
+
+	/**
+	 * Get the String residing on the clipboard.
+	 * 
+	 * @return any text found on the Clipboard; if none found, return an empty
+	 *         String.
+	 */
+	public String getClipboardContents() {
+		String result = null;
+		Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+		// odd: the Object param of getContents is not currently used
+		Transferable contents = clipboard.getContents(null);
+		boolean hasTransferableText = contents.isDataFlavorSupported(DataFlavor.stringFlavor);
+		if (hasTransferableText) {
+			try {
+				result = (String) contents.getTransferData(DataFlavor.stringFlavor);
+			} catch (Exception ex) {
+				logger.error(ex, ex);
+			}
+		}
+		return result;
+	}
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java b/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
index 6ae08f6169..12d7490398 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
@@ -1,56 +1,56 @@
-package lcsb.mapviewer.common;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.HashMap;
-import java.util.Map;
-
-/**
- * Class with util function to operate on text files.
- * 
- * @author Piotr Gawron
- *
- */
-public final class TextFileUtils {
-
-	/**
-	 * Default constructor that prevents instatiation.
-	 */
-	private TextFileUtils() {
-
-	}
-
-	/**
-	 * Parses input stream to get parameters from header. {@link InputStream}
-	 * should be a text file. Header parameters are lines at the beginning of the
-	 * file starting with '#' character.
-	 * 
-	 * @param is
-	 *          input stream for a file to process
-	 * @return map with paramteres parsed from input stream
-	 * @throws IOException
-	 *           thrown when there is a problem with accessing input stream
-	 */
-	public static Map<String, String> getHeaderParametersFromFile(InputStream is) throws IOException {
-		Map<String, String> result = new HashMap<String, String>();
-		BufferedReader in = new BufferedReader(new InputStreamReader(is));
-		String line = null;
-		while ((line = in.readLine()) != null) {
-			if (line.startsWith("#")) {
-				String tmp = line.substring(1);
-				if (tmp.indexOf("=") > 0) {
-					String key = tmp.substring(0, tmp.indexOf("=")).trim();
-					String value = tmp.substring(tmp.indexOf("=") + 1).trim();
-					result.put(key, value);
-				}
-			} else {
-				break;
-			}
-		}
-		is.close();
-		return result;
-	}
-
-}
+package lcsb.mapviewer.common;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Class with util function to operate on text files.
+ * 
+ * @author Piotr Gawron
+ *
+ */
+public final class TextFileUtils {
+
+	/**
+	 * Default constructor that prevents instatiation.
+	 */
+	private TextFileUtils() {
+
+	}
+
+	/**
+	 * Parses input stream to get parameters from header. {@link InputStream}
+	 * should be a text file. Header parameters are lines at the beginning of the
+	 * file starting with '#' character.
+	 * 
+	 * @param is
+	 *          input stream for a file to process
+	 * @return map with paramteres parsed from input stream
+	 * @throws IOException
+	 *           thrown when there is a problem with accessing input stream
+	 */
+	public static Map<String, String> getHeaderParametersFromFile(InputStream is) throws IOException {
+		Map<String, String> result = new HashMap<String, String>();
+		BufferedReader in = new BufferedReader(new InputStreamReader(is));
+		String line = null;
+		while ((line = in.readLine()) != null) {
+			if (line.startsWith("#")) {
+				String tmp = line.substring(1);
+				if (tmp.indexOf("=") > 0) {
+					String key = tmp.substring(0, tmp.indexOf("=")).trim();
+					String value = tmp.substring(tmp.indexOf("=") + 1).trim();
+					result.put(key, value);
+				}
+			} else {
+				break;
+			}
+		}
+		is.close();
+		return result;
+	}
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
index 8279792711..0f0530880c 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
@@ -1,357 +1,357 @@
-package lcsb.mapviewer.common;
-
-import java.awt.Color;
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringEscapeUtils;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-import org.w3c.dom.NamedNodeMap;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-
-/**
- * Abstract class with methods which help in parsing xml using DOM.
- * 
- * @author Piotr Gawron
- * 
- */
-public class XmlParser {
-	/**
-	 * Base of the hex representation.
-	 */
-	private static final int							HEX_BASE							 = 16;
-
-	/**
-	 * {@link DocumentBuilderFactory} used to create {@link DocumentBuilder}
-	 * objects that will manipulate xml nodes.
-	 */
-	private static DocumentBuilderFactory	documentBuilderFactory = DocumentBuilderFactory.newInstance();
-
-	/**
-	 * Default class logger.
-	 */
-	private Logger												logger								 = Logger.getLogger(XmlParser.class.getName());
-
-	/**
-	 * DOM document builder used for xml transformations.
-	 */
-	private DocumentBuilder								db;
-
-	/**
-	 * Default constructor that prevents from instatiation of the class and
-	 * initializes fields.
-	 */
-	protected XmlParser() {
-		try {
-			db = documentBuilderFactory.newDocumentBuilder();
-		} catch (ParserConfigurationException e) {
-			throw new InvalidStateException("Problem with xml parser");
-		}
-
-	}
-
-	/**
-	 * Method returns the node of xml nodelist 'nodes' with 'tagName' name. If
-	 * node could not be found then null is returned.
-	 * 
-	 * @param tagName
-	 *          name of node to look for
-	 * @param nodes
-	 *          list of nodes
-	 * @return node from nodes list with the tagName name, <b>null</b> if such
-	 *         node doesn't exist
-	 */
-	protected Node getNode(final String tagName, final NodeList nodes) {
-		for (int x = 0; x < nodes.getLength(); x++) {
-			Node node = nodes.item(x);
-			if (node.getNodeType() == Node.ELEMENT_NODE) {
-				if (node.getNodeName().equalsIgnoreCase(tagName)) {
-					return node;
-				}
-			}
-		}
-		return null;
-	}
-
-	/**
-	 * Method returns the child node of xml 'parentNode' with 'tagName' name. If
-	 * node could not be found then null is returned.
-	 * 
-	 * @param tagName
-	 *          name of node to look for
-	 * @param parentNode
-	 *          parent node
-	 * @return node from nodes list with the tagName name, <b>null</b> if such
-	 *         node doesn't exist
-	 */
-	protected Node getNode(final String tagName, final Node parentNode) {
-		return getNode(tagName, parentNode.getChildNodes());
-	}
-
-	/**
-	 * Method returns list of nodes with 'tagName' name. If node could not be
-	 * found then empty list is returned.
-	 * 
-	 * @param tagName
-	 *          name of node to look for
-	 * @param nodes
-	 *          list of input nodes
-	 * @return list of nodes with 'tagName' name
-	 */
-	protected List<Node> getNodes(final String tagName, final NodeList nodes) {
-		List<Node> result = new ArrayList<Node>();
-		for (int x = 0; x < nodes.getLength(); x++) {
-			Node node = nodes.item(x);
-			if (node.getNodeName().equalsIgnoreCase(tagName)) {
-				result.add(node);
-			}
-		}
-		return result;
-	}
-
-	/**
-	 * Method returns the value of node attribute. If attribute could not be found
-	 * then "" is returned.
-	 * 
-	 * @param attrName
-	 *          name of the attribute to look for
-	 * @param node
-	 *          a node
-	 * @return the value of node attribute, empty string("") if attribute doesn't
-	 *         exist
-	 */
-	protected String getNodeAttr(final String attrName, final Node node) {
-		NamedNodeMap attrs = node.getAttributes();
-		for (int y = 0; y < attrs.getLength(); y++) {
-			Node attr = attrs.item(y);
-			if (attr.getNodeName().equalsIgnoreCase(attrName)) {
-				return attr.getNodeValue();
-			}
-		}
-		return "";
-	}
-
-	/**
-	 * Method returns the text value of node. If text could not be found then ""
-	 * is returned.
-	 * 
-	 * @param node
-	 *          a node
-	 * @return the text value of node or empty string ("") if the text could be
-	 *         found.
-	 */
-	protected String getNodeValue(final Node node) {
-		if (node == null) {
-			return "";
-		}
-		NodeList childNodes = node.getChildNodes();
-		for (int x = 0; x < childNodes.getLength(); x++) {
-			Node data = childNodes.item(x);
-			if (data.getNodeType() == Node.TEXT_NODE) {
-				return data.getNodeValue();
-			}
-		}
-		return "";
-	}
-
-	/**
-	 * Method returns the xml Document from input source given as a parameter.
-	 * 
-	 * @param stream
-	 *          input stream with xml document
-	 * @return Document node for the input stream
-	 * @throws InvalidXmlSchemaException
-	 *           thrown when there is a problem with xml
-	 */
-	protected Document getXmlDocumentFromInputSource(final InputSource stream) throws InvalidXmlSchemaException {
-		try {
-			return db.parse(stream);
-		} catch (SAXException e) {
-			throw new InvalidXmlSchemaException("Problem with xml parser", e);
-		} catch (IOException e) {
-			throw new InvalidXmlSchemaException("Problem with xml parser", e);
-		}
-	}
-
-	/**
-	 * Method returns the xml Document from text given as a source.
-	 * 
-	 * @param text
-	 *          string representing xml document
-	 * @return Document for the xml document given in the input
-	 * @throws InvalidXmlSchemaException
-	 *           thrown when there is a problem with xml
-	 */
-	protected Document getXmlDocumentFromString(final String text) throws InvalidXmlSchemaException {
-		InputSource is = new InputSource();
-		is.setCharacterStream(new StringReader(text));
-		return getXmlDocumentFromInputSource(is);
-	}
-
-	/**
-	 * Transforms node into string xml format.
-	 * 
-	 * @param node
-	 *          node that should be transformed into xml string
-	 * @return string representation of the xml node
-	 */
-	protected String nodeToString(final Node node) {
-		return nodeToString(node, false);
-	}
-
-	/**
-	 * Transforms node into string xml format.
-	 * 
-	 * @param node
-	 *          node that should be transformed into xml string
-	 * @param includeHeadNode
-	 *          should the top level node exist in the output
-	 * @return string representation of the xml node
-	 */
-	protected String nodeToString(final Node node, final boolean includeHeadNode) {
-		if (node == null) {
-			return null;
-		}
-		StringWriter sw = new StringWriter();
-		try {
-			Transformer t = TransformerFactory.newInstance().newTransformer();
-			t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
-			t.setOutputProperty(OutputKeys.INDENT, "yes");
-			t.setOutputProperty(OutputKeys.METHOD, "xml");
-
-			NodeList list = node.getChildNodes();
-			for (int i = 0; i < list.getLength(); i++) {
-				Node element = list.item(i);
-				t.transform(new DOMSource(element), new StreamResult(sw));
-			}
-		} catch (TransformerException te) {
-			logger.debug("nodeToString Transformer Exception");
-		}
-		if (includeHeadNode) {
-			return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
-		}
-		return sw.toString();
-	}
-
-	/**
-	 * This method transform color encoded in string (CellDesigner format) into
-	 * Color.
-	 * 
-	 * @param color
-	 *          string representing color
-	 * @return Color object for the fiven string
-	 */
-	protected Color stringToColor(final String color) {
-		try {
-			String alpha = color.substring(0, 2);
-			Color tmp = new Color(hexToInteger(color.substring(2)));
-			return new Color(tmp.getRed(), tmp.getGreen(), tmp.getBlue(), hexToInteger(alpha));
-		} catch (Exception e) {
-			throw new InvalidArgumentException("Invalid color string: " + color);
-		}
-	}
-
-	/**
-	 * Transforms hex string into Integer.
-	 * 
-	 * @param hexString
-	 *          string representation in hex base
-	 * @return Integer value of the hex string
-	 */
-	private Integer hexToInteger(String hexString) {
-		return Integer.valueOf(hexString, HEX_BASE);
-	}
-
-	/**
-	 * Transforms Color object into string representing this color in RGB.
-	 * 
-	 * @param color
-	 *          color that should be converted into string
-	 * @return hex string representation of the color
-	 */
-	protected String colorToString(final Color color) {
-		return String.format("%08X", color.getRGB());
-	}
-
-	/**
-	 * Method that reads file and transforms it into a string.
-	 * 
-	 * @param fileName
-	 *          path to a file
-	 * @return string containing data from the file (default coding is used)
-	 * @throws IOException
-	 *           thrown when there are some problems with a file
-	 */
-	protected String fileToString(final String fileName) throws IOException {
-		BufferedReader reader = new BufferedReader(new FileReader(fileName));
-		String line = null;
-		StringBuilder stringBuilder = new StringBuilder();
-		String ls = System.getProperty("line.separator");
-
-		while ((line = reader.readLine()) != null) {
-			stringBuilder.append(line);
-			stringBuilder.append(ls);
-		}
-		reader.close();
-
-		return stringBuilder.toString();
-	}
-
-	/**
-	 * Method that reads all data from inputstream and transform it into a string.
-	 * UTF-8 coding is used.
-	 * 
-	 * @param inputStream
-	 *          stream from which we read data
-	 * @return string representing all data from input stream
-	 * @throws IOException
-	 *           thrown if there are some problems with input stream
-	 */
-	protected String inputStreamToString(final InputStream inputStream) throws IOException {
-		StringWriter writer = new StringWriter();
-		IOUtils.copy(inputStream, writer, "UTF-8");
-		String result = writer.toString();
-		return result;
-	}
-
-	/**
-	 * Method that encode string into a string that can be used in xml file.
-	 * 
-	 * @param string
-	 *          string to be escaped
-	 * @return escaped string, ready to be used in xml
-	 */
-	protected String escapeXml(final String string) {
-		if (string == null) {
-			return null;
-		}
-		// quite expensive
-		return StringEscapeUtils.escapeXml(string).replaceAll("\n", "&#10;").replace("\r", "&#13;");
-	}
-
-}
+package lcsb.mapviewer.common;
+
+import java.awt.Color;
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringEscapeUtils;
+import org.apache.log4j.Logger;
+import org.w3c.dom.Document;
+import org.w3c.dom.NamedNodeMap;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+
+/**
+ * Abstract class with methods which help in parsing xml using DOM.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public class XmlParser {
+	/**
+	 * Base of the hex representation.
+	 */
+	private static final int							HEX_BASE							 = 16;
+
+	/**
+	 * {@link DocumentBuilderFactory} used to create {@link DocumentBuilder}
+	 * objects that will manipulate xml nodes.
+	 */
+	private static DocumentBuilderFactory	documentBuilderFactory = DocumentBuilderFactory.newInstance();
+
+	/**
+	 * Default class logger.
+	 */
+	private Logger												logger								 = Logger.getLogger(XmlParser.class.getName());
+
+	/**
+	 * DOM document builder used for xml transformations.
+	 */
+	private DocumentBuilder								db;
+
+	/**
+	 * Default constructor that prevents from instatiation of the class and
+	 * initializes fields.
+	 */
+	protected XmlParser() {
+		try {
+			db = documentBuilderFactory.newDocumentBuilder();
+		} catch (ParserConfigurationException e) {
+			throw new InvalidStateException("Problem with xml parser");
+		}
+
+	}
+
+	/**
+	 * Method returns the node of xml nodelist 'nodes' with 'tagName' name. If
+	 * node could not be found then null is returned.
+	 * 
+	 * @param tagName
+	 *          name of node to look for
+	 * @param nodes
+	 *          list of nodes
+	 * @return node from nodes list with the tagName name, <b>null</b> if such
+	 *         node doesn't exist
+	 */
+	protected Node getNode(final String tagName, final NodeList nodes) {
+		for (int x = 0; x < nodes.getLength(); x++) {
+			Node node = nodes.item(x);
+			if (node.getNodeType() == Node.ELEMENT_NODE) {
+				if (node.getNodeName().equalsIgnoreCase(tagName)) {
+					return node;
+				}
+			}
+		}
+		return null;
+	}
+
+	/**
+	 * Method returns the child node of xml 'parentNode' with 'tagName' name. If
+	 * node could not be found then null is returned.
+	 * 
+	 * @param tagName
+	 *          name of node to look for
+	 * @param parentNode
+	 *          parent node
+	 * @return node from nodes list with the tagName name, <b>null</b> if such
+	 *         node doesn't exist
+	 */
+	protected Node getNode(final String tagName, final Node parentNode) {
+		return getNode(tagName, parentNode.getChildNodes());
+	}
+
+	/**
+	 * Method returns list of nodes with 'tagName' name. If node could not be
+	 * found then empty list is returned.
+	 * 
+	 * @param tagName
+	 *          name of node to look for
+	 * @param nodes
+	 *          list of input nodes
+	 * @return list of nodes with 'tagName' name
+	 */
+	protected List<Node> getNodes(final String tagName, final NodeList nodes) {
+		List<Node> result = new ArrayList<Node>();
+		for (int x = 0; x < nodes.getLength(); x++) {
+			Node node = nodes.item(x);
+			if (node.getNodeName().equalsIgnoreCase(tagName)) {
+				result.add(node);
+			}
+		}
+		return result;
+	}
+
+	/**
+	 * Method returns the value of node attribute. If attribute could not be found
+	 * then "" is returned.
+	 * 
+	 * @param attrName
+	 *          name of the attribute to look for
+	 * @param node
+	 *          a node
+	 * @return the value of node attribute, empty string("") if attribute doesn't
+	 *         exist
+	 */
+	protected String getNodeAttr(final String attrName, final Node node) {
+		NamedNodeMap attrs = node.getAttributes();
+		for (int y = 0; y < attrs.getLength(); y++) {
+			Node attr = attrs.item(y);
+			if (attr.getNodeName().equalsIgnoreCase(attrName)) {
+				return attr.getNodeValue();
+			}
+		}
+		return "";
+	}
+
+	/**
+	 * Method returns the text value of node. If text could not be found then ""
+	 * is returned.
+	 * 
+	 * @param node
+	 *          a node
+	 * @return the text value of node or empty string ("") if the text could be
+	 *         found.
+	 */
+	protected String getNodeValue(final Node node) {
+		if (node == null) {
+			return "";
+		}
+		NodeList childNodes = node.getChildNodes();
+		for (int x = 0; x < childNodes.getLength(); x++) {
+			Node data = childNodes.item(x);
+			if (data.getNodeType() == Node.TEXT_NODE) {
+				return data.getNodeValue();
+			}
+		}
+		return "";
+	}
+
+	/**
+	 * Method returns the xml Document from input source given as a parameter.
+	 * 
+	 * @param stream
+	 *          input stream with xml document
+	 * @return Document node for the input stream
+	 * @throws InvalidXmlSchemaException
+	 *           thrown when there is a problem with xml
+	 */
+	protected Document getXmlDocumentFromInputSource(final InputSource stream) throws InvalidXmlSchemaException {
+		try {
+			return db.parse(stream);
+		} catch (SAXException e) {
+			throw new InvalidXmlSchemaException("Problem with xml parser", e);
+		} catch (IOException e) {
+			throw new InvalidXmlSchemaException("Problem with xml parser", e);
+		}
+	}
+
+	/**
+	 * Method returns the xml Document from text given as a source.
+	 * 
+	 * @param text
+	 *          string representing xml document
+	 * @return Document for the xml document given in the input
+	 * @throws InvalidXmlSchemaException
+	 *           thrown when there is a problem with xml
+	 */
+	protected Document getXmlDocumentFromString(final String text) throws InvalidXmlSchemaException {
+		InputSource is = new InputSource();
+		is.setCharacterStream(new StringReader(text));
+		return getXmlDocumentFromInputSource(is);
+	}
+
+	/**
+	 * Transforms node into string xml format.
+	 * 
+	 * @param node
+	 *          node that should be transformed into xml string
+	 * @return string representation of the xml node
+	 */
+	protected String nodeToString(final Node node) {
+		return nodeToString(node, false);
+	}
+
+	/**
+	 * Transforms node into string xml format.
+	 * 
+	 * @param node
+	 *          node that should be transformed into xml string
+	 * @param includeHeadNode
+	 *          should the top level node exist in the output
+	 * @return string representation of the xml node
+	 */
+	protected String nodeToString(final Node node, final boolean includeHeadNode) {
+		if (node == null) {
+			return null;
+		}
+		StringWriter sw = new StringWriter();
+		try {
+			Transformer t = TransformerFactory.newInstance().newTransformer();
+			t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+			t.setOutputProperty(OutputKeys.INDENT, "yes");
+			t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+			NodeList list = node.getChildNodes();
+			for (int i = 0; i < list.getLength(); i++) {
+				Node element = list.item(i);
+				t.transform(new DOMSource(element), new StreamResult(sw));
+			}
+		} catch (TransformerException te) {
+			logger.debug("nodeToString Transformer Exception");
+		}
+		if (includeHeadNode) {
+			return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+		}
+		return sw.toString();
+	}
+
+	/**
+	 * This method transform color encoded in string (CellDesigner format) into
+	 * Color.
+	 * 
+	 * @param color
+	 *          string representing color
+	 * @return Color object for the fiven string
+	 */
+	protected Color stringToColor(final String color) {
+		try {
+			String alpha = color.substring(0, 2);
+			Color tmp = new Color(hexToInteger(color.substring(2)));
+			return new Color(tmp.getRed(), tmp.getGreen(), tmp.getBlue(), hexToInteger(alpha));
+		} catch (Exception e) {
+			throw new InvalidArgumentException("Invalid color string: " + color);
+		}
+	}
+
+	/**
+	 * Transforms hex string into Integer.
+	 * 
+	 * @param hexString
+	 *          string representation in hex base
+	 * @return Integer value of the hex string
+	 */
+	private Integer hexToInteger(String hexString) {
+		return Integer.valueOf(hexString, HEX_BASE);
+	}
+
+	/**
+	 * Transforms Color object into string representing this color in RGB.
+	 * 
+	 * @param color
+	 *          color that should be converted into string
+	 * @return hex string representation of the color
+	 */
+	protected String colorToString(final Color color) {
+		return String.format("%08X", color.getRGB());
+	}
+
+	/**
+	 * Method that reads file and transforms it into a string.
+	 * 
+	 * @param fileName
+	 *          path to a file
+	 * @return string containing data from the file (default coding is used)
+	 * @throws IOException
+	 *           thrown when there are some problems with a file
+	 */
+	protected String fileToString(final String fileName) throws IOException {
+		BufferedReader reader = new BufferedReader(new FileReader(fileName));
+		String line = null;
+		StringBuilder stringBuilder = new StringBuilder();
+		String ls = System.getProperty("line.separator");
+
+		while ((line = reader.readLine()) != null) {
+			stringBuilder.append(line);
+			stringBuilder.append(ls);
+		}
+		reader.close();
+
+		return stringBuilder.toString();
+	}
+
+	/**
+	 * Method that reads all data from inputstream and transform it into a string.
+	 * UTF-8 coding is used.
+	 * 
+	 * @param inputStream
+	 *          stream from which we read data
+	 * @return string representing all data from input stream
+	 * @throws IOException
+	 *           thrown if there are some problems with input stream
+	 */
+	protected String inputStreamToString(final InputStream inputStream) throws IOException {
+		StringWriter writer = new StringWriter();
+		IOUtils.copy(inputStream, writer, "UTF-8");
+		String result = writer.toString();
+		return result;
+	}
+
+	/**
+	 * Method that encode string into a string that can be used in xml file.
+	 * 
+	 * @param string
+	 *          string to be escaped
+	 * @return escaped string, ready to be used in xml
+	 */
+	protected String escapeXml(final String string) {
+		if (string == null) {
+			return null;
+		}
+		// quite expensive
+		return StringEscapeUtils.escapeXml(string).replaceAll("\n", "&#10;").replace("\r", "&#13;");
+	}
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java b/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
index 8c28d00230..561bc13f4a 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.common;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.common.comparator.AllComparatorTests;
-import lcsb.mapviewer.common.exception.AllExceptionTests;
-import lcsb.mapviewer.common.geometry.AllGeometryTests;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllComparatorTests.class, //
-		AllExceptionTests.class, //
-		AllGeometryTests.class, //
-		ConfigurationTest.class, //
-		EventStorageLoggerAppenderTest.class, //
-		HttpConnectionMethodTypeTest.class, //
-		MimeTypeTest.class, //
-		ObjectUtilsTest.class, //
-		PairTest.class, //
-		SystemClipboardTest.class, //
-		TextFileUtilsTest.class, //
-		XmlParserTest.class, //
-})
-public class AllCommonTests {
-
-}
+package lcsb.mapviewer.common;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.common.comparator.AllComparatorTests;
+import lcsb.mapviewer.common.exception.AllExceptionTests;
+import lcsb.mapviewer.common.geometry.AllGeometryTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllComparatorTests.class, //
+		AllExceptionTests.class, //
+		AllGeometryTests.class, //
+		ConfigurationTest.class, //
+		EventStorageLoggerAppenderTest.class, //
+		HttpConnectionMethodTypeTest.class, //
+		MimeTypeTest.class, //
+		ObjectUtilsTest.class, //
+		PairTest.class, //
+		SystemClipboardTest.class, //
+		TextFileUtilsTest.class, //
+		XmlParserTest.class, //
+})
+public class AllCommonTests {
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/EventStorageLoggerAppenderTest.java b/commons/src/test/java/lcsb/mapviewer/common/EventStorageLoggerAppenderTest.java
index 94a339ade8..9816f4b8aa 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/EventStorageLoggerAppenderTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/EventStorageLoggerAppenderTest.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class EventStorageLoggerAppenderTest {
-	Logger logger = Logger.getLogger(EventStorageLoggerAppenderTest.class);
-
-	@AfterClass
-	public static void tearDownAfterClass() throws Exception {
-	}
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testLogCatching() {
-		try {
-			EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
-			logger.addAppender(appender);
-			logger.warn("test");
-			logger.debug("1");
-			logger.error("2");
-			logger.info("3");
-			logger.fatal("4");
-			assertEquals(1, appender.getWarnings().size());
-			logger.removeAppender(appender);
-			logger.warn("test");
-			assertEquals(1, appender.getWarnings().size());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testGetters() {
-		try {
-			EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
-			appender.requiresLayout();
-			appender.close();
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class EventStorageLoggerAppenderTest {
+	Logger logger = Logger.getLogger(EventStorageLoggerAppenderTest.class);
+
+	@AfterClass
+	public static void tearDownAfterClass() throws Exception {
+	}
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testLogCatching() {
+		try {
+			EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+			logger.addAppender(appender);
+			logger.warn("test");
+			logger.debug("1");
+			logger.error("2");
+			logger.info("3");
+			logger.fatal("4");
+			assertEquals(1, appender.getWarnings().size());
+			logger.removeAppender(appender);
+			logger.warn("test");
+			assertEquals(1, appender.getWarnings().size());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testGetters() {
+		try {
+			EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+			appender.requiresLayout();
+			appender.close();
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/HttpConnectionMethodTypeTest.java b/commons/src/test/java/lcsb/mapviewer/common/HttpConnectionMethodTypeTest.java
index 2723073007..9789b766e9 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/HttpConnectionMethodTypeTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/HttpConnectionMethodTypeTest.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class HttpConnectionMethodTypeTest {
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testValidValues() {
-		for (HttpConnectionMethodType type : HttpConnectionMethodType.values()) {
-			assertNotNull(type);
-
-			// for coverage tests
-			HttpConnectionMethodType.valueOf(type.toString());
-		}
-	}
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class HttpConnectionMethodTypeTest {
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testValidValues() {
+		for (HttpConnectionMethodType type : HttpConnectionMethodType.values()) {
+			assertNotNull(type);
+
+			// for coverage tests
+			HttpConnectionMethodType.valueOf(type.toString());
+		}
+	}
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java b/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java
index 50189c2ae3..9087471b07 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class MimeTypeTest {
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testValidValues() {
-		for (MimeType type : MimeType.values()) {
-			assertNotNull(type);
-			assertNotNull(type.getTextRepresentation());
-			assertFalse(type.getTextRepresentation().isEmpty());
-			
-			//for coverage tests
-			MimeType.valueOf(type.toString());
-		}
-	}
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class MimeTypeTest {
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testValidValues() {
+		for (MimeType type : MimeType.values()) {
+			assertNotNull(type);
+			assertNotNull(type.getTextRepresentation());
+			assertFalse(type.getTextRepresentation().isEmpty());
+			
+			//for coverage tests
+			MimeType.valueOf(type.toString());
+		}
+	}
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/ObjectUtilsTest.java b/commons/src/test/java/lcsb/mapviewer/common/ObjectUtilsTest.java
index ff8b79effc..71ee157432 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/ObjectUtilsTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/ObjectUtilsTest.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.lang.reflect.Constructor;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-public class ObjectUtilsTest {
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testGetIdOfObject() {
-		Object obj = new Object() {
-			@SuppressWarnings("unused")
-			public int getId() {
-				return 107;
-			}
-		};
-		assertEquals((Integer) 107, ObjectUtils.getIdOfObject(obj));
-	}
-
-	@Test
-	public void testGetIdOfObjectWithoutId() {
-		Object obj = new Object();
-		try {
-			ObjectUtils.getIdOfObject(obj);
-			fail("Exception expected");
-		} catch (InvalidArgumentException e) {
-
-		}
-	}
-
-	@Test
-	public void testPrivateConstructor() throws Exception {
-		try {
-			Constructor<?> constr = ObjectUtils.class.getDeclaredConstructor(new Class<?>[] {});
-			constr.setAccessible(true);
-			assertNotNull(constr.newInstance(new Object[] {}));
-		} catch (Exception e) {
-			throw e;
-		}
-	}
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.lang.reflect.Constructor;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+public class ObjectUtilsTest {
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testGetIdOfObject() {
+		Object obj = new Object() {
+			@SuppressWarnings("unused")
+			public int getId() {
+				return 107;
+			}
+		};
+		assertEquals((Integer) 107, ObjectUtils.getIdOfObject(obj));
+	}
+
+	@Test
+	public void testGetIdOfObjectWithoutId() {
+		Object obj = new Object();
+		try {
+			ObjectUtils.getIdOfObject(obj);
+			fail("Exception expected");
+		} catch (InvalidArgumentException e) {
+
+		}
+	}
+
+	@Test
+	public void testPrivateConstructor() throws Exception {
+		try {
+			Constructor<?> constr = ObjectUtils.class.getDeclaredConstructor(new Class<?>[] {});
+			constr.setAccessible(true);
+			assertNotNull(constr.newInstance(new Object[] {}));
+		} catch (Exception e) {
+			throw e;
+		}
+	}
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/PairTest.java b/commons/src/test/java/lcsb/mapviewer/common/PairTest.java
index 33178d5e6a..286787b3f2 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/PairTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/PairTest.java
@@ -1,70 +1,70 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class PairTest {
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testConstructor() {
-		Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
-		assertEquals("test str", pair.getLeft());
-		assertEquals((Integer) 12, pair.getRight());
-	}
-
-	@Test
-	public void testEquals() {
-		Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
-		Pair<String, Integer> pair2 = new Pair<String, Integer>("test str", 12);
-		Pair<String, String> pair3 = new Pair<String, String>("test str", "str");
-		Pair<String, Integer> pair4 = new Pair<String, Integer>("test str", 124);
-		Pair<String, Integer> pair5 = new Pair<String, Integer>("test str1", 12);
-		assertTrue(pair.equals(pair2));
-		assertFalse(pair.equals(pair3));
-		assertFalse(pair.equals(pair4));
-		assertFalse(pair.equals(pair5));
-
-		assertTrue(pair2.equals(pair));
-		assertFalse(pair3.equals(pair));
-		assertFalse(pair4.equals(pair));
-		assertFalse(pair5.equals(pair));
-		assertFalse(pair4.equals(new Object()));
-	}
-
-	@Test
-	public void testHashCode() {
-		Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
-		Pair<String, Integer> pair2 = new Pair<String, Integer>("test str", 12);
-		Pair<String, Integer> pair3 = new Pair<String, Integer>("test str", 124);
-		assertEquals(pair.hashCode(), pair2.hashCode());
-		assertTrue(pair.hashCode() != pair3.hashCode());
-	}
-
-	@Test
-	public void testNullEquals() {
-		Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
-		Pair<String, Integer> pair2 = null;
-		assertFalse(pair.equals(pair2));
-	}
-
-	@Test
-	public void testToString() {
-		Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
-		assertTrue(pair.toString().contains(pair.getLeft().toString()));
-		assertTrue(pair.toString().contains(pair.getRight().toString()));
-	}
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class PairTest {
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testConstructor() {
+		Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+		assertEquals("test str", pair.getLeft());
+		assertEquals((Integer) 12, pair.getRight());
+	}
+
+	@Test
+	public void testEquals() {
+		Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+		Pair<String, Integer> pair2 = new Pair<String, Integer>("test str", 12);
+		Pair<String, String> pair3 = new Pair<String, String>("test str", "str");
+		Pair<String, Integer> pair4 = new Pair<String, Integer>("test str", 124);
+		Pair<String, Integer> pair5 = new Pair<String, Integer>("test str1", 12);
+		assertTrue(pair.equals(pair2));
+		assertFalse(pair.equals(pair3));
+		assertFalse(pair.equals(pair4));
+		assertFalse(pair.equals(pair5));
+
+		assertTrue(pair2.equals(pair));
+		assertFalse(pair3.equals(pair));
+		assertFalse(pair4.equals(pair));
+		assertFalse(pair5.equals(pair));
+		assertFalse(pair4.equals(new Object()));
+	}
+
+	@Test
+	public void testHashCode() {
+		Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+		Pair<String, Integer> pair2 = new Pair<String, Integer>("test str", 12);
+		Pair<String, Integer> pair3 = new Pair<String, Integer>("test str", 124);
+		assertEquals(pair.hashCode(), pair2.hashCode());
+		assertTrue(pair.hashCode() != pair3.hashCode());
+	}
+
+	@Test
+	public void testNullEquals() {
+		Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+		Pair<String, Integer> pair2 = null;
+		assertFalse(pair.equals(pair2));
+	}
+
+	@Test
+	public void testToString() {
+		Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+		assertTrue(pair.toString().contains(pair.getLeft().toString()));
+		assertTrue(pair.toString().contains(pair.getRight().toString()));
+	}
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java b/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java
index 88ba17059b..604262c4cf 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java
@@ -1,98 +1,98 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.Transferable;
-import java.awt.datatransfer.UnsupportedFlavorException;
-import java.io.IOException;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SystemClipboardTest {
-	Logger	logger	= Logger.getLogger(SystemClipboardTest.class);
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testClipboard() throws Exception {
-		try {
-			SystemClipboard sc = new SystemClipboard();
-			sc.setClipboardContents("TEST");
-
-			SystemClipboard sc2 = new SystemClipboard();
-			assertEquals("TEST",sc2.getClipboardContents());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testInvalidClipboard() throws Exception {
-		try {
-			SystemClipboard sc2 = new SystemClipboard();
-			
-			Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
-			clipboard.setContents(new Transferable() {
-				
-				@Override
-				public boolean isDataFlavorSupported(DataFlavor flavor) {
-					return true;
-				}
-				
-				@Override
-				public DataFlavor[] getTransferDataFlavors() {
-					return null;
-				}
-				
-				@Override
-				public Object getTransferData(DataFlavor flavor) throws UnsupportedFlavorException, IOException {
-					throw new UnsupportedFlavorException(flavor);
-				}
-			}, sc2);
-
-			assertEquals(null,sc2.getClipboardContents());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testLostOwnership() throws Exception {
-		try {
-			SystemClipboard sc = new SystemClipboard();
-			sc.lostOwnership(null, null);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testEmpty() throws Exception {
-		try {
-			SystemClipboard sc2 = new SystemClipboard();
-			sc2.setClipboardContents(null);
-			assertNull(sc2.getClipboardContents());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.datatransfer.UnsupportedFlavorException;
+import java.io.IOException;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class SystemClipboardTest {
+	Logger	logger	= Logger.getLogger(SystemClipboardTest.class);
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testClipboard() throws Exception {
+		try {
+			SystemClipboard sc = new SystemClipboard();
+			sc.setClipboardContents("TEST");
+
+			SystemClipboard sc2 = new SystemClipboard();
+			assertEquals("TEST",sc2.getClipboardContents());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testInvalidClipboard() throws Exception {
+		try {
+			SystemClipboard sc2 = new SystemClipboard();
+			
+			Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+			clipboard.setContents(new Transferable() {
+				
+				@Override
+				public boolean isDataFlavorSupported(DataFlavor flavor) {
+					return true;
+				}
+				
+				@Override
+				public DataFlavor[] getTransferDataFlavors() {
+					return null;
+				}
+				
+				@Override
+				public Object getTransferData(DataFlavor flavor) throws UnsupportedFlavorException, IOException {
+					throw new UnsupportedFlavorException(flavor);
+				}
+			}, sc2);
+
+			assertEquals(null,sc2.getClipboardContents());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testLostOwnership() throws Exception {
+		try {
+			SystemClipboard sc = new SystemClipboard();
+			sc.lostOwnership(null, null);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testEmpty() throws Exception {
+		try {
+			SystemClipboard sc2 = new SystemClipboard();
+			sc2.setClipboardContents(null);
+			assertNull(sc2.getClipboardContents());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java b/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java
index 6bc27c3ee4..a0136bd8eb 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java
@@ -1,76 +1,76 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import java.io.ByteArrayInputStream;
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.lang.reflect.Constructor;
-import java.nio.charset.StandardCharsets;
-import java.util.Map;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class TextFileUtilsTest {
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testGetHeaderParametersFromFile() throws Exception {
-		try {
-			String fileContent = "#header\n" + //
-					"#param1=value1\n" + //
-					"#\n" + //
-					"no header\n" + //
-					"#param2=value\n";
-
-			Map<String, String> params = TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(fileContent.getBytes(StandardCharsets.UTF_8)));
-			assertEquals(1, params.keySet().size());
-			assertNull(params.get("param2"));
-			assertEquals("value1", params.get("param1"));
-			assertNull(params.get("header"));
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-	@Test
-	public void testParseHeader() throws Exception {
-		try {
-			InputStream is = new FileInputStream("testFiles/fileHeader.txt");
-			Map<String, String> map = TextFileUtils.getHeaderParametersFromFile(is);
-
-			assertEquals("1.0", map.get("VERSION"));
-			assertEquals("example name", map.get("NAME"));
-			assertEquals("layout description", map.get("DESCRIPTION"));
-			assertEquals("", map.get("MISSING"));
-			assertEquals("A=B", map.get("TRICKY"));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testPrivateConstructor() throws Exception {
-		try {
-			Constructor<?> constr = TextFileUtils.class.getDeclaredConstructor(new Class<?>[] {});
-			constr.setAccessible(true);
-			assertNotNull(constr.newInstance(new Object[] {}));
-		} catch (Exception e) {
-			throw e;
-		}
-	}
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import java.io.ByteArrayInputStream;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.lang.reflect.Constructor;
+import java.nio.charset.StandardCharsets;
+import java.util.Map;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class TextFileUtilsTest {
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testGetHeaderParametersFromFile() throws Exception {
+		try {
+			String fileContent = "#header\n" + //
+					"#param1=value1\n" + //
+					"#\n" + //
+					"no header\n" + //
+					"#param2=value\n";
+
+			Map<String, String> params = TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(fileContent.getBytes(StandardCharsets.UTF_8)));
+			assertEquals(1, params.keySet().size());
+			assertNull(params.get("param2"));
+			assertEquals("value1", params.get("param1"));
+			assertNull(params.get("header"));
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+	@Test
+	public void testParseHeader() throws Exception {
+		try {
+			InputStream is = new FileInputStream("testFiles/fileHeader.txt");
+			Map<String, String> map = TextFileUtils.getHeaderParametersFromFile(is);
+
+			assertEquals("1.0", map.get("VERSION"));
+			assertEquals("example name", map.get("NAME"));
+			assertEquals("layout description", map.get("DESCRIPTION"));
+			assertEquals("", map.get("MISSING"));
+			assertEquals("A=B", map.get("TRICKY"));
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testPrivateConstructor() throws Exception {
+		try {
+			Constructor<?> constr = TextFileUtils.class.getDeclaredConstructor(new Class<?>[] {});
+			constr.setAccessible(true);
+			assertNotNull(constr.newInstance(new Object[] {}));
+		} catch (Exception e) {
+			throw e;
+		}
+	}
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java b/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
index a2bd25fb39..5e2188cfd4 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
@@ -1,474 +1,474 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.lang.reflect.Field;
-import java.nio.charset.StandardCharsets;
-import java.util.List;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.apache.log4j.Logger;
-import org.apache.xerces.dom.DocumentImpl;
-import org.apache.xerces.dom.ElementImpl;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.NamedNodeMap;
-import org.w3c.dom.Node;
-import org.xml.sax.InputSource;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-
-public class XmlParserTest {
-	Logger		logger = Logger.getLogger(XmlParserTest.class);
-
-	XmlParser	parser = new XmlParser();
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testColorParsing() {
-		try {
-			String strColor = "ffcbcd09";
-
-			Color c = parser.stringToColor(strColor);
-			String resultString = parser.colorToString(c);
-			assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
-
-			Color c2 = parser.stringToColor(resultString);
-
-			assertEquals(c.getRed(), c2.getRed());
-			assertEquals(c.getGreen(), c2.getGreen());
-			assertEquals(c.getBlue(), c2.getBlue());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testInvalidColorParsing() {
-		try {
-			String strColor = "hello world";
-
-			parser.stringToColor(strColor);
-			fail("Exception expected");
-		} catch (InvalidArgumentException e) {
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testColorParsingWithAlpha() {
-		try {
-			String strColor = "fecbcd09";
-
-			Color c = parser.stringToColor(strColor);
-			String resultString = parser.colorToString(c);
-			assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
-
-			Color c2 = parser.stringToColor(resultString);
-
-			assertEquals(c.getRed(), c2.getRed());
-			assertEquals(c.getGreen(), c2.getGreen());
-			assertEquals(c.getBlue(), c2.getBlue());
-			assertEquals(c.getAlpha(), c2.getAlpha());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testGetXmlDocumentFromString() throws Exception {
-		try {
-			Document validDoc = parser.getXmlDocumentFromString("<node>test</node>");
-			assertNotNull(validDoc);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testNodeToString() throws Exception {
-		try {
-			String xml = "<test_node>test_x</test_node>";
-			Document validDoc = parser.getXmlDocumentFromString(xml);
-			String str = parser.nodeToString(validDoc);
-			assertEquals(xml.trim(), str.trim());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testEmptyNodeToString() throws Exception {
-		try {
-			String str = parser.nodeToString(null);
-			assertNull(str);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testNodeToStringWithHeader() throws Exception {
-		try {
-			String xml = "<test_node>test_x</test_node>";
-			Document validDoc = parser.getXmlDocumentFromString(xml);
-			String str = parser.nodeToString(validDoc, true);
-			assertTrue(str.contains(xml));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testInvalidNodeToString() throws Exception {
-		try {
-			final DocumentImpl xmlDoc = new DocumentImpl();
-
-			Element root = xmlDoc.createElement("booking");
-
-			class Tmp extends ElementImpl {
-				/**
-				 * 
-				 */
-				private static final long serialVersionUID = 1L;
-
-				public Tmp() {
-					this.ownerDocument = xmlDoc;
-				}
-
-				@Override
-				public NamedNodeMap getAttributes() {
-					return null;
-				}
-
-			}
-			;
-			Element el = new Tmp();
-			root.appendChild(el);
-			assertNotNull(parser.nodeToString(root, true));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testGetXmlDocumentFromInvalidString() throws Exception {
-		try {
-			parser.getXmlDocumentFromString("<node>test<node>");
-			fail("Exception expected");
-		} catch (InvalidXmlSchemaException e) {
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testGetXmlDocumentFromInvalidInputStream() throws Exception {
-		try {
-			parser.getXmlDocumentFromInputSource(new InputSource());
-			fail("Exception expected");
-		} catch (InvalidXmlSchemaException e) {
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testEscapeXml() throws Exception {
-		try {
-			String str = parser.escapeXml("<xml>node</xml>");
-			assertFalse(str.contains("<"));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testEscapeNullXml() throws Exception {
-		try {
-			String str = parser.escapeXml(null);
-			assertNull(str);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testFileToString() throws Exception {
-		try {
-			String str = parser.fileToString("testFiles/test.txt");
-			assertTrue(str.contains("test"));
-			assertTrue(str.contains("file"));
-			assertTrue(str.contains("with some content"));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testInputStreamToString() throws Exception {
-		try {
-			InputStream stream = new ByteArrayInputStream("stream string".getBytes(StandardCharsets.UTF_8));
-			String str = parser.inputStreamToString(stream);
-			assertEquals("stream string", str);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testGetNodeValue() throws Exception {
-		try {
-			Document document = parser.getXmlDocumentFromString("<node>content</node>");
-			Node node = parser.getNode("node", document);
-			String str = parser.getNodeValue(node);
-			assertEquals("content", str);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testGetNodeValue2() throws Exception {
-		try {
-			String str = parser.getNodeValue(null);
-			assertEquals("", str);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testGetNodeValue3() throws Exception {
-		try {
-			Document document = parser.getXmlDocumentFromString("<node></node>");
-			Node node = parser.getNode("node", document);
-			String str = parser.getNodeValue(node);
-			assertEquals("", str);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testGetNodeValue4() throws Exception {
-		try {
-			Document document = parser.getXmlDocumentFromString("<node><subnode/></node>");
-			Node node = parser.getNode("node", document);
-			String str = parser.getNodeValue(node);
-			assertEquals("", str);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testInputStreamToStringThrowsException() throws Exception {
-		try {
-			parser.inputStreamToString(new InputStream() {
-				@Override
-				public int read() throws IOException {
-					throw new IOException();
-				}
-			});
-			fail("Exception expected");
-		} catch (IOException e) {
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testFileToStringThrowsException() throws Exception {
-		try {
-			parser.fileToString("testFiles/unknown file.txt");
-			fail("Exception expected");
-		} catch (IOException e) {
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testGetNodeAttr() throws Exception {
-		try {
-			Document document = parser.getXmlDocumentFromString("<node attr=\"val\">content</node>");
-			Node node = parser.getNode("node", document);
-			String str = parser.getNodeAttr("attr", node);
-			assertEquals("val", str);
-			str = parser.getNodeAttr("attr2", node);
-			assertEquals("", str);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testGetNodes() throws Exception {
-		try {
-			Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
-			Node node = parser.getNode("node", document);
-			List<Node> nodes = parser.getNodes("subnode", node.getChildNodes());
-			assertEquals(2, nodes.size());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testGetNode() throws Exception {
-		try {
-			Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
-			Node node = parser.getNode("node", document);
-			Node child = parser.getNode("other", node.getChildNodes());
-			assertNotNull(child);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testGetNode2() throws Exception {
-		try {
-			Document document = parser.getXmlDocumentFromString("<node attr=\"x\"><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
-			Node node = parser.getNode("node", document);
-			Node child = parser.getNode("other2", node.getChildNodes());
-			assertNull(child);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testGetNode3() throws Exception {
-		try {
-			Document document = parser.getXmlDocumentFromString("<node attr=\"x\">xxx</node>");
-			Node node = parser.getNode("node", document);
-			Node child = parser.getNode("other2", node.getChildNodes());
-			assertNull(child);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testExceptionInConstructor() throws Exception {
-		DocumentBuilderFactory factory = null;
-		Field privateStringField = XmlParser.class.getDeclaredField("documentBuilderFactory");
-		try {
-
-			privateStringField.setAccessible(true);
-
-			factory = (DocumentBuilderFactory) privateStringField.get(parser);
-			privateStringField.set(parser, new DocumentBuilderFactory() {
-
-				@Override
-				public void setFeature(String name, boolean value) throws ParserConfigurationException {
-					// TODO Auto-generated method stub
-
-				}
-
-				@Override
-				public void setAttribute(String name, Object value) throws IllegalArgumentException {
-					// TODO Auto-generated method stub
-
-				}
-
-				@Override
-				public DocumentBuilder newDocumentBuilder() throws ParserConfigurationException {
-					throw new ParserConfigurationException();
-				}
-
-				@Override
-				public boolean getFeature(String name) throws ParserConfigurationException {
-					// TODO Auto-generated method stub
-					return false;
-				}
-
-				@Override
-				public Object getAttribute(String name) throws IllegalArgumentException {
-					// TODO Auto-generated method stub
-					return null;
-				}
-			});
-			new XmlParser();
-			fail("Exception expected");
-		} catch (InvalidStateException e) {
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		} finally {
-			privateStringField.set(parser, factory);
-		}
-	}
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.lang.reflect.Field;
+import java.nio.charset.StandardCharsets;
+import java.util.List;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.apache.log4j.Logger;
+import org.apache.xerces.dom.DocumentImpl;
+import org.apache.xerces.dom.ElementImpl;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.NamedNodeMap;
+import org.w3c.dom.Node;
+import org.xml.sax.InputSource;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+
+public class XmlParserTest {
+	Logger		logger = Logger.getLogger(XmlParserTest.class);
+
+	XmlParser	parser = new XmlParser();
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testColorParsing() {
+		try {
+			String strColor = "ffcbcd09";
+
+			Color c = parser.stringToColor(strColor);
+			String resultString = parser.colorToString(c);
+			assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
+
+			Color c2 = parser.stringToColor(resultString);
+
+			assertEquals(c.getRed(), c2.getRed());
+			assertEquals(c.getGreen(), c2.getGreen());
+			assertEquals(c.getBlue(), c2.getBlue());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testInvalidColorParsing() {
+		try {
+			String strColor = "hello world";
+
+			parser.stringToColor(strColor);
+			fail("Exception expected");
+		} catch (InvalidArgumentException e) {
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testColorParsingWithAlpha() {
+		try {
+			String strColor = "fecbcd09";
+
+			Color c = parser.stringToColor(strColor);
+			String resultString = parser.colorToString(c);
+			assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
+
+			Color c2 = parser.stringToColor(resultString);
+
+			assertEquals(c.getRed(), c2.getRed());
+			assertEquals(c.getGreen(), c2.getGreen());
+			assertEquals(c.getBlue(), c2.getBlue());
+			assertEquals(c.getAlpha(), c2.getAlpha());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testGetXmlDocumentFromString() throws Exception {
+		try {
+			Document validDoc = parser.getXmlDocumentFromString("<node>test</node>");
+			assertNotNull(validDoc);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testNodeToString() throws Exception {
+		try {
+			String xml = "<test_node>test_x</test_node>";
+			Document validDoc = parser.getXmlDocumentFromString(xml);
+			String str = parser.nodeToString(validDoc);
+			assertEquals(xml.trim(), str.trim());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testEmptyNodeToString() throws Exception {
+		try {
+			String str = parser.nodeToString(null);
+			assertNull(str);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testNodeToStringWithHeader() throws Exception {
+		try {
+			String xml = "<test_node>test_x</test_node>";
+			Document validDoc = parser.getXmlDocumentFromString(xml);
+			String str = parser.nodeToString(validDoc, true);
+			assertTrue(str.contains(xml));
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testInvalidNodeToString() throws Exception {
+		try {
+			final DocumentImpl xmlDoc = new DocumentImpl();
+
+			Element root = xmlDoc.createElement("booking");
+
+			class Tmp extends ElementImpl {
+				/**
+				 * 
+				 */
+				private static final long serialVersionUID = 1L;
+
+				public Tmp() {
+					this.ownerDocument = xmlDoc;
+				}
+
+				@Override
+				public NamedNodeMap getAttributes() {
+					return null;
+				}
+
+			}
+			;
+			Element el = new Tmp();
+			root.appendChild(el);
+			assertNotNull(parser.nodeToString(root, true));
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testGetXmlDocumentFromInvalidString() throws Exception {
+		try {
+			parser.getXmlDocumentFromString("<node>test<node>");
+			fail("Exception expected");
+		} catch (InvalidXmlSchemaException e) {
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testGetXmlDocumentFromInvalidInputStream() throws Exception {
+		try {
+			parser.getXmlDocumentFromInputSource(new InputSource());
+			fail("Exception expected");
+		} catch (InvalidXmlSchemaException e) {
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testEscapeXml() throws Exception {
+		try {
+			String str = parser.escapeXml("<xml>node</xml>");
+			assertFalse(str.contains("<"));
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testEscapeNullXml() throws Exception {
+		try {
+			String str = parser.escapeXml(null);
+			assertNull(str);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testFileToString() throws Exception {
+		try {
+			String str = parser.fileToString("testFiles/test.txt");
+			assertTrue(str.contains("test"));
+			assertTrue(str.contains("file"));
+			assertTrue(str.contains("with some content"));
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testInputStreamToString() throws Exception {
+		try {
+			InputStream stream = new ByteArrayInputStream("stream string".getBytes(StandardCharsets.UTF_8));
+			String str = parser.inputStreamToString(stream);
+			assertEquals("stream string", str);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testGetNodeValue() throws Exception {
+		try {
+			Document document = parser.getXmlDocumentFromString("<node>content</node>");
+			Node node = parser.getNode("node", document);
+			String str = parser.getNodeValue(node);
+			assertEquals("content", str);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testGetNodeValue2() throws Exception {
+		try {
+			String str = parser.getNodeValue(null);
+			assertEquals("", str);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testGetNodeValue3() throws Exception {
+		try {
+			Document document = parser.getXmlDocumentFromString("<node></node>");
+			Node node = parser.getNode("node", document);
+			String str = parser.getNodeValue(node);
+			assertEquals("", str);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testGetNodeValue4() throws Exception {
+		try {
+			Document document = parser.getXmlDocumentFromString("<node><subnode/></node>");
+			Node node = parser.getNode("node", document);
+			String str = parser.getNodeValue(node);
+			assertEquals("", str);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testInputStreamToStringThrowsException() throws Exception {
+		try {
+			parser.inputStreamToString(new InputStream() {
+				@Override
+				public int read() throws IOException {
+					throw new IOException();
+				}
+			});
+			fail("Exception expected");
+		} catch (IOException e) {
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testFileToStringThrowsException() throws Exception {
+		try {
+			parser.fileToString("testFiles/unknown file.txt");
+			fail("Exception expected");
+		} catch (IOException e) {
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testGetNodeAttr() throws Exception {
+		try {
+			Document document = parser.getXmlDocumentFromString("<node attr=\"val\">content</node>");
+			Node node = parser.getNode("node", document);
+			String str = parser.getNodeAttr("attr", node);
+			assertEquals("val", str);
+			str = parser.getNodeAttr("attr2", node);
+			assertEquals("", str);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testGetNodes() throws Exception {
+		try {
+			Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
+			Node node = parser.getNode("node", document);
+			List<Node> nodes = parser.getNodes("subnode", node.getChildNodes());
+			assertEquals(2, nodes.size());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testGetNode() throws Exception {
+		try {
+			Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
+			Node node = parser.getNode("node", document);
+			Node child = parser.getNode("other", node.getChildNodes());
+			assertNotNull(child);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testGetNode2() throws Exception {
+		try {
+			Document document = parser.getXmlDocumentFromString("<node attr=\"x\"><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
+			Node node = parser.getNode("node", document);
+			Node child = parser.getNode("other2", node.getChildNodes());
+			assertNull(child);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testGetNode3() throws Exception {
+		try {
+			Document document = parser.getXmlDocumentFromString("<node attr=\"x\">xxx</node>");
+			Node node = parser.getNode("node", document);
+			Node child = parser.getNode("other2", node.getChildNodes());
+			assertNull(child);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testExceptionInConstructor() throws Exception {
+		DocumentBuilderFactory factory = null;
+		Field privateStringField = XmlParser.class.getDeclaredField("documentBuilderFactory");
+		try {
+
+			privateStringField.setAccessible(true);
+
+			factory = (DocumentBuilderFactory) privateStringField.get(parser);
+			privateStringField.set(parser, new DocumentBuilderFactory() {
+
+				@Override
+				public void setFeature(String name, boolean value) throws ParserConfigurationException {
+					// TODO Auto-generated method stub
+
+				}
+
+				@Override
+				public void setAttribute(String name, Object value) throws IllegalArgumentException {
+					// TODO Auto-generated method stub
+
+				}
+
+				@Override
+				public DocumentBuilder newDocumentBuilder() throws ParserConfigurationException {
+					throw new ParserConfigurationException();
+				}
+
+				@Override
+				public boolean getFeature(String name) throws ParserConfigurationException {
+					// TODO Auto-generated method stub
+					return false;
+				}
+
+				@Override
+				public Object getAttribute(String name) throws IllegalArgumentException {
+					// TODO Auto-generated method stub
+					return null;
+				}
+			});
+			new XmlParser();
+			fail("Exception expected");
+		} catch (InvalidStateException e) {
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		} finally {
+			privateStringField.set(parser, factory);
+		}
+	}
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/BellExport.java b/console/src/main/java/lcsb/mapviewer/run/BellExport.java
index d22ed9fe9d..d280b38887 100644
--- a/console/src/main/java/lcsb/mapviewer/run/BellExport.java
+++ b/console/src/main/java/lcsb/mapviewer/run/BellExport.java
@@ -1,140 +1,140 @@
-package lcsb.mapviewer.run;
-
-import lcsb.mapviewer.annotation.services.ModelAnnotator;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.services.interfaces.IExporterService;
-import lcsb.mapviewer.services.interfaces.IExporterService.ExporterParameters;
-import lcsb.mapviewer.services.utils.data.ExportFileType;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * This class prepare data for Bell format (further transformation is done by
- * Marek).
- * 
- * @author Piotr Gawron
- * 
- */
-public class BellExport {
-	/**
-	 * Default class logger.
-	 */
-	private static Logger			logger	= Logger.getLogger(BellExport.class.getName());
-
-	/**
-	 * Object that performs different types of export transformation.
-	 */
-	@Autowired
-	private IExporterService	exporter;
-
-	/**
-	 * Object used to annotate the model.
-	 */
-	@Autowired
-	private ModelAnnotator		modelAnnotator;
-
-	/**
-	 * Object used to annotate the model.
-	 */
-	@Autowired
-	private DbUtils						dbUtils;
-
-	/**
-	 * Static main method used to run this stand alone code.
-	 * 
-	 * @param args
-	 *          command line arguments
-	 */
-	public static void main(String[] args) {
-		ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
-		BellExport main = new BellExport();
-		ApplicationContextLoader.injectDependencies(main);
-		main.run();
-	}
-
-	/**
-	 * Default constructor.
-	 */
-	public BellExport() {
-
-	}
-
-	/**
-	 * Method that export pd map into file that can be exported to bell (by
-	 * Marek).
-	 * 
-	 */
-	private void run() {
-		CellDesignerXmlParser p = new CellDesignerXmlParser();
-		try {
-			String filename = PdMapAnnotations.getLastPdFilename();
-			String version = PdMapAnnotations.getLastPdVersion();
-			
-			//filename = "testFiles/other_full/ASTHMAP18000X8000V1_38.xml";
-			//version = "1.1.38";
-			dbUtils.createSessionForCurrentThread();
-			Model model = p.createModel(new ConverterParams().filename(filename));
-
-			modelAnnotator.performAnnotations(model, new IProgressUpdater() {
-
-				@Override
-				public void setProgress(double progress) {
-					// TODO Auto-generated method stub
-
-				}
-			});
-
-			ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
-			fileName("out/bell/" + version + "-reactions.txt").//
-					fileType(ExportFileType.TAB_SEPARATED).//
-					type(Species.class).//
-					moleculeEdges(false);
-
-			exporter.exportReactions(params);
-
-			params = new IExporterService.ExporterParameters().model(model).//
-			fileName("out/bell/" + version + "-species.txt").//
-					fileType(ExportFileType.TAB_SEPARATED).//
-					type(Species.class).//
-//					column(ExportColumn.FULL).//
-					moleculeEdges(false);
-			exporter.exportSpecies(params);
-
-			params = new IExporterService.ExporterParameters().model(model).//
-			fileName("out/bell/" + version + "-compartments.txt").//
-					fileType(ExportFileType.TAB_SEPARATED).//
-					type(Object.class); //
-//					column(ExportColumn.FULL);
-			exporter.exportCompartments(params);
-
-		} catch (Exception e) {
-			logger.error(e.getMessage(), e);
-		} finally {
-			dbUtils.closeSessionForCurrentThread();
-		}
-	}
-
-	/**
-	 * @return the modelAnnotator
-	 * @see #modelAnnotator
-	 */
-	public ModelAnnotator getModelAnnotator() {
-		return modelAnnotator;
-	}
-
-	/**
-	 * @param modelAnnotator
-	 *          the modelAnnotator to set
-	 * @see #modelAnnotator
-	 */
-	public void setModelAnnotator(ModelAnnotator modelAnnotator) {
-		this.modelAnnotator = modelAnnotator;
-	}
-}
+package lcsb.mapviewer.run;
+
+import lcsb.mapviewer.annotation.services.ModelAnnotator;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.persist.ApplicationContextLoader;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.services.interfaces.IExporterService;
+import lcsb.mapviewer.services.interfaces.IExporterService.ExporterParameters;
+import lcsb.mapviewer.services.utils.data.ExportFileType;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * This class prepare data for Bell format (further transformation is done by
+ * Marek).
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public class BellExport {
+	/**
+	 * Default class logger.
+	 */
+	private static Logger			logger	= Logger.getLogger(BellExport.class.getName());
+
+	/**
+	 * Object that performs different types of export transformation.
+	 */
+	@Autowired
+	private IExporterService	exporter;
+
+	/**
+	 * Object used to annotate the model.
+	 */
+	@Autowired
+	private ModelAnnotator		modelAnnotator;
+
+	/**
+	 * Object used to annotate the model.
+	 */
+	@Autowired
+	private DbUtils						dbUtils;
+
+	/**
+	 * Static main method used to run this stand alone code.
+	 * 
+	 * @param args
+	 *          command line arguments
+	 */
+	public static void main(String[] args) {
+		ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+		BellExport main = new BellExport();
+		ApplicationContextLoader.injectDependencies(main);
+		main.run();
+	}
+
+	/**
+	 * Default constructor.
+	 */
+	public BellExport() {
+
+	}
+
+	/**
+	 * Method that export pd map into file that can be exported to bell (by
+	 * Marek).
+	 * 
+	 */
+	private void run() {
+		CellDesignerXmlParser p = new CellDesignerXmlParser();
+		try {
+			String filename = PdMapAnnotations.getLastPdFilename();
+			String version = PdMapAnnotations.getLastPdVersion();
+			
+			//filename = "testFiles/other_full/ASTHMAP18000X8000V1_38.xml";
+			//version = "1.1.38";
+			dbUtils.createSessionForCurrentThread();
+			Model model = p.createModel(new ConverterParams().filename(filename));
+
+			modelAnnotator.performAnnotations(model, new IProgressUpdater() {
+
+				@Override
+				public void setProgress(double progress) {
+					// TODO Auto-generated method stub
+
+				}
+			});
+
+			ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
+			fileName("out/bell/" + version + "-reactions.txt").//
+					fileType(ExportFileType.TAB_SEPARATED).//
+					type(Species.class).//
+					moleculeEdges(false);
+
+			exporter.exportReactions(params);
+
+			params = new IExporterService.ExporterParameters().model(model).//
+			fileName("out/bell/" + version + "-species.txt").//
+					fileType(ExportFileType.TAB_SEPARATED).//
+					type(Species.class).//
+//					column(ExportColumn.FULL).//
+					moleculeEdges(false);
+			exporter.exportSpecies(params);
+
+			params = new IExporterService.ExporterParameters().model(model).//
+			fileName("out/bell/" + version + "-compartments.txt").//
+					fileType(ExportFileType.TAB_SEPARATED).//
+					type(Object.class); //
+//					column(ExportColumn.FULL);
+			exporter.exportCompartments(params);
+
+		} catch (Exception e) {
+			logger.error(e.getMessage(), e);
+		} finally {
+			dbUtils.closeSessionForCurrentThread();
+		}
+	}
+
+	/**
+	 * @return the modelAnnotator
+	 * @see #modelAnnotator
+	 */
+	public ModelAnnotator getModelAnnotator() {
+		return modelAnnotator;
+	}
+
+	/**
+	 * @param modelAnnotator
+	 *          the modelAnnotator to set
+	 * @see #modelAnnotator
+	 */
+	public void setModelAnnotator(ModelAnnotator modelAnnotator) {
+		this.modelAnnotator = modelAnnotator;
+	}
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
index 09c6c27d63..3f6ad5730d 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
@@ -1,467 +1,467 @@
-package lcsb.mapviewer.run;
-
-import java.awt.geom.Point2D;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.io.UnsupportedEncodingException;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.annotation.services.MiriamConnector;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-/**
- * This class is entry point for console tool to convert data from tab separated
- * file a CellDesigner format.
- * 
- * @author Piotr Gawron
- * 
- */
-public class ConsoleConverter {
-
-	/**
-	 * Default class logger.
-	 */
-	private final Logger		logger				= Logger.getLogger(ConsoleConverter.class);
-
-	/**
-	 * Options from the input.
-	 */
-	private RunOptions			inputOptions;
-
-	/**
-	 * Connector used for accessing data from miriam registry.
-	 */
-	private MiriamConnector	mc = new MiriamConnector();
-
-	/**
-	 * Util class used to access some information about {@link Element}.
-	 */
-	private ElementUtils		elementUtils	= new ElementUtils();
-
-	/**
-	 * Default constructor.
-	 * 
-	 * @param args
-	 *          parameters with which the program was run
-	 */
-	public ConsoleConverter(String[] args) {
-		inputOptions = new RunOptions(args);
-	}
-
-	/**
-	 * Main entry point to the program.
-	 * 
-	 * @param args
-	 *          parameters with which the program was run
-	 */
-	public static void main(String[] args) {
-//		ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
-		ConsoleConverter main = new ConsoleConverter(args);
-//		ApplicationContextLoader.injectDependencies(main);
-		try {
-			main.run();
-		} catch (InvalidInputDataExecption e) {
-			main.logger.error(e, e);
-		}
-	}
-
-	/**
-	 * This method transform {@link #inputOptions input data}.
-	 * 
-	 * @throws InvalidInputDataExecption
-	 *           thrown when the input data are invalid
-	 */
-	private void run() throws InvalidInputDataExecption {
-		if (inputOptions.isFormat()) {
-			inputOptions.printFormat();
-		} else if (!inputOptions.isValidInput() || inputOptions.isHelpOption()) {
-			inputOptions.printHelp();
-		} else {
-			logger.debug("Running...");
-
-			String nodesFilename = inputOptions.getNodesFilename();
-
-			Model model = new ModelFullIndexed(null);
-			model.setWidth(inputOptions.getModelSize());
-			model.setHeight(inputOptions.getModelSize());
-			model.addCompartment(new Compartment("default"));
-
-			Set<Element> elements = null;
-			try {
-				elements = getNodes(nodesFilename);
-			} catch (IOException e) {
-				throw new InvalidInputDataExecption("Problem with input file: " + nodesFilename, e);
-			}
-
-			for (Element element : elements) {
-				model.addElement(element);
-			}
-
-			double middleX = inputOptions.getModelSize() / 2;
-			double middleY = inputOptions.getModelSize() / 2;
-
-			double size = model.getSpecies().size();
-			double x = 0;
-
-			for (Species species : model.getSpecies()) {
-				SpeciesAlias alias = new SpeciesAlias(species);
-				alias.setAliasId("al" + species.getElementId());
-				alias.setWidth(inputOptions.getAliasWidth());
-				alias.setHeight(inputOptions.getAliasHeight());
-				double angle = x / size * 2 * Math.PI;
-				alias.setX(middleX + Math.sin(angle) * inputOptions.getRadius());
-				alias.setY(middleY + Math.cos(angle) * inputOptions.getRadius());
-				model.addAlias(alias);
-				x++;
-			}
-
-			String reactionsFilename = inputOptions.getReactionsFilename();
-
-			List<Reaction> reactions;
-			try {
-				reactions = getReactions(reactionsFilename, model);
-			} catch (IOException e) {
-				throw new InvalidInputDataExecption("Problem with input file: " + reactionsFilename, e);
-			}
-			model.addReactions(reactions);
-			String outputFilename = inputOptions.getOutputFilename();
-
-			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			PrintWriter writer = null;
-			try {
-				writer = new PrintWriter(outputFilename, "UTF-8");
-				writer.println(parser.toXml(model));
-			} catch (FileNotFoundException e) {
-				throw new InvalidInputDataExecption("Problem with output file: " + outputFilename, e);
-			} catch (UnsupportedEncodingException e) {
-				logger.error(e, e);
-			} catch (InconsistentModelException e) {
-				throw new InvalidStateException(e);
-			} finally {
-				writer.close();
-			}
-
-		}
-	}
-
-	/**
-	 * Returns list of {@link Reaction reactions} obtained from input file.
-	 * 
-	 * @param filename
-	 *          file with information about reactions
-	 * @param model
-	 *          {@link Model} where the data about nodes is stored
-	 * @return list of {@link Reaction reactions} obtained from input file
-	 * @throws InvalidInputDataExecption
-	 *           thrown when the file is invalid
-	 * @throws IOException
-	 *           thrown when there is a problem with acceesing input file
-	 */
-	private List<Reaction> getReactions(String filename, Model model) throws InvalidInputDataExecption, IOException {
-		List<Reaction> result = new ArrayList<Reaction>();
-		Integer identifierColumn = null;
-		Integer typeColumn = null;
-		Integer reactantsColumn = null;
-		Integer modifiersColumn = null;
-		Integer productsColumn = null;
-		Integer annotationsColumn = null;
-		Set<Integer> ids = new HashSet<Integer>();
-		BufferedReader br = new BufferedReader(new FileReader(new File(filename)));
-		try {
-			String line = br.readLine();
-			String[] cols = line.split("\t", -1);
-			int columns = cols.length;
-			for (int i = 0; i < cols.length; i++) {
-				if (cols[i].equalsIgnoreCase(RunOptions.IDENTIFIER_REACTIONS_HEADER)) {
-					identifierColumn = i;
-				} else if (cols[i].equalsIgnoreCase(RunOptions.TYPE_REACTIONS_HEADER)) {
-					typeColumn = i;
-				} else if (cols[i].equalsIgnoreCase(RunOptions.REACTANTS_REACTIONS_HEADER)) {
-					reactantsColumn = i;
-				} else if (cols[i].equalsIgnoreCase(RunOptions.MODIFIERS_REACTIONS_HEADER)) {
-					modifiersColumn = i;
-				} else if (cols[i].equalsIgnoreCase(RunOptions.PRODUCTS_REACTIONS_HEADER)) {
-					productsColumn = i;
-				} else if (cols[i].equalsIgnoreCase(RunOptions.ANNOTATIONS_REACTIONS_HEADER)) {
-					annotationsColumn = i;
-				} else {
-					throw new InvalidInputDataExecption("Unknown column name " + cols[i], filename);
-				}
-			}
-			if (identifierColumn == null) {
-				throw new InvalidInputDataExecption("No \"" + RunOptions.IDENTIFIER_REACTIONS_HEADER + "\" defined.", filename);
-			} else if (typeColumn == null) {
-				throw new InvalidInputDataExecption("No \"" + RunOptions.TYPE_REACTIONS_HEADER + "\" defined.", filename);
-			} else if (reactantsColumn == null) {
-				throw new InvalidInputDataExecption("No \"" + RunOptions.REACTANTS_REACTIONS_HEADER + "\" defined.", filename);
-			} else if (modifiersColumn == null) {
-				throw new InvalidInputDataExecption("No \"" + RunOptions.MODIFIERS_REACTIONS_HEADER + "\" defined.", filename);
-			} else if (productsColumn == null) {
-				throw new InvalidInputDataExecption("No \"" + RunOptions.PRODUCTS_REACTIONS_HEADER + "\" defined.", filename);
-			} else if (annotationsColumn == null) {
-				throw new InvalidInputDataExecption("No \"" + RunOptions.ANNOTATIONS_REACTIONS_HEADER + "\" defined.", filename);
-			}
-			int row = 2;
-			while ((line = br.readLine()) != null) {
-				cols = line.split("\t", -1);
-				if (cols.length != columns) {
-					throw new InvalidInputDataExecption("Invalid number of columns in row " + row, filename);
-				}
-				String id = cols[identifierColumn];
-				if (ids.contains(id)) {
-					throw new InvalidInputDataExecption("Id \"" + id + "\" is not unique.", filename);
-				}
-
-				String className = cols[typeColumn];
-				Class<? extends AnnotatedObject> clazz = elementUtils.getClassByName(className);
-				if (clazz == null) {
-					throw new InvalidInputDataExecption("Unknown element type: " + className, filename);
-				}
-				List<Product> products = new ArrayList<Product>();
-				String productString = cols[productsColumn];
-				for (String string : productString.split(",")) {
-					if (!string.isEmpty()) {
-						Element element = model.getSpeciesBySpeciesId(string.trim());
-						SpeciesAlias alias = model.getAliasesBySpeciesId(string.trim()).get(0);
-						Product product = new Product(alias, element);
-						products.add(product);
-					}
-				}
-				if (products.size() == 0) {
-					throw new InvalidInputDataExecption("List of products cannot be empty (row: " + row + ")", filename);
-				}
-
-				List<Reactant> reactants = new ArrayList<Reactant>();
-				String reactantString = cols[reactantsColumn];
-				for (String string : reactantString.split(",")) {
-					if (!string.isEmpty()) {
-						Element element = model.getSpeciesBySpeciesId(string.trim());
-						SpeciesAlias alias = model.getAliasesBySpeciesId(string.trim()).get(0);
-						Reactant product = new Reactant(alias, element);
-						reactants.add(product);
-					}
-				}
-				if (reactants.size() == 0) {
-					throw new InvalidInputDataExecption("List of reactants cannot be empty (row: " + row + ")", filename);
-				}
-
-				List<Modifier> modifiers = new ArrayList<Modifier>();
-				String modifierString = cols[modifiersColumn];
-				for (String string : modifierString.split(",")) {
-					if (!string.isEmpty()) {
-						Element element = model.getSpeciesBySpeciesId(string.trim());
-						SpeciesAlias alias = model.getAliasesBySpeciesId(string.trim()).get(0);
-						Modifier modifier = new Catalysis(alias, element);
-						modifiers.add(modifier);
-					}
-				}
-				Alias alias1 = products.get(0).getAlias();
-				Alias alias2 = reactants.get(0).getAlias();
-
-				Point2D middle = new Point2D.Double((alias1.getCenterX() + alias2.getCenterX()) / 2, (alias1.getCenterY() + alias2.getCenterY()) / 2);
-
-				Set<MiriamData> annotations = new HashSet<MiriamData>();
-				if (annotationsColumn != null) {
-					String[] annotationString = cols[annotationsColumn].split(",");
-					for (String string : annotationString) {
-						if (!string.isEmpty()) {
-							try {
-								annotations.add(MiriamType.getMiriamByUri(string));
-							} catch (InvalidArgumentException e) {
-								throw new InvalidInputDataExecption("Invalid miriam urn: " + string, filename);
-							}
-						}
-					}
-				}
-
-				try {
-					if (!Reaction.class.isAssignableFrom(clazz)) {
-						throw new InvalidInputDataExecption("Invalid reaction type type: " + className, filename);
-					}
-					Reaction reaction = (Reaction) clazz.newInstance();
-					for (Product product : products) {
-						product.setLine(new PolylineData(middle, product.getAlias().getCenter()));
-						reaction.addProduct(product);
-					}
-					for (Reactant reactant : reactants) {
-						reactant.setLine(new PolylineData(reactant.getAlias().getCenter(), middle));
-						reaction.addReactant(reactant);
-					}
-					for (Modifier modifier : modifiers) {
-						modifier.setLine(new PolylineData(middle, modifier.getAlias().getCenter()));
-						reaction.addModifier(modifier);
-					}
-					reaction.addMiriamData(annotations);
-					reaction.setElementId(id);
-					result.add(reaction);
-				} catch (InstantiationException e) {
-					throw new InvalidStateException(e);
-				} catch (IllegalAccessException e) {
-					throw new InvalidStateException(e);
-				}
-				row++;
-			}
-		} finally {
-			br.close();
-		}
-		return result;
-	}
-
-	/**
-	 * This method parses the data from input file into set of {@link Element
-	 * elements}.
-	 * 
-	 * @param filename
-	 *          nam of input file
-	 * @return set of {@link Element elements}
-	 * @throws InvalidInputDataExecption
-	 *           thrown when the input data is invalid
-	 * @throws IOException
-	 *           thrown when there is a problem with input file
-	 */
-	private Set<Element> getNodes(String filename) throws InvalidInputDataExecption, IOException {
-		ElementUtils elementUtils = new ElementUtils();
-
-		Set<Element> result = new HashSet<Element>();
-		Set<String> ids = new HashSet<String>();
-
-		Integer identifierColumn = null;
-		Integer typeColumn = null;
-		Integer nameColumn = null;
-		Integer annotationsColumn = null;
-
-		BufferedReader br = new BufferedReader(new FileReader(new File(filename)));
-		try {
-			String line = br.readLine();
-			String[] cols = line.split("\t", -1);
-			int columns = cols.length;
-			for (int i = 0; i < cols.length; i++) {
-				if (cols[i].equalsIgnoreCase(RunOptions.IDENTIFIER_NODES_HEADER)) {
-					identifierColumn = i;
-				} else if (cols[i].equalsIgnoreCase(RunOptions.TYPE_NODES_HEADER)) {
-					typeColumn = i;
-				} else if (cols[i].equalsIgnoreCase(RunOptions.NAME_NODES_HEADER)) {
-					nameColumn = i;
-				} else if (cols[i].equalsIgnoreCase(RunOptions.ANNOTATIONS_NODES_HEADER)) {
-					annotationsColumn = i;
-				} else {
-					throw new InvalidInputDataExecption("Unknown column name " + cols[i], filename);
-				}
-			}
-			if (identifierColumn == null) {
-				throw new InvalidInputDataExecption("No \"" + RunOptions.IDENTIFIER_NODES_HEADER + "\" defined.", filename);
-			}
-			if (typeColumn == null) {
-				throw new InvalidInputDataExecption("No \"" + RunOptions.TYPE_NODES_HEADER + "\" defined.", filename);
-			}
-			if (nameColumn == null) {
-				throw new InvalidInputDataExecption("No \"" + RunOptions.NAME_NODES_HEADER + "\" defined.", filename);
-			}
-			int row = 2;
-			while ((line = br.readLine()) != null) {
-				if (line.isEmpty()) {
-					continue;
-				}
-				cols = line.split("\t", -1);
-				if (cols.length != columns) {
-					throw new InvalidInputDataExecption(
-							"Invalid number of columns in row " + row + ". Expected " + columns + ", but " + cols.length + " found", filename);
-				}
-				String id = cols[identifierColumn];
-				if (ids.contains(id)) {
-					throw new InvalidInputDataExecption("Id \"" + id + "\" is not unique.", filename);
-				}
-
-				String className = cols[typeColumn];
-				Class<? extends AnnotatedObject> clazz = elementUtils.getClassByName(className);
-				if (clazz == null) {
-					throw new InvalidInputDataExecption("Unknown element type: " + className, filename);
-				}
-				String name = cols[nameColumn];
-				if (name.isEmpty()) {
-					throw new InvalidInputDataExecption("Name cannot be empty (row " + row + ").", filename);
-				}
-				Set<MiriamData> annotations = new HashSet<MiriamData>();
-				if (annotationsColumn != null) {
-					String[] annotationString = cols[annotationsColumn].split(",");
-					for (String string : annotationString) {
-						if (!string.isEmpty()) {
-							try {
-								annotations.add(MiriamType.getMiriamByUri(string));
-							} catch (InvalidArgumentException e) {
-								throw new InvalidInputDataExecption("Invalid miriam urn: " + string, filename);
-							}
-						}
-					}
-				}
-
-				try {
-					if (!Element.class.isAssignableFrom(clazz)) {
-						throw new InvalidInputDataExecption("Invliad element type: " + className, filename);
-					}
-					Element element = (Element) clazz.newInstance();
-					element.setName(name);
-					element.addMiriamData(annotations);
-					element.setElementId(id);
-					result.add(element);
-				} catch (InstantiationException e) {
-					throw new InvalidStateException(e);
-				} catch (IllegalAccessException e) {
-					throw new InvalidStateException(e);
-				}
-				row++;
-			}
-		} finally {
-			br.close();
-		}
-
-		return result;
-	}
-
-	/**
-	 * @return the mc
-	 * @see #mc
-	 */
-	public MiriamConnector getMc() {
-		return mc;
-	}
-
-	/**
-	 * @param mc
-	 *          the mc to set
-	 * @see #mc
-	 */
-	public void setMc(MiriamConnector mc) {
-		this.mc = mc;
-	}
-}
+package lcsb.mapviewer.run;
+
+import java.awt.geom.Point2D;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.annotation.services.MiriamConnector;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * This class is entry point for console tool to convert data from tab separated
+ * file a CellDesigner format.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public class ConsoleConverter {
+
+	/**
+	 * Default class logger.
+	 */
+	private final Logger		logger				= Logger.getLogger(ConsoleConverter.class);
+
+	/**
+	 * Options from the input.
+	 */
+	private RunOptions			inputOptions;
+
+	/**
+	 * Connector used for accessing data from miriam registry.
+	 */
+	private MiriamConnector	mc = new MiriamConnector();
+
+	/**
+	 * Util class used to access some information about {@link Element}.
+	 */
+	private ElementUtils		elementUtils	= new ElementUtils();
+
+	/**
+	 * Default constructor.
+	 * 
+	 * @param args
+	 *          parameters with which the program was run
+	 */
+	public ConsoleConverter(String[] args) {
+		inputOptions = new RunOptions(args);
+	}
+
+	/**
+	 * Main entry point to the program.
+	 * 
+	 * @param args
+	 *          parameters with which the program was run
+	 */
+	public static void main(String[] args) {
+//		ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+		ConsoleConverter main = new ConsoleConverter(args);
+//		ApplicationContextLoader.injectDependencies(main);
+		try {
+			main.run();
+		} catch (InvalidInputDataExecption e) {
+			main.logger.error(e, e);
+		}
+	}
+
+	/**
+	 * This method transform {@link #inputOptions input data}.
+	 * 
+	 * @throws InvalidInputDataExecption
+	 *           thrown when the input data are invalid
+	 */
+	private void run() throws InvalidInputDataExecption {
+		if (inputOptions.isFormat()) {
+			inputOptions.printFormat();
+		} else if (!inputOptions.isValidInput() || inputOptions.isHelpOption()) {
+			inputOptions.printHelp();
+		} else {
+			logger.debug("Running...");
+
+			String nodesFilename = inputOptions.getNodesFilename();
+
+			Model model = new ModelFullIndexed(null);
+			model.setWidth(inputOptions.getModelSize());
+			model.setHeight(inputOptions.getModelSize());
+			model.addCompartment(new Compartment("default"));
+
+			Set<Element> elements = null;
+			try {
+				elements = getNodes(nodesFilename);
+			} catch (IOException e) {
+				throw new InvalidInputDataExecption("Problem with input file: " + nodesFilename, e);
+			}
+
+			for (Element element : elements) {
+				model.addElement(element);
+			}
+
+			double middleX = inputOptions.getModelSize() / 2;
+			double middleY = inputOptions.getModelSize() / 2;
+
+			double size = model.getSpecies().size();
+			double x = 0;
+
+			for (Species species : model.getSpecies()) {
+				SpeciesAlias alias = new SpeciesAlias(species);
+				alias.setAliasId("al" + species.getElementId());
+				alias.setWidth(inputOptions.getAliasWidth());
+				alias.setHeight(inputOptions.getAliasHeight());
+				double angle = x / size * 2 * Math.PI;
+				alias.setX(middleX + Math.sin(angle) * inputOptions.getRadius());
+				alias.setY(middleY + Math.cos(angle) * inputOptions.getRadius());
+				model.addAlias(alias);
+				x++;
+			}
+
+			String reactionsFilename = inputOptions.getReactionsFilename();
+
+			List<Reaction> reactions;
+			try {
+				reactions = getReactions(reactionsFilename, model);
+			} catch (IOException e) {
+				throw new InvalidInputDataExecption("Problem with input file: " + reactionsFilename, e);
+			}
+			model.addReactions(reactions);
+			String outputFilename = inputOptions.getOutputFilename();
+
+			CellDesignerXmlParser parser = new CellDesignerXmlParser();
+			PrintWriter writer = null;
+			try {
+				writer = new PrintWriter(outputFilename, "UTF-8");
+				writer.println(parser.toXml(model));
+			} catch (FileNotFoundException e) {
+				throw new InvalidInputDataExecption("Problem with output file: " + outputFilename, e);
+			} catch (UnsupportedEncodingException e) {
+				logger.error(e, e);
+			} catch (InconsistentModelException e) {
+				throw new InvalidStateException(e);
+			} finally {
+				writer.close();
+			}
+
+		}
+	}
+
+	/**
+	 * Returns list of {@link Reaction reactions} obtained from input file.
+	 * 
+	 * @param filename
+	 *          file with information about reactions
+	 * @param model
+	 *          {@link Model} where the data about nodes is stored
+	 * @return list of {@link Reaction reactions} obtained from input file
+	 * @throws InvalidInputDataExecption
+	 *           thrown when the file is invalid
+	 * @throws IOException
+	 *           thrown when there is a problem with acceesing input file
+	 */
+	private List<Reaction> getReactions(String filename, Model model) throws InvalidInputDataExecption, IOException {
+		List<Reaction> result = new ArrayList<Reaction>();
+		Integer identifierColumn = null;
+		Integer typeColumn = null;
+		Integer reactantsColumn = null;
+		Integer modifiersColumn = null;
+		Integer productsColumn = null;
+		Integer annotationsColumn = null;
+		Set<Integer> ids = new HashSet<Integer>();
+		BufferedReader br = new BufferedReader(new FileReader(new File(filename)));
+		try {
+			String line = br.readLine();
+			String[] cols = line.split("\t", -1);
+			int columns = cols.length;
+			for (int i = 0; i < cols.length; i++) {
+				if (cols[i].equalsIgnoreCase(RunOptions.IDENTIFIER_REACTIONS_HEADER)) {
+					identifierColumn = i;
+				} else if (cols[i].equalsIgnoreCase(RunOptions.TYPE_REACTIONS_HEADER)) {
+					typeColumn = i;
+				} else if (cols[i].equalsIgnoreCase(RunOptions.REACTANTS_REACTIONS_HEADER)) {
+					reactantsColumn = i;
+				} else if (cols[i].equalsIgnoreCase(RunOptions.MODIFIERS_REACTIONS_HEADER)) {
+					modifiersColumn = i;
+				} else if (cols[i].equalsIgnoreCase(RunOptions.PRODUCTS_REACTIONS_HEADER)) {
+					productsColumn = i;
+				} else if (cols[i].equalsIgnoreCase(RunOptions.ANNOTATIONS_REACTIONS_HEADER)) {
+					annotationsColumn = i;
+				} else {
+					throw new InvalidInputDataExecption("Unknown column name " + cols[i], filename);
+				}
+			}
+			if (identifierColumn == null) {
+				throw new InvalidInputDataExecption("No \"" + RunOptions.IDENTIFIER_REACTIONS_HEADER + "\" defined.", filename);
+			} else if (typeColumn == null) {
+				throw new InvalidInputDataExecption("No \"" + RunOptions.TYPE_REACTIONS_HEADER + "\" defined.", filename);
+			} else if (reactantsColumn == null) {
+				throw new InvalidInputDataExecption("No \"" + RunOptions.REACTANTS_REACTIONS_HEADER + "\" defined.", filename);
+			} else if (modifiersColumn == null) {
+				throw new InvalidInputDataExecption("No \"" + RunOptions.MODIFIERS_REACTIONS_HEADER + "\" defined.", filename);
+			} else if (productsColumn == null) {
+				throw new InvalidInputDataExecption("No \"" + RunOptions.PRODUCTS_REACTIONS_HEADER + "\" defined.", filename);
+			} else if (annotationsColumn == null) {
+				throw new InvalidInputDataExecption("No \"" + RunOptions.ANNOTATIONS_REACTIONS_HEADER + "\" defined.", filename);
+			}
+			int row = 2;
+			while ((line = br.readLine()) != null) {
+				cols = line.split("\t", -1);
+				if (cols.length != columns) {
+					throw new InvalidInputDataExecption("Invalid number of columns in row " + row, filename);
+				}
+				String id = cols[identifierColumn];
+				if (ids.contains(id)) {
+					throw new InvalidInputDataExecption("Id \"" + id + "\" is not unique.", filename);
+				}
+
+				String className = cols[typeColumn];
+				Class<? extends AnnotatedObject> clazz = elementUtils.getClassByName(className);
+				if (clazz == null) {
+					throw new InvalidInputDataExecption("Unknown element type: " + className, filename);
+				}
+				List<Product> products = new ArrayList<Product>();
+				String productString = cols[productsColumn];
+				for (String string : productString.split(",")) {
+					if (!string.isEmpty()) {
+						Element element = model.getSpeciesBySpeciesId(string.trim());
+						SpeciesAlias alias = model.getAliasesBySpeciesId(string.trim()).get(0);
+						Product product = new Product(alias, element);
+						products.add(product);
+					}
+				}
+				if (products.size() == 0) {
+					throw new InvalidInputDataExecption("List of products cannot be empty (row: " + row + ")", filename);
+				}
+
+				List<Reactant> reactants = new ArrayList<Reactant>();
+				String reactantString = cols[reactantsColumn];
+				for (String string : reactantString.split(",")) {
+					if (!string.isEmpty()) {
+						Element element = model.getSpeciesBySpeciesId(string.trim());
+						SpeciesAlias alias = model.getAliasesBySpeciesId(string.trim()).get(0);
+						Reactant product = new Reactant(alias, element);
+						reactants.add(product);
+					}
+				}
+				if (reactants.size() == 0) {
+					throw new InvalidInputDataExecption("List of reactants cannot be empty (row: " + row + ")", filename);
+				}
+
+				List<Modifier> modifiers = new ArrayList<Modifier>();
+				String modifierString = cols[modifiersColumn];
+				for (String string : modifierString.split(",")) {
+					if (!string.isEmpty()) {
+						Element element = model.getSpeciesBySpeciesId(string.trim());
+						SpeciesAlias alias = model.getAliasesBySpeciesId(string.trim()).get(0);
+						Modifier modifier = new Catalysis(alias, element);
+						modifiers.add(modifier);
+					}
+				}
+				Alias alias1 = products.get(0).getAlias();
+				Alias alias2 = reactants.get(0).getAlias();
+
+				Point2D middle = new Point2D.Double((alias1.getCenterX() + alias2.getCenterX()) / 2, (alias1.getCenterY() + alias2.getCenterY()) / 2);
+
+				Set<MiriamData> annotations = new HashSet<MiriamData>();
+				if (annotationsColumn != null) {
+					String[] annotationString = cols[annotationsColumn].split(",");
+					for (String string : annotationString) {
+						if (!string.isEmpty()) {
+							try {
+								annotations.add(MiriamType.getMiriamByUri(string));
+							} catch (InvalidArgumentException e) {
+								throw new InvalidInputDataExecption("Invalid miriam urn: " + string, filename);
+							}
+						}
+					}
+				}
+
+				try {
+					if (!Reaction.class.isAssignableFrom(clazz)) {
+						throw new InvalidInputDataExecption("Invalid reaction type type: " + className, filename);
+					}
+					Reaction reaction = (Reaction) clazz.newInstance();
+					for (Product product : products) {
+						product.setLine(new PolylineData(middle, product.getAlias().getCenter()));
+						reaction.addProduct(product);
+					}
+					for (Reactant reactant : reactants) {
+						reactant.setLine(new PolylineData(reactant.getAlias().getCenter(), middle));
+						reaction.addReactant(reactant);
+					}
+					for (Modifier modifier : modifiers) {
+						modifier.setLine(new PolylineData(middle, modifier.getAlias().getCenter()));
+						reaction.addModifier(modifier);
+					}
+					reaction.addMiriamData(annotations);
+					reaction.setElementId(id);
+					result.add(reaction);
+				} catch (InstantiationException e) {
+					throw new InvalidStateException(e);
+				} catch (IllegalAccessException e) {
+					throw new InvalidStateException(e);
+				}
+				row++;
+			}
+		} finally {
+			br.close();
+		}
+		return result;
+	}
+
+	/**
+	 * This method parses the data from input file into set of {@link Element
+	 * elements}.
+	 * 
+	 * @param filename
+	 *          nam of input file
+	 * @return set of {@link Element elements}
+	 * @throws InvalidInputDataExecption
+	 *           thrown when the input data is invalid
+	 * @throws IOException
+	 *           thrown when there is a problem with input file
+	 */
+	private Set<Element> getNodes(String filename) throws InvalidInputDataExecption, IOException {
+		ElementUtils elementUtils = new ElementUtils();
+
+		Set<Element> result = new HashSet<Element>();
+		Set<String> ids = new HashSet<String>();
+
+		Integer identifierColumn = null;
+		Integer typeColumn = null;
+		Integer nameColumn = null;
+		Integer annotationsColumn = null;
+
+		BufferedReader br = new BufferedReader(new FileReader(new File(filename)));
+		try {
+			String line = br.readLine();
+			String[] cols = line.split("\t", -1);
+			int columns = cols.length;
+			for (int i = 0; i < cols.length; i++) {
+				if (cols[i].equalsIgnoreCase(RunOptions.IDENTIFIER_NODES_HEADER)) {
+					identifierColumn = i;
+				} else if (cols[i].equalsIgnoreCase(RunOptions.TYPE_NODES_HEADER)) {
+					typeColumn = i;
+				} else if (cols[i].equalsIgnoreCase(RunOptions.NAME_NODES_HEADER)) {
+					nameColumn = i;
+				} else if (cols[i].equalsIgnoreCase(RunOptions.ANNOTATIONS_NODES_HEADER)) {
+					annotationsColumn = i;
+				} else {
+					throw new InvalidInputDataExecption("Unknown column name " + cols[i], filename);
+				}
+			}
+			if (identifierColumn == null) {
+				throw new InvalidInputDataExecption("No \"" + RunOptions.IDENTIFIER_NODES_HEADER + "\" defined.", filename);
+			}
+			if (typeColumn == null) {
+				throw new InvalidInputDataExecption("No \"" + RunOptions.TYPE_NODES_HEADER + "\" defined.", filename);
+			}
+			if (nameColumn == null) {
+				throw new InvalidInputDataExecption("No \"" + RunOptions.NAME_NODES_HEADER + "\" defined.", filename);
+			}
+			int row = 2;
+			while ((line = br.readLine()) != null) {
+				if (line.isEmpty()) {
+					continue;
+				}
+				cols = line.split("\t", -1);
+				if (cols.length != columns) {
+					throw new InvalidInputDataExecption(
+							"Invalid number of columns in row " + row + ". Expected " + columns + ", but " + cols.length + " found", filename);
+				}
+				String id = cols[identifierColumn];
+				if (ids.contains(id)) {
+					throw new InvalidInputDataExecption("Id \"" + id + "\" is not unique.", filename);
+				}
+
+				String className = cols[typeColumn];
+				Class<? extends AnnotatedObject> clazz = elementUtils.getClassByName(className);
+				if (clazz == null) {
+					throw new InvalidInputDataExecption("Unknown element type: " + className, filename);
+				}
+				String name = cols[nameColumn];
+				if (name.isEmpty()) {
+					throw new InvalidInputDataExecption("Name cannot be empty (row " + row + ").", filename);
+				}
+				Set<MiriamData> annotations = new HashSet<MiriamData>();
+				if (annotationsColumn != null) {
+					String[] annotationString = cols[annotationsColumn].split(",");
+					for (String string : annotationString) {
+						if (!string.isEmpty()) {
+							try {
+								annotations.add(MiriamType.getMiriamByUri(string));
+							} catch (InvalidArgumentException e) {
+								throw new InvalidInputDataExecption("Invalid miriam urn: " + string, filename);
+							}
+						}
+					}
+				}
+
+				try {
+					if (!Element.class.isAssignableFrom(clazz)) {
+						throw new InvalidInputDataExecption("Invliad element type: " + className, filename);
+					}
+					Element element = (Element) clazz.newInstance();
+					element.setName(name);
+					element.addMiriamData(annotations);
+					element.setElementId(id);
+					result.add(element);
+				} catch (InstantiationException e) {
+					throw new InvalidStateException(e);
+				} catch (IllegalAccessException e) {
+					throw new InvalidStateException(e);
+				}
+				row++;
+			}
+		} finally {
+			br.close();
+		}
+
+		return result;
+	}
+
+	/**
+	 * @return the mc
+	 * @see #mc
+	 */
+	public MiriamConnector getMc() {
+		return mc;
+	}
+
+	/**
+	 * @param mc
+	 *          the mc to set
+	 * @see #mc
+	 */
+	public void setMc(MiriamConnector mc) {
+		this.mc = mc;
+	}
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/PdMapAnnotations.java b/console/src/main/java/lcsb/mapviewer/run/PdMapAnnotations.java
index fdd4685430..2ddc3a1ee4 100644
--- a/console/src/main/java/lcsb/mapviewer/run/PdMapAnnotations.java
+++ b/console/src/main/java/lcsb/mapviewer/run/PdMapAnnotations.java
@@ -1,82 +1,82 @@
-package lcsb.mapviewer.run;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * Class with some PD map specific information.
- * 
- * @author Piotr Gawron
- * 
- */
-public final class PdMapAnnotations {
-
-	/**
-	 * Default class constructor. Prevent initialization.
-	 */
-	private PdMapAnnotations() {
-
-	}
-
-	/**
-	 * Returns url to pdmap with reaction selected on it.
-	 * 
-	 * @param reaction
-	 *          reaction to be selected
-	 * @return url to the reaction in pd map
-	 */
-	public static String getLinkForReaction(Reaction reaction) {
-		return Configuration.PUBLICALY_AVAILABLE_PD_MAP + "&search=reaction:" + reaction.getIdReaction();
-	}
-
-	/**
-	 * Returns filename of the last available version of pd project from testFiles
-	 * directory.
-	 * 
-	 * @return filename of the last available version of pd project
-	 * @throws FileNotFoundException
-	 *           thrown when file cannpt be found
-	 */
-	public static String getLastPdFilename() throws FileNotFoundException {
-		String result = null;
-		File folder = new File("testFiles/PD_full/");
-		File[] listOfFiles = folder.listFiles();
-
-		for (int i = 0; i < listOfFiles.length; i++) {
-
-			if (listOfFiles[i].isFile() && listOfFiles[i].getAbsolutePath().toLowerCase().endsWith("xml")) {
-				if (result == null) {
-					result = listOfFiles[i].getAbsolutePath();
-				} else {
-					if (result.compareTo(listOfFiles[i].getAbsolutePath()) < 0) {
-						result = listOfFiles[i].getAbsolutePath();
-					}
-				}
-			}
-		}
-		if (result == null) {
-			throw new FileNotFoundException();
-		} else {
-			return result;
-		}
-	}
-
-	/**
-	 * Returns version of the last pd file project.
-	 * 
-	 * @return version of the last pd file project
-	 */
-	public static String getLastPdVersion() {
-		String result = null;
-		try {
-			String[] tokens = getLastPdFilename().split("[\\/\\\\]");
-			result = tokens[tokens.length - 1].replace(".xml", "");
-		} catch (FileNotFoundException e) {
-			return null;
-		}
-		return result;
-	}
-}
+package lcsb.mapviewer.run;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * Class with some PD map specific information.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public final class PdMapAnnotations {
+
+	/**
+	 * Default class constructor. Prevent initialization.
+	 */
+	private PdMapAnnotations() {
+
+	}
+
+	/**
+	 * Returns url to pdmap with reaction selected on it.
+	 * 
+	 * @param reaction
+	 *          reaction to be selected
+	 * @return url to the reaction in pd map
+	 */
+	public static String getLinkForReaction(Reaction reaction) {
+		return Configuration.PUBLICALY_AVAILABLE_PD_MAP + "&search=reaction:" + reaction.getIdReaction();
+	}
+
+	/**
+	 * Returns filename of the last available version of pd project from testFiles
+	 * directory.
+	 * 
+	 * @return filename of the last available version of pd project
+	 * @throws FileNotFoundException
+	 *           thrown when file cannpt be found
+	 */
+	public static String getLastPdFilename() throws FileNotFoundException {
+		String result = null;
+		File folder = new File("testFiles/PD_full/");
+		File[] listOfFiles = folder.listFiles();
+
+		for (int i = 0; i < listOfFiles.length; i++) {
+
+			if (listOfFiles[i].isFile() && listOfFiles[i].getAbsolutePath().toLowerCase().endsWith("xml")) {
+				if (result == null) {
+					result = listOfFiles[i].getAbsolutePath();
+				} else {
+					if (result.compareTo(listOfFiles[i].getAbsolutePath()) < 0) {
+						result = listOfFiles[i].getAbsolutePath();
+					}
+				}
+			}
+		}
+		if (result == null) {
+			throw new FileNotFoundException();
+		} else {
+			return result;
+		}
+	}
+
+	/**
+	 * Returns version of the last pd file project.
+	 * 
+	 * @return version of the last pd file project
+	 */
+	public static String getLastPdVersion() {
+		String result = null;
+		try {
+			String[] tokens = getLastPdFilename().split("[\\/\\\\]");
+			result = tokens[tokens.length - 1].replace(".xml", "");
+		} catch (FileNotFoundException e) {
+			return null;
+		}
+		return result;
+	}
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java b/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
index d155f5dcd0..74ea907a17 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
@@ -1,405 +1,405 @@
-package lcsb.mapviewer.run;
-
-import static org.junit.Assert.fail;
-
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.io.UnsupportedEncodingException;
-import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
-import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
-import lcsb.mapviewer.reactome.utils.ComparatorException;
-import lcsb.mapviewer.reactome.utils.DataFormatter;
-import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
-import lcsb.mapviewer.reactome.utils.ReactionComparator;
-import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
-import lcsb.mapviewer.reactome.utils.comparators.MatchResult;
-import lcsb.mapviewer.reactome.utils.comparators.MatchResult.MatchStatus;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.PropertyConfigurator;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * This class generates report of comparison between data on PD-map and
- * reactome.
- * 
- * @author Piotr Gawron
- * 
- */
-
-public class ReactomeComparison {
-	/**
-	 * Number of nanoseconds in second :).
-	 */
-	private static final double	NANOSECONDS_IN_SECOND	= 1000000000.0;
-
-	/**
-	 * Local model used for comparison.
-	 */
-	private Model								model;
-
-	/**
-	 * Default class logger.
-	 */
-	private static Logger				logger								= Logger.getLogger(ReactomeComparison.class);
-
-
-	/**
-	 * Comparator of reactions between our model and reactome.
-	 */
-	@Autowired
-	private ReactionComparator	reactionComparator;
-
-	/**
-	 * Class used for accessing reactome data.
-	 */
-	@Autowired
-	private DataSourceUpdater		rc;
-
-	/**
-	 * Util class used for manipulating information in reactome objects.
-	 */
-	@Autowired
-	private ReactomeQueryUtil		rcu;
-
-	/**
-	 * Formatter used for reaction comparison.
-	 */
-	@Autowired
-	private DataFormatter				dataFormatter;
-
-	/**
-	 * Static main method used to run this stand alone code.
-	 * 
-	 * @param args
-	 *          command line arguments
-	 */
-	public static void main(String[] args) {
-		long startTime = System.nanoTime();
-		PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
-		ReactomeComparison main = new ReactomeComparison();
-		ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
-		ApplicationContextLoader.injectDependencies(main);
-		main.run();
-		long endTime = System.nanoTime();
-
-		long duration = endTime - startTime;
-		double sec = duration / NANOSECONDS_IN_SECOND;
-		System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
-	}
-
-	/**
-	 * Executes comparison between model and reactome representation.
-	 */
-	public void run() {
-		try {
-			model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
-
-			Set<String> list = new HashSet<String>();
-
-			for (Element element : model.getElements()) {
-				if (element instanceof Species) {
-					list.add(((Species) element).getName());
-				}
-			}
-			logger.debug("Species: " + list.size());
-
-			List<String> ids = new ArrayList<String>();
-			for (Reaction reaction : model.getReactions()) {
-				ids.add(reaction.getIdReaction());
-			}
-			Collections.sort(ids);
-			List<MatchResult> results = new ArrayList<MatchResult>();
-
-			printHeader();
-			int i = 0;
-			for (String string : ids) {
-				Reaction reaction = model.getReactionByReactionId(string);
-				logger.info("Reaction: " + string + "; " + (i++) + "/" + ids.size());
-				if (rcu.getReactomeIdentifierForReaction(reaction) != null) {
-					MatchResult result = checkReaction(string);
-					if (result != null) {
-						results.add(result);
-						printResult(result);
-					}
-				} else {
-					ReactomeReactionlikeEvent reactomReaction = rcu.getSimilarReaction(reaction);
-					if (reactomReaction != null) {
-						MatchResult matchResult = new MatchResult();
-						matchResult.setStatus(MatchStatus.SIMILAR_REACTION_FOUND);
-						matchResult.setLocalReaction(reaction);
-						matchResult.setReactomeReaction(reactomReaction);
-						results.add(matchResult);
-						printResult(matchResult);
-
-					}
-				}
-			}
-			printFooter(results);
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			fail("Unknown exception");
-		}
-
-	}
-
-	/**
-	 * Prints report footer.
-	 * 
-	 * @param results
-	 *          results used in the report
-	 */
-	private void printFooter(List<MatchResult> results) {
-		writer.println("</table>");
-
-		int ok = 0;
-		int mismatch = 0;
-		int severe = 0;
-		int similar = 0;
-		for (MatchResult matchResult : results) {
-			if (matchResult.getStatus() == MatchStatus.OK) {
-				ok++;
-			} else if (matchResult.getStatus() == MatchStatus.MISMATCH) {
-				mismatch++;
-			} else if (matchResult.getStatus() == MatchStatus.SIMILAR_REACTION_FOUND) {
-				similar++;
-			} else {
-				severe++;
-			}
-		}
-		writer.println("<p>Reactions checked: " + (results.size()) + "</p>");
-		writer.println("<p>OK: " + ok + "</p>");
-		writer.println("<p>MISMATCH: " + mismatch + "</p>");
-		writer.println("<p>SEVERE PROBLEMS: " + severe + "</p>");
-		writer.println("<p>SIMILAR: " + similar + "</p>");
-
-		writer.println("</body></html>");
-		writer.close();
-
-	}
-
-	/**
-	 * Object to which the report is written.
-	 */
-	private PrintWriter	writer;
-
-	/**
-	 * Creates report stream and prints header of the report.
-	 * 
-	 * @throws FileNotFoundException
-	 *           if there is a problem with creating report file
-	 * @throws UnsupportedEncodingException
-	 *           thrown when there are problems with encoding
-	 */
-	private void printHeader() throws FileNotFoundException, UnsupportedEncodingException {
-		writer = new PrintWriter("out/report/report.html", "UTF-8");
-		writer.println("<html><head></head><body>");
-		writer.println("<table cellspacing=\"0\">");
-
-		String resultString = "<tr>";
-		resultString += "<td" + style + ">Reaction</td>";
-		resultString += "<td" + style + ">REACTOME ID</td>";
-		resultString += "<td" + style + ">Status</td>";
-		resultString += "<td" + style + ">Similarity</td>";
-		resultString += "<td" + style + ">Unknown reaction input</td>";
-		resultString += "<td" + style + ">Unknown reaction modifier</td>";
-		resultString += "<td" + style + ">Unknown reaction output</td>";
-		resultString += "<td" + style + ">Unknown reactome input</td>";
-		resultString += "<td" + style + ">Unknown reactome modifier</td>";
-		resultString += "<td" + style + ">Unknown reactome output</td>";
-		resultString += "</tr>";
-		writer.println(resultString);
-
-	}
-
-	/**
-	 * Formatter of decimal numbers.
-	 */
-	private DecimalFormat	df		= new DecimalFormat("#.##");
-
-	/**
-	 * Style used by report cells.
-	 */
-	private String				style	= " style=\"border-width:1;border-style:solid;border-color:#000000;\" ";
-
-	/**
-	 * Prints result row.
-	 * 
-	 * @param result
-	 *          result to be printed
-	 * @throws IOException 
-	 * @throws AnnotatorException 
-	 */
-	private void printResult(MatchResult result) throws IOException, AnnotatorException {
-		String color = "#000000";
-		String status = "";
-		String error = "";
-		switch (result.getStatus()) {
-			case OK:
-				color = "#52D017";
-				status = "OK";
-				error = "<td colspan=\"6\" " + style + "></td>";
-				return;
-			case SIMILAR_REACTION_FOUND:
-				color = "#5757E0";
-				status = "SIMILAR";
-				error = "<td colspan=\"6\" " + style + "></td>";
-				return;
-			case MISMATCH:
-				color = "#FFFF00";
-				status = "MISMATCH";
-				error += "<td" + style + ">" + dataFormatter.getInvalidLocalInputString(result) + "&nbsp;</td>";
-				error += "<td" + style + ">" + dataFormatter.getInvalidLocalModifierString(result) + "&nbsp;</td>";
-				error += "<td" + style + ">" + dataFormatter.getInvalidLocalOutputString(result) + "&nbsp;</td>";
-				error += "<td" + style + ">" + dataFormatter.getInvalidReactomeInputString(result) + "&nbsp;</td>";
-				error += "<td" + style + ">" + dataFormatter.getInvalidReactomeModifierString(result) + "&nbsp;</td>";
-				error += "<td" + style + ">" + dataFormatter.getInvalidReactomeOutputString(result) + "&nbsp;</td>";
-				break;
-			case INVALID_REACTOME_ID:
-				color = "#FF0000";
-				status = "REACTOME id does not point to reaction";
-				error = "<td colspan=\"6\" " + style + "></td>";
-				return;
-			case INVALID_REACTION_WITH_PHEONTYPE:
-				color = "#FF0000";
-				status = "Impossible to map reaction to reactome - reaction contains Phenotype";
-				error = "<td colspan=\"6\" " + style + "></td>";
-				return;
-			default:
-				return;
-		}
-		String resultString = "<tr bgcolor = \"" + color + "\">";
-		String reactionId = result.getLocalReaction().getIdReaction();
-		String reactomId = null;
-		reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
-
-		resultString += "<td" + style + "><a target=\"_blank\" href=\"" + PdMapAnnotations.getLinkForReaction(result.getLocalReaction()) + "\">" + reactionId
-				+ "</a> ";
-		resultString += "<a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
-
-		if (result.getReactomeReaction() != null) {
-			reactomId = result.getReactomeReaction().getStableIdentifier().getIdentifier() + "."
-					+ result.getReactomeReaction().getStableIdentifier().getIdentifierVersion();
-		} else {
-			reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
-		}
-
-		resultString += "<td" + style + "><a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
-		resultString += "<td" + style + ">" + status + "</td>";
-		resultString += "<td" + style + ">" + df.format(result.getScore() * IProgressUpdater.MAX_PROGRESS) + "%</td>";
-		resultString += error;
-		resultString += "</tr>";
-		writer.println(resultString);
-		System.out.println(resultString);
-	}
-
-	/**
-	 * Compares our model reaction to reactome representation.
-	 * 
-	 * @param id
-	 *          identifier of our reaction
-	 * @return result of reaction comparison
-	 * @throws IOException
-	 *           thrown whene there are problems accessing reactome reaction
-	 * @throws ComparatorException 
-	 */
-	private MatchResult checkReaction(String id) throws IOException, ComparatorException {
-		return checkReaction(model.getReactionByReactionId(id));
-	}
-
-	/**
-	 * Compares our model reaction to reactome representation.
-	 * 
-	 * @param reaction
-	 *          our reaction
-	 * @return result of reaction comparison
-	 * @throws IOException
-	 *           thrown whene there are problems accessing reactome reaction
-	 * @throws ComparatorException 
-	 */
-	private MatchResult checkReaction(Reaction reaction) throws IOException, ComparatorException {
-		String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
-		if (stableIdentifier != null) {
-			String identifier = stableIdentifier.split("\\.")[0];
-			String version = stableIdentifier.split("\\.")[1];
-
-			ReactomeDatabaseObject object = rc.getFullObjectForStableIdentifier(identifier, version);
-			if (object != null && object instanceof ReactomeReactionlikeEvent) {
-				return reactionComparator.compareReactions(reaction, (ReactomeReactionlikeEvent) object);
-
-			} else {
-				MatchResult result = new MatchResult();
-				result.setLocalReaction(reaction);
-				result.setStatus(MatchStatus.INVALID_REACTOME_ID);
-				return result;
-			}
-		}
-		return null;
-	}
-
-	/**
-	 * @return the reactionComparator
-	 */
-	public ReactionComparator getReactionComparator() {
-		return reactionComparator;
-	}
-
-	/**
-	 * @param reactionComparator
-	 *          the reactionComparator to set
-	 */
-	public void setReactionComparator(ReactionComparator reactionComparator) {
-		this.reactionComparator = reactionComparator;
-	}
-
-	/**
-	 * @return the dataFormatter
-	 */
-	public DataFormatter getDataFormatter() {
-		return dataFormatter;
-	}
-
-	/**
-	 * @param dataFormatter
-	 *          the dataFormatter to set
-	 */
-	public void setDataFormatter(DataFormatter dataFormatter) {
-		this.dataFormatter = dataFormatter;
-	}
-
-	/**
-	 * @return the rc
-	 * @see #rc
-	 */
-	public DataSourceUpdater getRc() {
-		return rc;
-	}
-
-	/**
-	 * @param rc
-	 *          the rc to set
-	 * @see #rc
-	 */
-	public void setRc(DataSourceUpdater rc) {
-		this.rc = rc;
-	}
-
-}
+package lcsb.mapviewer.run;
+
+import static org.junit.Assert.fail;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.UnsupportedEncodingException;
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.persist.ApplicationContextLoader;
+import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
+import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
+import lcsb.mapviewer.reactome.utils.ComparatorException;
+import lcsb.mapviewer.reactome.utils.DataFormatter;
+import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
+import lcsb.mapviewer.reactome.utils.ReactionComparator;
+import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
+import lcsb.mapviewer.reactome.utils.comparators.MatchResult;
+import lcsb.mapviewer.reactome.utils.comparators.MatchResult.MatchStatus;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.PropertyConfigurator;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * This class generates report of comparison between data on PD-map and
+ * reactome.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+
+public class ReactomeComparison {
+	/**
+	 * Number of nanoseconds in second :).
+	 */
+	private static final double	NANOSECONDS_IN_SECOND	= 1000000000.0;
+
+	/**
+	 * Local model used for comparison.
+	 */
+	private Model								model;
+
+	/**
+	 * Default class logger.
+	 */
+	private static Logger				logger								= Logger.getLogger(ReactomeComparison.class);
+
+
+	/**
+	 * Comparator of reactions between our model and reactome.
+	 */
+	@Autowired
+	private ReactionComparator	reactionComparator;
+
+	/**
+	 * Class used for accessing reactome data.
+	 */
+	@Autowired
+	private DataSourceUpdater		rc;
+
+	/**
+	 * Util class used for manipulating information in reactome objects.
+	 */
+	@Autowired
+	private ReactomeQueryUtil		rcu;
+
+	/**
+	 * Formatter used for reaction comparison.
+	 */
+	@Autowired
+	private DataFormatter				dataFormatter;
+
+	/**
+	 * Static main method used to run this stand alone code.
+	 * 
+	 * @param args
+	 *          command line arguments
+	 */
+	public static void main(String[] args) {
+		long startTime = System.nanoTime();
+		PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
+		ReactomeComparison main = new ReactomeComparison();
+		ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+		ApplicationContextLoader.injectDependencies(main);
+		main.run();
+		long endTime = System.nanoTime();
+
+		long duration = endTime - startTime;
+		double sec = duration / NANOSECONDS_IN_SECOND;
+		System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
+	}
+
+	/**
+	 * Executes comparison between model and reactome representation.
+	 */
+	public void run() {
+		try {
+			model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
+
+			Set<String> list = new HashSet<String>();
+
+			for (Element element : model.getElements()) {
+				if (element instanceof Species) {
+					list.add(((Species) element).getName());
+				}
+			}
+			logger.debug("Species: " + list.size());
+
+			List<String> ids = new ArrayList<String>();
+			for (Reaction reaction : model.getReactions()) {
+				ids.add(reaction.getIdReaction());
+			}
+			Collections.sort(ids);
+			List<MatchResult> results = new ArrayList<MatchResult>();
+
+			printHeader();
+			int i = 0;
+			for (String string : ids) {
+				Reaction reaction = model.getReactionByReactionId(string);
+				logger.info("Reaction: " + string + "; " + (i++) + "/" + ids.size());
+				if (rcu.getReactomeIdentifierForReaction(reaction) != null) {
+					MatchResult result = checkReaction(string);
+					if (result != null) {
+						results.add(result);
+						printResult(result);
+					}
+				} else {
+					ReactomeReactionlikeEvent reactomReaction = rcu.getSimilarReaction(reaction);
+					if (reactomReaction != null) {
+						MatchResult matchResult = new MatchResult();
+						matchResult.setStatus(MatchStatus.SIMILAR_REACTION_FOUND);
+						matchResult.setLocalReaction(reaction);
+						matchResult.setReactomeReaction(reactomReaction);
+						results.add(matchResult);
+						printResult(matchResult);
+
+					}
+				}
+			}
+			printFooter(results);
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			fail("Unknown exception");
+		}
+
+	}
+
+	/**
+	 * Prints report footer.
+	 * 
+	 * @param results
+	 *          results used in the report
+	 */
+	private void printFooter(List<MatchResult> results) {
+		writer.println("</table>");
+
+		int ok = 0;
+		int mismatch = 0;
+		int severe = 0;
+		int similar = 0;
+		for (MatchResult matchResult : results) {
+			if (matchResult.getStatus() == MatchStatus.OK) {
+				ok++;
+			} else if (matchResult.getStatus() == MatchStatus.MISMATCH) {
+				mismatch++;
+			} else if (matchResult.getStatus() == MatchStatus.SIMILAR_REACTION_FOUND) {
+				similar++;
+			} else {
+				severe++;
+			}
+		}
+		writer.println("<p>Reactions checked: " + (results.size()) + "</p>");
+		writer.println("<p>OK: " + ok + "</p>");
+		writer.println("<p>MISMATCH: " + mismatch + "</p>");
+		writer.println("<p>SEVERE PROBLEMS: " + severe + "</p>");
+		writer.println("<p>SIMILAR: " + similar + "</p>");
+
+		writer.println("</body></html>");
+		writer.close();
+
+	}
+
+	/**
+	 * Object to which the report is written.
+	 */
+	private PrintWriter	writer;
+
+	/**
+	 * Creates report stream and prints header of the report.
+	 * 
+	 * @throws FileNotFoundException
+	 *           if there is a problem with creating report file
+	 * @throws UnsupportedEncodingException
+	 *           thrown when there are problems with encoding
+	 */
+	private void printHeader() throws FileNotFoundException, UnsupportedEncodingException {
+		writer = new PrintWriter("out/report/report.html", "UTF-8");
+		writer.println("<html><head></head><body>");
+		writer.println("<table cellspacing=\"0\">");
+
+		String resultString = "<tr>";
+		resultString += "<td" + style + ">Reaction</td>";
+		resultString += "<td" + style + ">REACTOME ID</td>";
+		resultString += "<td" + style + ">Status</td>";
+		resultString += "<td" + style + ">Similarity</td>";
+		resultString += "<td" + style + ">Unknown reaction input</td>";
+		resultString += "<td" + style + ">Unknown reaction modifier</td>";
+		resultString += "<td" + style + ">Unknown reaction output</td>";
+		resultString += "<td" + style + ">Unknown reactome input</td>";
+		resultString += "<td" + style + ">Unknown reactome modifier</td>";
+		resultString += "<td" + style + ">Unknown reactome output</td>";
+		resultString += "</tr>";
+		writer.println(resultString);
+
+	}
+
+	/**
+	 * Formatter of decimal numbers.
+	 */
+	private DecimalFormat	df		= new DecimalFormat("#.##");
+
+	/**
+	 * Style used by report cells.
+	 */
+	private String				style	= " style=\"border-width:1;border-style:solid;border-color:#000000;\" ";
+
+	/**
+	 * Prints result row.
+	 * 
+	 * @param result
+	 *          result to be printed
+	 * @throws IOException 
+	 * @throws AnnotatorException 
+	 */
+	private void printResult(MatchResult result) throws IOException, AnnotatorException {
+		String color = "#000000";
+		String status = "";
+		String error = "";
+		switch (result.getStatus()) {
+			case OK:
+				color = "#52D017";
+				status = "OK";
+				error = "<td colspan=\"6\" " + style + "></td>";
+				return;
+			case SIMILAR_REACTION_FOUND:
+				color = "#5757E0";
+				status = "SIMILAR";
+				error = "<td colspan=\"6\" " + style + "></td>";
+				return;
+			case MISMATCH:
+				color = "#FFFF00";
+				status = "MISMATCH";
+				error += "<td" + style + ">" + dataFormatter.getInvalidLocalInputString(result) + "&nbsp;</td>";
+				error += "<td" + style + ">" + dataFormatter.getInvalidLocalModifierString(result) + "&nbsp;</td>";
+				error += "<td" + style + ">" + dataFormatter.getInvalidLocalOutputString(result) + "&nbsp;</td>";
+				error += "<td" + style + ">" + dataFormatter.getInvalidReactomeInputString(result) + "&nbsp;</td>";
+				error += "<td" + style + ">" + dataFormatter.getInvalidReactomeModifierString(result) + "&nbsp;</td>";
+				error += "<td" + style + ">" + dataFormatter.getInvalidReactomeOutputString(result) + "&nbsp;</td>";
+				break;
+			case INVALID_REACTOME_ID:
+				color = "#FF0000";
+				status = "REACTOME id does not point to reaction";
+				error = "<td colspan=\"6\" " + style + "></td>";
+				return;
+			case INVALID_REACTION_WITH_PHEONTYPE:
+				color = "#FF0000";
+				status = "Impossible to map reaction to reactome - reaction contains Phenotype";
+				error = "<td colspan=\"6\" " + style + "></td>";
+				return;
+			default:
+				return;
+		}
+		String resultString = "<tr bgcolor = \"" + color + "\">";
+		String reactionId = result.getLocalReaction().getIdReaction();
+		String reactomId = null;
+		reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
+
+		resultString += "<td" + style + "><a target=\"_blank\" href=\"" + PdMapAnnotations.getLinkForReaction(result.getLocalReaction()) + "\">" + reactionId
+				+ "</a> ";
+		resultString += "<a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
+
+		if (result.getReactomeReaction() != null) {
+			reactomId = result.getReactomeReaction().getStableIdentifier().getIdentifier() + "."
+					+ result.getReactomeReaction().getStableIdentifier().getIdentifierVersion();
+		} else {
+			reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
+		}
+
+		resultString += "<td" + style + "><a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
+		resultString += "<td" + style + ">" + status + "</td>";
+		resultString += "<td" + style + ">" + df.format(result.getScore() * IProgressUpdater.MAX_PROGRESS) + "%</td>";
+		resultString += error;
+		resultString += "</tr>";
+		writer.println(resultString);
+		System.out.println(resultString);
+	}
+
+	/**
+	 * Compares our model reaction to reactome representation.
+	 * 
+	 * @param id
+	 *          identifier of our reaction
+	 * @return result of reaction comparison
+	 * @throws IOException
+	 *           thrown whene there are problems accessing reactome reaction
+	 * @throws ComparatorException 
+	 */
+	private MatchResult checkReaction(String id) throws IOException, ComparatorException {
+		return checkReaction(model.getReactionByReactionId(id));
+	}
+
+	/**
+	 * Compares our model reaction to reactome representation.
+	 * 
+	 * @param reaction
+	 *          our reaction
+	 * @return result of reaction comparison
+	 * @throws IOException
+	 *           thrown whene there are problems accessing reactome reaction
+	 * @throws ComparatorException 
+	 */
+	private MatchResult checkReaction(Reaction reaction) throws IOException, ComparatorException {
+		String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
+		if (stableIdentifier != null) {
+			String identifier = stableIdentifier.split("\\.")[0];
+			String version = stableIdentifier.split("\\.")[1];
+
+			ReactomeDatabaseObject object = rc.getFullObjectForStableIdentifier(identifier, version);
+			if (object != null && object instanceof ReactomeReactionlikeEvent) {
+				return reactionComparator.compareReactions(reaction, (ReactomeReactionlikeEvent) object);
+
+			} else {
+				MatchResult result = new MatchResult();
+				result.setLocalReaction(reaction);
+				result.setStatus(MatchStatus.INVALID_REACTOME_ID);
+				return result;
+			}
+		}
+		return null;
+	}
+
+	/**
+	 * @return the reactionComparator
+	 */
+	public ReactionComparator getReactionComparator() {
+		return reactionComparator;
+	}
+
+	/**
+	 * @param reactionComparator
+	 *          the reactionComparator to set
+	 */
+	public void setReactionComparator(ReactionComparator reactionComparator) {
+		this.reactionComparator = reactionComparator;
+	}
+
+	/**
+	 * @return the dataFormatter
+	 */
+	public DataFormatter getDataFormatter() {
+		return dataFormatter;
+	}
+
+	/**
+	 * @param dataFormatter
+	 *          the dataFormatter to set
+	 */
+	public void setDataFormatter(DataFormatter dataFormatter) {
+		this.dataFormatter = dataFormatter;
+	}
+
+	/**
+	 * @return the rc
+	 * @see #rc
+	 */
+	public DataSourceUpdater getRc() {
+		return rc;
+	}
+
+	/**
+	 * @param rc
+	 *          the rc to set
+	 * @see #rc
+	 */
+	public void setRc(DataSourceUpdater rc) {
+		this.rc = rc;
+	}
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java b/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
index 40882f8f5d..556976542d 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
@@ -1,616 +1,616 @@
-package lcsb.mapviewer.run;
-
-import java.awt.Rectangle;
-import java.awt.geom.Point2D;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
-import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
-import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.PropertyConfigurator;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * This class create a data that could be used by visualized in reactome
- * visualization framework. It was developed only for test purpose and has no
- * real value.
- */
-public class ReactomeExport {
-	/**
-	 * Size of the map to vizualize.
-	 */
-	private static final int	DEFAULT_SIZE	= 30000;
-	/**
-	 * Bounds of the map to vizualize.
-	 */
-	private static Rectangle	bound					= new Rectangle(0, 0, DEFAULT_SIZE, DEFAULT_SIZE);
-	/**
-	 * Default class logger.
-	 */
-	private static Logger			logger				= Logger.getLogger(ReactomeExport.class.getName());
-
-	/**
-	 * Class used for accessing reactome data.
-	 */
-	@Autowired
-	private DataSourceUpdater	rc;
-
-	/**
-	 * Util class used for manipulating information in reactome objects.
-	 */
-	@Autowired
-	private ReactomeQueryUtil	rcu;
-
-	/**
-	 * Static main method used to run this stand alone code.
-	 * 
-	 * @param args
-	 *          command line arguments
-	 */
-	public static void main(String[] args) {
-		PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
-		ReactomeExport main = new ReactomeExport();
-		ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
-		ApplicationContextLoader.injectDependencies(main);
-		main.run();
-
-	}
-
-	/**
-	 * String containing the result of export.
-	 */
-	private String	result	= "";
-
-	/**
-	 * Adds text to the output.
-	 * 
-	 * @param str
-	 *          text to add
-	 */
-	private void print(String str) {
-		result += str;
-	}
-
-	/**
-	 * Identifier counter used for generating identifiers in the reactome
-	 * visualization model.
-	 */
-	private int									id			= 0;
-
-	/**
-	 * Map between aliases in our model and identifiers that will be used in the
-	 * reactome vizualization model.
-	 */
-	private Map<Alias, Integer>	tempIds	= new HashMap<Alias, Integer>();
-
-	/**
-	 * Creates reactome identifier for alias.
-	 * 
-	 * @param alias
-	 *          object for which identifier is created
-	 * @return identifier of the alias
-	 */
-	public int addElement(Alias alias) {
-		int result = -1;
-		if (tempIds.containsKey(alias)) {
-			result = tempIds.get(alias);
-		} else {
-			tempIds.put(alias, ++id);
-			result = id;
-
-			if (alias instanceof ComplexAlias) {
-				for (Alias a : ((ComplexAlias) alias).getAliases()) {
-					addElement(a);
-				}
-			} else if (alias instanceof CompartmentAlias) {
-				for (Alias a : ((CompartmentAlias) alias).getAliases()) {
-					addElement(a);
-				}
-			}
-		}
-
-		return result;
-	}
-
-	/**
-	 * Creates file with reactome vizualization.
-	 */
-	private void run() {
-		CellDesignerXmlParser p = new CellDesignerXmlParser();
-		try {
-			Model model = p.createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
-			print("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
-			print("<Process reactomeId=\"0\">\n");
-			print("<Properties>\n");
-			print("<displayName>PD map</displayName>\n");
-			print("</Properties>\n");
-			printAliases(model);
-			printReactions(model);
-			print("</Process>\n");
-
-			PrintWriter writer = new PrintWriter("out/report/reactome-viewer.xml", "UTF-8");
-			writer.print(result);
-			writer.close();
-
-		} catch (Exception e) {
-			logger.error(e.getMessage());
-			e.printStackTrace();
-		}
-
-	}
-
-	/**
-	 * Creates representation of the aliases in the reactome visualization model.
-	 * 
-	 * @param model
-	 *          our model to be visualized
-	 * @throws IOException
-	 *           thrown when there are problems accessing reactome database
-	 */
-	private void printAliases(Model model) throws IOException {
-		print("<Nodes>\n");
-		List<Alias> aliases = new ArrayList<Alias>();
-		aliases.addAll(model.getAliases());
-		Collections.sort(aliases, Alias.SIZE_COMPARATOR);
-		for (Alias alias : aliases) {
-			if (!aliasFeasible(alias)) {
-				continue;
-			}
-			int currId = addElement(alias);
-			Element element = null;
-			Map<String, String> parameters = new HashMap<String, String>();
-			Map<String, String> attributes = new HashMap<String, String>();
-
-			attributes.put("id", currId + "");
-			attributes.put("position", (int) alias.getCenterX() + " " + (int) alias.getCenterY());
-			attributes.put("bounds", alias.getX().intValue() + " " + alias.getY().intValue() + " " + alias.getWidth().intValue() + " "
-					+ alias.getHeight().intValue());
-			attributes.put("textPosition", (int) alias.getCenterX() + " " + (int) alias.getCenterY());
-			attributes.put("reactomeId", "0");
-
-			Set<Integer> components = new HashSet<Integer>();
-			String type = "";
-			if (alias instanceof SpeciesAlias) {
-				element = ((SpeciesAlias) alias).getSpecies();
-				String stableIdentifier = rcu.getReactomeIdentifierForSpecies(((SpeciesAlias) alias).getSpecies());
-				if (stableIdentifier != null) {
-					ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
-					if (obj != null && obj.getDbId() != null) {
-						attributes.put("reactomeId", obj.getDbId() + "");
-					}
-				}
-				parameters.put("displayName", ((Species) element).getName());
-				if (alias instanceof ComplexAlias) {
-					for (Alias a : ((ComplexAlias) alias).getAliases()) {
-						components.add(addElement(a));
-					}
-				}
-			}
-			if (alias instanceof CompartmentAlias) {
-				element = ((CompartmentAlias) alias).getCompartment();
-				parameters.put("displayName", ((Compartment) element).getName());
-				for (Alias a : ((CompartmentAlias) alias).getAliases()) {
-					components.add(addElement(a));
-				}
-			}
-
-			if (element instanceof ComplexSpecies) {
-				type = "org.gk.render.RenderableComplex";
-				attributes.put("hideComponents", "true");
-				attributes.put("textPosition", (int) alias.getCenterX() + " " + (int) (alias.getY() + alias.getHeight()));
-			} else if (element instanceof SimpleMolecule) {
-				type = "org.gk.render.RenderableChemical";
-			} else if (element instanceof Ion) {
-				type = "org.gk.render.RenderableChemical";
-			} else if (element instanceof Protein) {
-				type = "org.gk.render.RenderableProtein";
-			} else if (element instanceof Species) {
-				type = "org.gk.render.RenderableEntity";
-			} else if (element instanceof Compartment) {
-				type = "org.gk.render.RenderableCompartment";
-			} else {
-				logger.debug("Ignoring: " + parameters.get("displayName") + "(" + element.getClass() + ")");
-				continue;
-			}
-			print("<" + type);
-			for (String string : attributes.keySet()) {
-				print(" " + string + "=\"" + attributes.get(string) + "\"");
-			}
-			print(">");
-			for (String key : parameters.keySet()) {
-				print("<" + key + ">" + parameters.get(key) + "</" + key + ">");
-			}
-
-			if (components.size() != 0) {
-				print("\n <Components>\n");
-				for (Integer i : components) {
-					print("  <Component id=\"" + i + "\"/>\n");
-				}
-				print(" </Components>\n");
-			}
-			print("</" + type + ">\n");
-
-		}
-		print("</Nodes>\n");
-	}
-
-	/**
-	 * Creates reactions in reactome visuazliation model from our model.
-	 * 
-	 * @param model
-	 *          model to be visualized
-	 * @throws IOException
-	 *           thrown when there are problems with accessing reactome database
-	 */
-	private void printReactions(Model model) throws IOException {
-		print("<Edges>\n");
-		for (Reaction reaction : model.getReactions()) {
-			if (!isReactionFeasible(reaction)) {
-				continue;
-			}
-			int currId = ++id;
-			Map<String, String> parameters = new HashMap<String, String>();
-			Map<Integer, String> inputs = new HashMap<Integer, String>();
-			Map<Integer, String> outputs = new HashMap<Integer, String>();
-			Map<Integer, String> catalysts = new HashMap<Integer, String>();
-
-			Map<String, String> attributes = new HashMap<String, String>();
-
-			attributes.put("id", currId + "");
-			attributes.put("position", (int) reaction.getCenterPoint().getX() + " " + (int) reaction.getCenterPoint().getY());
-			attributes.put("points", getReactionMiddlePoints(reaction));
-			attributes.put("lineWidth", "1.0");
-			attributes.put("reactomeId", "0");
-
-			parameters.put("displayName", reaction.getIdReaction());
-
-			String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
-			if (stableIdentifier != null) {
-				ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
-				if (obj != null && obj.getDbId() != null) {
-					attributes.put("reactomeId", obj.getDbId() + "");
-				}
-			}
-
-			for (ReactionNode node : reaction.getReactionNodes()) {
-				Integer id = tempIds.get(node.getAlias());
-				if (node instanceof Reactant) {
-					inputs.put(id, getInputString((Reactant) node));
-				} else if (node instanceof Product) {
-					outputs.put(id, getOutputString((Product) node));
-				} else if (node instanceof Modifier) {
-					catalysts.put(id, getModifierString((Modifier) node));
-				}
-			}
-
-			String type = "org.gk.render.RenderableReaction";
-
-			print("<" + type);
-			for (String string : attributes.keySet()) {
-				print(" " + string + "=\"" + attributes.get(string) + "\"");
-			}
-			print(">\n");
-			print(" <Properties>\n");
-			for (String key : parameters.keySet()) {
-				print("  <" + key + ">" + parameters.get(key) + "</" + key + ">\n");
-			}
-			print(" </Properties>\n");
-
-			if (inputs.size() != 0) {
-				print(" <Inputs>\n");
-				for (Integer i : inputs.keySet()) {
-					print("  <Input  id=\"" + i + "\" points=\"" + inputs.get(i) + "\"/>\n");
-				}
-				print(" </Inputs>\n");
-			}
-			if (outputs.size() != 0) {
-				print(" <Outputs>\n");
-				for (Integer i : outputs.keySet()) {
-					print("  <Output  id=\"" + i + "\" points=\"" + outputs.get(i) + "\"/>\n");
-				}
-				print(" </Outputs>\n");
-			}
-			if (catalysts.size() != 0) {
-				print(" <Catalysts>\n");
-				for (Integer i : catalysts.keySet()) {
-					print("  <Catalyst  id=\"" + i + "\" points=\"" + catalysts.get(i) + "\"/>\n");
-				}
-				print(" </Catalysts>\n");
-			}
-			print("</" + type + ">\n");
-
-		}
-
-		print("</Edges>\n");
-	}
-
-	/**
-	 * Returns string representing modifier.
-	 * 
-	 * @param node
-	 *          modifier in our model
-	 * @return string representing modifier that can be used in reactome
-	 *         visualization
-	 */
-	private String getModifierString(ReactionNode node) {
-		String result = null;
-		List<Point2D> points = node.getLine().getPoints();
-		for (int i = 0; i < points.size() - 1; i++) {
-			if (result == null) {
-				result = "";
-			} else {
-				result += ", ";
-			}
-			Point2D point = points.get(i);
-			result += (int) point.getX() + " " + (int) point.getY();
-		}
-		return result;
-	}
-
-	/**
-	 * Returns string representing product.
-	 * 
-	 * @param node
-	 *          product in our model
-	 * @return string representing product that can be used in reactome
-	 *         visualization
-	 */
-	private String getOutputString(ReactionNode node) {
-		for (NodeOperator tmpNode : node.getReaction().getOperators()) {
-			if (tmpNode.isProductOperator()) {
-				String result = null;
-				List<Point2D> points = node.getLine().getPoints();
-				for (int i = points.size() - 1; i >= 0; i--) {
-					if (result == null) {
-						result = "";
-					} else {
-						result += ", ";
-					}
-					Point2D point = points.get(i);
-					result += (int) point.getX() + " " + (int) point.getY();
-				}
-				return result;
-			}
-		}
-		Point2D point = node.getLine().getEndPoint();
-		String result = (int) point.getX() + " " + (int) point.getY();
-		return result;
-	}
-
-	/**
-	 * Returns string representing reactant.
-	 * 
-	 * @param node
-	 *          reactant in our model
-	 * @return string representing reactant that can be used in reactome
-	 *         visualization
-	 */
-	private String getInputString(ReactionNode node) {
-		for (NodeOperator tmpNode : node.getReaction().getOperators()) {
-			if (tmpNode.isReactantOperator()) {
-				String result = null;
-				List<Point2D> points = node.getLine().getPoints();
-				for (int i = 0; i < points.size(); i++) {
-					if (result == null) {
-						result = "";
-					} else {
-						result += ", ";
-					}
-					Point2D point = points.get(i);
-					result += (int) point.getX() + " " + (int) point.getY();
-				}
-				return result;
-			}
-		}
-		Point2D point = node.getLine().getPoints().get(0);
-		String result = (int) point.getX() + " " + (int) point.getY();
-		return result;
-	}
-
-	/**
-	 * Check if reaction can be easily transformed into reactome vizualization
-	 * tool.
-	 * 
-	 * @param reaction
-	 *          reaction to be checked
-	 * @return <code>true</code> if reaction can be easily transformed,
-	 *         <code>false</code> otherwise
-	 */
-	private boolean isReactionFeasible(Reaction reaction) {
-		for (ReactionNode node : reaction.getReactionNodes()) {
-			if (!aliasFeasible(node.getAlias())) {
-				return false;
-			}
-		}
-		int counter = 0;
-		for (NodeOperator node : reaction.getOperators()) {
-			if (node.isProductOperator()) {
-				counter++;
-			}
-			if (counter > 1) {
-				logger.debug("To many operators in the input: " + reaction.getIdReaction());
-				return false;
-			}
-		}
-		counter = 0;
-		for (NodeOperator node : reaction.getOperators()) {
-			if (node.isReactantOperator()) {
-				counter++;
-			}
-			if (counter > 1) {
-				logger.debug("To many operators in the output: " + reaction.getIdReaction());
-				return false;
-			}
-		}
-		counter = 0;
-		for (NodeOperator node : reaction.getOperators()) {
-			if (node.isModifierOperator()) {
-				logger.debug("To complicated catalyst: " + reaction.getIdReaction());
-				return false;
-			}
-		}
-		return true;
-	}
-
-	/**
-	 * Returns string representing reaction line.
-	 * 
-	 * @param reaction
-	 *          reaction to be transformed
-	 * @return string representing reaction line
-	 */
-	private String getReactionMiddlePoints(Reaction reaction) {
-		String result = null;
-		NodeOperator node = null;
-		for (NodeOperator n : reaction.getOperators()) {
-			if (n.isReactantOperator()) {
-				node = n;
-			}
-		}
-		if (node != null) {
-			for (Point2D point : node.getLine().getPoints()) {
-				if (result == null) {
-					result = (int) point.getX() + " " + (int) point.getY();
-				} else {
-					result += ", " + (int) point.getX() + " " + (int) point.getY();
-				}
-			}
-		} else {
-			AbstractNode tmp = null;
-			for (AbstractNode reactionNode : reaction.getNodes()) {
-				if (reactionNode instanceof Reactant) {
-					tmp = reactionNode;
-				}
-			}
-			List<Point2D> points = tmp.getLine().getPoints();
-			for (int i = 0; i < points.size(); i++) {
-				Point2D point = points.get(i);
-				if (result == null) {
-					result = (int) point.getX() + " " + (int) point.getY();
-				} else {
-					result += ", " + (int) point.getX() + " " + (int) point.getY();
-				}
-			}
-		}
-
-		node = null;
-		for (NodeOperator n : reaction.getOperators()) {
-			if (n.isProductOperator()) {
-				node = n;
-			}
-		}
-		if (node != null) {
-			List<Point2D> points = node.getLine().getPoints();
-			for (int i = points.size() - 1; i >= 0; i--) {
-				Point2D point = points.get(i);
-				if (result == null) {
-					result = (int) point.getX() + " " + (int) point.getY();
-				} else {
-					result += ", " + (int) point.getX() + " " + (int) point.getY();
-				}
-			}
-		} else {
-			AbstractNode tmp = null;
-			for (AbstractNode reactionNode : reaction.getNodes()) {
-				if (reactionNode instanceof Product) {
-					tmp = reactionNode;
-				}
-			}
-			List<Point2D> points = tmp.getLine().getPoints();
-			for (int i = 0; i < points.size(); i++) {
-				Point2D point = points.get(i);
-				if (result == null) {
-					result = (int) point.getX() + " " + (int) point.getY();
-				} else {
-					result += ", " + (int) point.getX() + " " + (int) point.getY();
-				}
-			}
-		}
-
-		return result;
-	}
-
-	/**
-	 * Checks if alias can be put into reactome vizualization.
-	 * 
-	 * @param alias
-	 *          alias to check
-	 * @return <code>true</code> if alias can be put into reactome vizualization,
-	 *         <code>false</code> otherwise
-	 */
-	public boolean aliasFeasible(Alias alias) {
-		Point2D point = new Point2D.Double(alias.getX(), alias.getY());
-		Point2D point2 = new Point2D.Double(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
-		if (bound.contains(point) && bound.contains(point2)) {
-			return true;
-		}
-		return false;
-	}
-
-	/**
-	 * @return the rc
-	 * @see #rc
-	 */
-	public DataSourceUpdater getRc() {
-		return rc;
-	}
-
-	/**
-	 * @param rc
-	 *          the rc to set
-	 * @see #rc
-	 */
-	public void setRc(DataSourceUpdater rc) {
-		this.rc = rc;
-	}
-
-	/**
-	 * @return the rcu
-	 * @see #rcu
-	 */
-	public ReactomeQueryUtil getRcu() {
-		return rcu;
-	}
-
-	/**
-	 * @param rcu
-	 *          the rcu to set
-	 * @see #rcu
-	 */
-	public void setRcu(ReactomeQueryUtil rcu) {
-		this.rcu = rcu;
-	}
-
-}
+package lcsb.mapviewer.run;
+
+import java.awt.Rectangle;
+import java.awt.geom.Point2D;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.ComplexSpecies;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.persist.ApplicationContextLoader;
+import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
+import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
+import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.PropertyConfigurator;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * This class create a data that could be used by visualized in reactome
+ * visualization framework. It was developed only for test purpose and has no
+ * real value.
+ */
+public class ReactomeExport {
+	/**
+	 * Size of the map to vizualize.
+	 */
+	private static final int	DEFAULT_SIZE	= 30000;
+	/**
+	 * Bounds of the map to vizualize.
+	 */
+	private static Rectangle	bound					= new Rectangle(0, 0, DEFAULT_SIZE, DEFAULT_SIZE);
+	/**
+	 * Default class logger.
+	 */
+	private static Logger			logger				= Logger.getLogger(ReactomeExport.class.getName());
+
+	/**
+	 * Class used for accessing reactome data.
+	 */
+	@Autowired
+	private DataSourceUpdater	rc;
+
+	/**
+	 * Util class used for manipulating information in reactome objects.
+	 */
+	@Autowired
+	private ReactomeQueryUtil	rcu;
+
+	/**
+	 * Static main method used to run this stand alone code.
+	 * 
+	 * @param args
+	 *          command line arguments
+	 */
+	public static void main(String[] args) {
+		PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
+		ReactomeExport main = new ReactomeExport();
+		ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+		ApplicationContextLoader.injectDependencies(main);
+		main.run();
+
+	}
+
+	/**
+	 * String containing the result of export.
+	 */
+	private String	result	= "";
+
+	/**
+	 * Adds text to the output.
+	 * 
+	 * @param str
+	 *          text to add
+	 */
+	private void print(String str) {
+		result += str;
+	}
+
+	/**
+	 * Identifier counter used for generating identifiers in the reactome
+	 * visualization model.
+	 */
+	private int									id			= 0;
+
+	/**
+	 * Map between aliases in our model and identifiers that will be used in the
+	 * reactome vizualization model.
+	 */
+	private Map<Alias, Integer>	tempIds	= new HashMap<Alias, Integer>();
+
+	/**
+	 * Creates reactome identifier for alias.
+	 * 
+	 * @param alias
+	 *          object for which identifier is created
+	 * @return identifier of the alias
+	 */
+	public int addElement(Alias alias) {
+		int result = -1;
+		if (tempIds.containsKey(alias)) {
+			result = tempIds.get(alias);
+		} else {
+			tempIds.put(alias, ++id);
+			result = id;
+
+			if (alias instanceof ComplexAlias) {
+				for (Alias a : ((ComplexAlias) alias).getAliases()) {
+					addElement(a);
+				}
+			} else if (alias instanceof CompartmentAlias) {
+				for (Alias a : ((CompartmentAlias) alias).getAliases()) {
+					addElement(a);
+				}
+			}
+		}
+
+		return result;
+	}
+
+	/**
+	 * Creates file with reactome vizualization.
+	 */
+	private void run() {
+		CellDesignerXmlParser p = new CellDesignerXmlParser();
+		try {
+			Model model = p.createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
+			print("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
+			print("<Process reactomeId=\"0\">\n");
+			print("<Properties>\n");
+			print("<displayName>PD map</displayName>\n");
+			print("</Properties>\n");
+			printAliases(model);
+			printReactions(model);
+			print("</Process>\n");
+
+			PrintWriter writer = new PrintWriter("out/report/reactome-viewer.xml", "UTF-8");
+			writer.print(result);
+			writer.close();
+
+		} catch (Exception e) {
+			logger.error(e.getMessage());
+			e.printStackTrace();
+		}
+
+	}
+
+	/**
+	 * Creates representation of the aliases in the reactome visualization model.
+	 * 
+	 * @param model
+	 *          our model to be visualized
+	 * @throws IOException
+	 *           thrown when there are problems accessing reactome database
+	 */
+	private void printAliases(Model model) throws IOException {
+		print("<Nodes>\n");
+		List<Alias> aliases = new ArrayList<Alias>();
+		aliases.addAll(model.getAliases());
+		Collections.sort(aliases, Alias.SIZE_COMPARATOR);
+		for (Alias alias : aliases) {
+			if (!aliasFeasible(alias)) {
+				continue;
+			}
+			int currId = addElement(alias);
+			Element element = null;
+			Map<String, String> parameters = new HashMap<String, String>();
+			Map<String, String> attributes = new HashMap<String, String>();
+
+			attributes.put("id", currId + "");
+			attributes.put("position", (int) alias.getCenterX() + " " + (int) alias.getCenterY());
+			attributes.put("bounds", alias.getX().intValue() + " " + alias.getY().intValue() + " " + alias.getWidth().intValue() + " "
+					+ alias.getHeight().intValue());
+			attributes.put("textPosition", (int) alias.getCenterX() + " " + (int) alias.getCenterY());
+			attributes.put("reactomeId", "0");
+
+			Set<Integer> components = new HashSet<Integer>();
+			String type = "";
+			if (alias instanceof SpeciesAlias) {
+				element = ((SpeciesAlias) alias).getSpecies();
+				String stableIdentifier = rcu.getReactomeIdentifierForSpecies(((SpeciesAlias) alias).getSpecies());
+				if (stableIdentifier != null) {
+					ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
+					if (obj != null && obj.getDbId() != null) {
+						attributes.put("reactomeId", obj.getDbId() + "");
+					}
+				}
+				parameters.put("displayName", ((Species) element).getName());
+				if (alias instanceof ComplexAlias) {
+					for (Alias a : ((ComplexAlias) alias).getAliases()) {
+						components.add(addElement(a));
+					}
+				}
+			}
+			if (alias instanceof CompartmentAlias) {
+				element = ((CompartmentAlias) alias).getCompartment();
+				parameters.put("displayName", ((Compartment) element).getName());
+				for (Alias a : ((CompartmentAlias) alias).getAliases()) {
+					components.add(addElement(a));
+				}
+			}
+
+			if (element instanceof ComplexSpecies) {
+				type = "org.gk.render.RenderableComplex";
+				attributes.put("hideComponents", "true");
+				attributes.put("textPosition", (int) alias.getCenterX() + " " + (int) (alias.getY() + alias.getHeight()));
+			} else if (element instanceof SimpleMolecule) {
+				type = "org.gk.render.RenderableChemical";
+			} else if (element instanceof Ion) {
+				type = "org.gk.render.RenderableChemical";
+			} else if (element instanceof Protein) {
+				type = "org.gk.render.RenderableProtein";
+			} else if (element instanceof Species) {
+				type = "org.gk.render.RenderableEntity";
+			} else if (element instanceof Compartment) {
+				type = "org.gk.render.RenderableCompartment";
+			} else {
+				logger.debug("Ignoring: " + parameters.get("displayName") + "(" + element.getClass() + ")");
+				continue;
+			}
+			print("<" + type);
+			for (String string : attributes.keySet()) {
+				print(" " + string + "=\"" + attributes.get(string) + "\"");
+			}
+			print(">");
+			for (String key : parameters.keySet()) {
+				print("<" + key + ">" + parameters.get(key) + "</" + key + ">");
+			}
+
+			if (components.size() != 0) {
+				print("\n <Components>\n");
+				for (Integer i : components) {
+					print("  <Component id=\"" + i + "\"/>\n");
+				}
+				print(" </Components>\n");
+			}
+			print("</" + type + ">\n");
+
+		}
+		print("</Nodes>\n");
+	}
+
+	/**
+	 * Creates reactions in reactome visuazliation model from our model.
+	 * 
+	 * @param model
+	 *          model to be visualized
+	 * @throws IOException
+	 *           thrown when there are problems with accessing reactome database
+	 */
+	private void printReactions(Model model) throws IOException {
+		print("<Edges>\n");
+		for (Reaction reaction : model.getReactions()) {
+			if (!isReactionFeasible(reaction)) {
+				continue;
+			}
+			int currId = ++id;
+			Map<String, String> parameters = new HashMap<String, String>();
+			Map<Integer, String> inputs = new HashMap<Integer, String>();
+			Map<Integer, String> outputs = new HashMap<Integer, String>();
+			Map<Integer, String> catalysts = new HashMap<Integer, String>();
+
+			Map<String, String> attributes = new HashMap<String, String>();
+
+			attributes.put("id", currId + "");
+			attributes.put("position", (int) reaction.getCenterPoint().getX() + " " + (int) reaction.getCenterPoint().getY());
+			attributes.put("points", getReactionMiddlePoints(reaction));
+			attributes.put("lineWidth", "1.0");
+			attributes.put("reactomeId", "0");
+
+			parameters.put("displayName", reaction.getIdReaction());
+
+			String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
+			if (stableIdentifier != null) {
+				ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
+				if (obj != null && obj.getDbId() != null) {
+					attributes.put("reactomeId", obj.getDbId() + "");
+				}
+			}
+
+			for (ReactionNode node : reaction.getReactionNodes()) {
+				Integer id = tempIds.get(node.getAlias());
+				if (node instanceof Reactant) {
+					inputs.put(id, getInputString((Reactant) node));
+				} else if (node instanceof Product) {
+					outputs.put(id, getOutputString((Product) node));
+				} else if (node instanceof Modifier) {
+					catalysts.put(id, getModifierString((Modifier) node));
+				}
+			}
+
+			String type = "org.gk.render.RenderableReaction";
+
+			print("<" + type);
+			for (String string : attributes.keySet()) {
+				print(" " + string + "=\"" + attributes.get(string) + "\"");
+			}
+			print(">\n");
+			print(" <Properties>\n");
+			for (String key : parameters.keySet()) {
+				print("  <" + key + ">" + parameters.get(key) + "</" + key + ">\n");
+			}
+			print(" </Properties>\n");
+
+			if (inputs.size() != 0) {
+				print(" <Inputs>\n");
+				for (Integer i : inputs.keySet()) {
+					print("  <Input  id=\"" + i + "\" points=\"" + inputs.get(i) + "\"/>\n");
+				}
+				print(" </Inputs>\n");
+			}
+			if (outputs.size() != 0) {
+				print(" <Outputs>\n");
+				for (Integer i : outputs.keySet()) {
+					print("  <Output  id=\"" + i + "\" points=\"" + outputs.get(i) + "\"/>\n");
+				}
+				print(" </Outputs>\n");
+			}
+			if (catalysts.size() != 0) {
+				print(" <Catalysts>\n");
+				for (Integer i : catalysts.keySet()) {
+					print("  <Catalyst  id=\"" + i + "\" points=\"" + catalysts.get(i) + "\"/>\n");
+				}
+				print(" </Catalysts>\n");
+			}
+			print("</" + type + ">\n");
+
+		}
+
+		print("</Edges>\n");
+	}
+
+	/**
+	 * Returns string representing modifier.
+	 * 
+	 * @param node
+	 *          modifier in our model
+	 * @return string representing modifier that can be used in reactome
+	 *         visualization
+	 */
+	private String getModifierString(ReactionNode node) {
+		String result = null;
+		List<Point2D> points = node.getLine().getPoints();
+		for (int i = 0; i < points.size() - 1; i++) {
+			if (result == null) {
+				result = "";
+			} else {
+				result += ", ";
+			}
+			Point2D point = points.get(i);
+			result += (int) point.getX() + " " + (int) point.getY();
+		}
+		return result;
+	}
+
+	/**
+	 * Returns string representing product.
+	 * 
+	 * @param node
+	 *          product in our model
+	 * @return string representing product that can be used in reactome
+	 *         visualization
+	 */
+	private String getOutputString(ReactionNode node) {
+		for (NodeOperator tmpNode : node.getReaction().getOperators()) {
+			if (tmpNode.isProductOperator()) {
+				String result = null;
+				List<Point2D> points = node.getLine().getPoints();
+				for (int i = points.size() - 1; i >= 0; i--) {
+					if (result == null) {
+						result = "";
+					} else {
+						result += ", ";
+					}
+					Point2D point = points.get(i);
+					result += (int) point.getX() + " " + (int) point.getY();
+				}
+				return result;
+			}
+		}
+		Point2D point = node.getLine().getEndPoint();
+		String result = (int) point.getX() + " " + (int) point.getY();
+		return result;
+	}
+
+	/**
+	 * Returns string representing reactant.
+	 * 
+	 * @param node
+	 *          reactant in our model
+	 * @return string representing reactant that can be used in reactome
+	 *         visualization
+	 */
+	private String getInputString(ReactionNode node) {
+		for (NodeOperator tmpNode : node.getReaction().getOperators()) {
+			if (tmpNode.isReactantOperator()) {
+				String result = null;
+				List<Point2D> points = node.getLine().getPoints();
+				for (int i = 0; i < points.size(); i++) {
+					if (result == null) {
+						result = "";
+					} else {
+						result += ", ";
+					}
+					Point2D point = points.get(i);
+					result += (int) point.getX() + " " + (int) point.getY();
+				}
+				return result;
+			}
+		}
+		Point2D point = node.getLine().getPoints().get(0);
+		String result = (int) point.getX() + " " + (int) point.getY();
+		return result;
+	}
+
+	/**
+	 * Check if reaction can be easily transformed into reactome vizualization
+	 * tool.
+	 * 
+	 * @param reaction
+	 *          reaction to be checked
+	 * @return <code>true</code> if reaction can be easily transformed,
+	 *         <code>false</code> otherwise
+	 */
+	private boolean isReactionFeasible(Reaction reaction) {
+		for (ReactionNode node : reaction.getReactionNodes()) {
+			if (!aliasFeasible(node.getAlias())) {
+				return false;
+			}
+		}
+		int counter = 0;
+		for (NodeOperator node : reaction.getOperators()) {
+			if (node.isProductOperator()) {
+				counter++;
+			}
+			if (counter > 1) {
+				logger.debug("To many operators in the input: " + reaction.getIdReaction());
+				return false;
+			}
+		}
+		counter = 0;
+		for (NodeOperator node : reaction.getOperators()) {
+			if (node.isReactantOperator()) {
+				counter++;
+			}
+			if (counter > 1) {
+				logger.debug("To many operators in the output: " + reaction.getIdReaction());
+				return false;
+			}
+		}
+		counter = 0;
+		for (NodeOperator node : reaction.getOperators()) {
+			if (node.isModifierOperator()) {
+				logger.debug("To complicated catalyst: " + reaction.getIdReaction());
+				return false;
+			}
+		}
+		return true;
+	}
+
+	/**
+	 * Returns string representing reaction line.
+	 * 
+	 * @param reaction
+	 *          reaction to be transformed
+	 * @return string representing reaction line
+	 */
+	private String getReactionMiddlePoints(Reaction reaction) {
+		String result = null;
+		NodeOperator node = null;
+		for (NodeOperator n : reaction.getOperators()) {
+			if (n.isReactantOperator()) {
+				node = n;
+			}
+		}
+		if (node != null) {
+			for (Point2D point : node.getLine().getPoints()) {
+				if (result == null) {
+					result = (int) point.getX() + " " + (int) point.getY();
+				} else {
+					result += ", " + (int) point.getX() + " " + (int) point.getY();
+				}
+			}
+		} else {
+			AbstractNode tmp = null;
+			for (AbstractNode reactionNode : reaction.getNodes()) {
+				if (reactionNode instanceof Reactant) {
+					tmp = reactionNode;
+				}
+			}
+			List<Point2D> points = tmp.getLine().getPoints();
+			for (int i = 0; i < points.size(); i++) {
+				Point2D point = points.get(i);
+				if (result == null) {
+					result = (int) point.getX() + " " + (int) point.getY();
+				} else {
+					result += ", " + (int) point.getX() + " " + (int) point.getY();
+				}
+			}
+		}
+
+		node = null;
+		for (NodeOperator n : reaction.getOperators()) {
+			if (n.isProductOperator()) {
+				node = n;
+			}
+		}
+		if (node != null) {
+			List<Point2D> points = node.getLine().getPoints();
+			for (int i = points.size() - 1; i >= 0; i--) {
+				Point2D point = points.get(i);
+				if (result == null) {
+					result = (int) point.getX() + " " + (int) point.getY();
+				} else {
+					result += ", " + (int) point.getX() + " " + (int) point.getY();
+				}
+			}
+		} else {
+			AbstractNode tmp = null;
+			for (AbstractNode reactionNode : reaction.getNodes()) {
+				if (reactionNode instanceof Product) {
+					tmp = reactionNode;
+				}
+			}
+			List<Point2D> points = tmp.getLine().getPoints();
+			for (int i = 0; i < points.size(); i++) {
+				Point2D point = points.get(i);
+				if (result == null) {
+					result = (int) point.getX() + " " + (int) point.getY();
+				} else {
+					result += ", " + (int) point.getX() + " " + (int) point.getY();
+				}
+			}
+		}
+
+		return result;
+	}
+
+	/**
+	 * Checks if alias can be put into reactome vizualization.
+	 * 
+	 * @param alias
+	 *          alias to check
+	 * @return <code>true</code> if alias can be put into reactome vizualization,
+	 *         <code>false</code> otherwise
+	 */
+	public boolean aliasFeasible(Alias alias) {
+		Point2D point = new Point2D.Double(alias.getX(), alias.getY());
+		Point2D point2 = new Point2D.Double(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
+		if (bound.contains(point) && bound.contains(point2)) {
+			return true;
+		}
+		return false;
+	}
+
+	/**
+	 * @return the rc
+	 * @see #rc
+	 */
+	public DataSourceUpdater getRc() {
+		return rc;
+	}
+
+	/**
+	 * @param rc
+	 *          the rc to set
+	 * @see #rc
+	 */
+	public void setRc(DataSourceUpdater rc) {
+		this.rc = rc;
+	}
+
+	/**
+	 * @return the rcu
+	 * @see #rcu
+	 */
+	public ReactomeQueryUtil getRcu() {
+		return rcu;
+	}
+
+	/**
+	 * @param rcu
+	 *          the rcu to set
+	 * @see #rcu
+	 */
+	public void setRcu(ReactomeQueryUtil rcu) {
+		this.rcu = rcu;
+	}
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java b/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
index 63122b2de2..32f4a07f0f 100644
--- a/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
+++ b/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
@@ -1,116 +1,116 @@
-package lcsb.mapviewer.run;
-
-import java.io.FileNotFoundException;
-import java.text.DecimalFormat;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-
-/**
- * This class is a snippet for Vibine collaboration project. It shows how to
- * access our internal data structures and source files.
- * 
- * @author Piotr Gawron
- * 
- */
-public class VibineSnippet {
-
-	/**
-	 * Number of nanoseconds in second.
-	 */
-	private static final double	NANOSECONDS_IN_SECOND	= 1000000000.0;
-
-	/**
-	 * CellDesigner file on with some data that is used in this snippet (it's PD
-	 * map from June 2015).
-	 */
-	private static final String	INPUT_FILE						= "testFiles/pd_full/PD_150625_3.xml";
-
-	/**
-	 * Default class logger.
-	 */
-	private final Logger				logger								= Logger.getLogger(VibineSnippet.class);
-
-	/**
-	 * Main entry point to the program.
-	 * 
-	 * @param args
-	 *          parameters with which the program was run
-	 */
-	public static void main(String[] args) {
-		VibineSnippet main = new VibineSnippet();
-		long startTime = System.nanoTime();
-
-		try {
-			main.run();
-		} catch (Exception e) {
-			main.logger.error(e, e);
-		} finally {
-			long endTime = System.nanoTime();
-			long duration = endTime - startTime;
-			double sec = duration / NANOSECONDS_IN_SECOND;
-			System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
-		}
-	}
-
-	/**
-	 * This method transform {@link #inputOptions input data}.
-	 * 
-	 * @throws FileNotFoundException
-	 * 
-	 * @throws Exception
-	 *           thrown when the there is a problem...
-	 */
-	private void run() throws Exception {
-		logger.debug("Opening file: " + INPUT_FILE);
-
-		CellDesignerXmlParser parser = new CellDesignerXmlParser();
-		Model model = parser.createModel(new ConverterParams().filename(INPUT_FILE));
-
-		logger.debug("File processed.");
-
-		logger.debug("-------------------------------");
-		logger.debug("Number of elements: " + model.getElements().size());
-		logger.debug("Number of aliases for these elements: " + model.getAliases().size());
-
-		logger.debug("Number of reactions: " + model.getReactions().size());
-
-		logger.debug("-------------------------------");
-		String speciesId = "s4351";
-		String reactionId = "re332";
-		Element element = model.getElementByElementId(speciesId);
-
-		List<SpeciesAlias> aliases = model.getAliasesBySpeciesId(speciesId);
-
-		logger.debug("Element with id: " + speciesId);
-		logger.debug("Element type: " + element.getClass());
-		logger.debug("Element name: " + element.getName());
-		logger.debug("Element is located in " + aliases.size() + " places on the map.");
-		logger.debug("Here are coordinates: ");
-		for (SpeciesAlias speciesAlias : aliases) {
-			logger.debug(
-					speciesAlias.getAliasId() + " - " + speciesAlias.getX() + "," + speciesAlias.getY() + "," + speciesAlias.getWidth() + ","
-							+ speciesAlias.getHeight());
-		}
-
-		logger.debug("-------------------------------");
-		Reaction reaction = model.getReactionByReactionId(reactionId);
-
-		logger.debug("Reaction with id: " + reactionId);
-		logger.debug("Reaction has " + reaction.getReactionNodes().size() + " members.");
-		for (ReactionNode node : reaction.getReactionNodes()) {
-			logger.debug(
-					node.getClass().getSimpleName() + "; points to " + node.getElement().getClass().getSimpleName() + "[" + node.getElement().getElementId() + "]");
-		}
-		logger.debug("-------------------------------");
-	}
-
-}
+package lcsb.mapviewer.run;
+
+import java.io.FileNotFoundException;
+import java.text.DecimalFormat;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+
+/**
+ * This class is a snippet for Vibine collaboration project. It shows how to
+ * access our internal data structures and source files.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public class VibineSnippet {
+
+	/**
+	 * Number of nanoseconds in second.
+	 */
+	private static final double	NANOSECONDS_IN_SECOND	= 1000000000.0;
+
+	/**
+	 * CellDesigner file on with some data that is used in this snippet (it's PD
+	 * map from June 2015).
+	 */
+	private static final String	INPUT_FILE						= "testFiles/pd_full/PD_150625_3.xml";
+
+	/**
+	 * Default class logger.
+	 */
+	private final Logger				logger								= Logger.getLogger(VibineSnippet.class);
+
+	/**
+	 * Main entry point to the program.
+	 * 
+	 * @param args
+	 *          parameters with which the program was run
+	 */
+	public static void main(String[] args) {
+		VibineSnippet main = new VibineSnippet();
+		long startTime = System.nanoTime();
+
+		try {
+			main.run();
+		} catch (Exception e) {
+			main.logger.error(e, e);
+		} finally {
+			long endTime = System.nanoTime();
+			long duration = endTime - startTime;
+			double sec = duration / NANOSECONDS_IN_SECOND;
+			System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
+		}
+	}
+
+	/**
+	 * This method transform {@link #inputOptions input data}.
+	 * 
+	 * @throws FileNotFoundException
+	 * 
+	 * @throws Exception
+	 *           thrown when the there is a problem...
+	 */
+	private void run() throws Exception {
+		logger.debug("Opening file: " + INPUT_FILE);
+
+		CellDesignerXmlParser parser = new CellDesignerXmlParser();
+		Model model = parser.createModel(new ConverterParams().filename(INPUT_FILE));
+
+		logger.debug("File processed.");
+
+		logger.debug("-------------------------------");
+		logger.debug("Number of elements: " + model.getElements().size());
+		logger.debug("Number of aliases for these elements: " + model.getAliases().size());
+
+		logger.debug("Number of reactions: " + model.getReactions().size());
+
+		logger.debug("-------------------------------");
+		String speciesId = "s4351";
+		String reactionId = "re332";
+		Element element = model.getElementByElementId(speciesId);
+
+		List<SpeciesAlias> aliases = model.getAliasesBySpeciesId(speciesId);
+
+		logger.debug("Element with id: " + speciesId);
+		logger.debug("Element type: " + element.getClass());
+		logger.debug("Element name: " + element.getName());
+		logger.debug("Element is located in " + aliases.size() + " places on the map.");
+		logger.debug("Here are coordinates: ");
+		for (SpeciesAlias speciesAlias : aliases) {
+			logger.debug(
+					speciesAlias.getAliasId() + " - " + speciesAlias.getX() + "," + speciesAlias.getY() + "," + speciesAlias.getWidth() + ","
+							+ speciesAlias.getHeight());
+		}
+
+		logger.debug("-------------------------------");
+		Reaction reaction = model.getReactionByReactionId(reactionId);
+
+		logger.debug("Reaction with id: " + reactionId);
+		logger.debug("Reaction has " + reaction.getReactionNodes().size() + " members.");
+		for (ReactionNode node : reaction.getReactionNodes()) {
+			logger.debug(
+					node.getClass().getSimpleName() + "; points to " + node.getElement().getClass().getSimpleName() + "[" + node.getElement().getElementId() + "]");
+		}
+		logger.debug("-------------------------------");
+	}
+
+}
diff --git a/console/src/test/java/lcsb/mapviewer/run/PdMapAnnotationsTest.java b/console/src/test/java/lcsb/mapviewer/run/PdMapAnnotationsTest.java
index 587c930333..3c0f4bfef1 100644
--- a/console/src/test/java/lcsb/mapviewer/run/PdMapAnnotationsTest.java
+++ b/console/src/test/java/lcsb/mapviewer/run/PdMapAnnotationsTest.java
@@ -1,40 +1,40 @@
-package lcsb.mapviewer.run;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.File;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.run.PdMapAnnotations;
-
-public class PdMapAnnotationsTest {
-	Logger logger = Logger.getLogger(PdMapAnnotationsTest.class);
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void test() {
-		try {
-			String fileName = PdMapAnnotations.getLastPdFilename();
-			assertNotNull(fileName);
-			File file = new File(fileName);
-			assertTrue(file.exists());
-		} catch (Exception e) {
-			e.printStackTrace();
-			fail("Unknown exception occurred");
-		}
-	}
-
-}
+package lcsb.mapviewer.run;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.File;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.run.PdMapAnnotations;
+
+public class PdMapAnnotationsTest {
+	Logger logger = Logger.getLogger(PdMapAnnotationsTest.class);
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void test() {
+		try {
+			String fileName = PdMapAnnotations.getLastPdFilename();
+			assertNotNull(fileName);
+			File file = new File(fileName);
+			assertTrue(file.exists());
+		} catch (Exception e) {
+			e.printStackTrace();
+			fail("Unknown exception occurred");
+		}
+	}
+
+}
diff --git a/console/testFiles/pd_full/PD_151217_2/layouts/PD substantia nigra.txt b/console/testFiles/pd_full/PD_151217_2/layouts/PD substantia nigra.txt
index 8f57d5c9d2..5ed3ee8742 100644
--- a/console/testFiles/pd_full/PD_151217_2/layouts/PD substantia nigra.txt	
+++ b/console/testFiles/pd_full/PD_151217_2/layouts/PD substantia nigra.txt	
@@ -1,4342 +1,4342 @@
-# VERSION=1.0
-# NAME=PD substantia nigra
+# VERSION=1.0
+# NAME=PD substantia nigra
 # DESCRIPTION=Differential transcriptome expression from post mortem tissue. Meta-analysis from 8 published datasets, FDR = 0.05, see PMIDs 23832570 and 25447234.
-name	value
-GBE1	-0,943978048
-SLC18A2	-0,941309505
-KCNJ6	-0,894120983
-DLK1	-0,887122171
-PTDSS1	-0,851959645
-FGF13	-0,842876271
-PCDH8	-0,83524894
-ZNF226	-0,82900335
-SLC6A3	-0,824713365
-PIP5K1B	-0,812285785
-DENR	-0,81101551
-TPBG	-0,806963209
-PRKAR2B	-0,805288865
-OSBPL10	-0,80406299
-ALDH1A1	-0,795042129
-GGCX	-0,795035797
-ACP2	-0,794853979
-SLITRK5	-0,793842132
-FAM70A	-0,793715412
-HPRT1	-0,792370336
-CCNH	-0,790971864
-MYRIP	-0,78490295
-TUBB2A	-0,783142444
-ACTR10	-0,782043082
-BASP1	-0,778702387
-CADPS2	-0,777552826
-PID1	-0,775106213
-SV2C	-0,774895093
-RBM3	-0,77091551
-REEP1	-0,770000111
-RIMBP2	-0,766421185
-CNIH3	-0,765790316
-DMXL2	-0,765309344
-LOC10431	-0,762992699
-SV2B	-0,759985564
-AGK	-0,756506198
-RCAN2	-0,753762002
-LPPR4	-0,753018962
-RALYL	-0,75270126
-L1CAM	-0,751978689
-BCAS2	-0,751241508
-LOC100131795	-0,750350108
-TH	-0,748260596
-AV756161	-0,747351587
-TRIM36	-0,746057792
-MPPED2	-0,743864716
-NELL2	-0,742513977
-MAGED1	-0,739190733
-LRRC49	-0,738776851
-SYNGR3	-0,734846774
-ERC2	-0,734619705
-VBP1	-0,73223558
-UQCC	-0,729749962
-DCLK1	-0,725139215
-GSS	-0,724321987
-OPA1	-0,723790592
-PPP2R2B	-0,720892147
-COPS4	-0,720599852
-NSF	-0,720580224
-DLD	-0,72035948
-DYNC1I1	-0,719837984
-GABARAPL3	-0,717235008
-GPRASP1	-0,71302626
-NAP1L2	-0,712876929
-AMPH	-0,711957162
-PNMAL1	-0,70952389
-RGS6	-0,706463
-LDB2	-0,704777497
-TTC19	-0,704232585
-SCN3B	-0,703738866
-ATPIF1	-0,702603531
-BEX1	-0,700382911
-LMO3	-0,699029823
-TBC1D9	-0,698189481
-NDUFS1	-0,697230219
-INSM1	-0,696524737
-PARL	-0,696362568
-MRPL15	-0,688780959
-C3orf14	-0,687875821
-C19orf62	-0,687403479
-PCYOX1L	-0,686812669
-VRK1	-0,685016241
-MDH2	-0,684889561
-SMYD3	-0,684642724
-ASAH1	-0,68459801
-GSTA4	-0,684021936
-NDUFA9	-0,683116722
-ATP5C1	-0,682289667
-DDX25	-0,681511867
-GNG3	-0,681122999
-MUDENG	-0,67996077
-SCG2	-0,679728044
-MOAP1	-0,679575281
-SYT1	-0,678979261
-ATP6V1H	-0,6786546
-SHOC2	-0,677754756
-PCSK1	-0,677441918
-LBH	-0,67710638
-HK1	-0,676818391
-KIAA0319	-0,676346138
-SMAP1	-0,67618103
-EHBP1	-0,675429621
-RAP1GAP2	-0,673705297
-FABP7	-0,673485271
-LRRN3	-0,6731503
-AHNAK2	-0,672875949
-DHDDS	-0,671959403
-SNAPC5	-0,670824633
-C17orf108	-0,670563093
-AL390170	-0,67026906
-PTS	-0,669577055
-NUDT11	-0,668061506
-HMP19	-0,66794356
-IMMT	-0,667541939
-RGS4	-0,667109174
-RET	-0,667088994
-PBLD	-0,666164981
-AP3M2	-0,666056972
-WDR7	-0,665751643
-ATP6V0D1	-0,665487037
-RTF1	-0,664652469
-TUBB3	-0,664644351
-CHCHD2	-0,664529051
-DYNLT3	-0,663584428
-RAB6B	-0,662755469
-CHGB	-0,661865706
-NGFRAP1	-0,659441958
-AZIN1	-0,659394366
-EN1	-0,659313013
-SNX10	-0,659251628
-MIA3	-0,65882244
-ANK1	-0,657621479
-NR4A2	-0,65598531
-ANAPC13	-0,655864214
-RGS7	-0,654445938
-NME5	-0,652754395
-TXNDC9	-0,652019899
-PPIP5K2	-0,651763237
-RFK	-0,651442652
-BE674466	-0,651048329
-PEG10	-0,650932122
-PIAS2	-0,650823358
-CUX2	-0,649970555
-SEPT6	-0,649422911
-FKBP1B	-0,649416387
-C12orf10	-0,648407487
-HMGCS1	-0,648164918
-WDR61	-0,648133373
-GFPT1	-0,647751981
-MLLT11	-0,647471245
-AGTR1	-0,645674318
-CSNK1D	-0,645408463
-WDR47	-0,64495088
-PSMD14	-0,644669314
-CISD1	-0,643780748
-PSMD11	-0,642982055
-KCNS3	-0,642919136
-TIMM8B	-0,642730563
-RUNDC3B	-0,641744336
-ANKRD6	-0,640032629
-MDH1	-0,639623665
-STMN2	-0,639070421
-BAI3	-0,638894116
-STX12	-0,638382169
-NECAP1	-0,638376593
-NIT2	-0,638223243
-CIRBP	-0,637859912
-XK	-0,636787355
-KIAA1797	-0,636384728
-ICMT	-0,636379567
-GALT	-0,636138691
-SPINT2	-0,635454321
-PAIP1	-0,634724103
-TAGLN3	-0,63459569
-CADPS	-0,634245008
-GALNT11	-0,634168707
-SLC9A6	-0,632805526
-ANKRD34C	-0,63217094
-COPG2IT1	-0,63213856
-VPS4B	-0,63135628
-ATP6V0E2	-0,631164455
-SC5DL	-0,631137699
-CNPY2	-0,630875303
-GCC2	-0,630691438
-CRYZL1	-0,63015348
-MOBKL3	-0,630076244
-SNCA	-0,629316875
-STAM	-0,628134338
-TUBA4A	-0,627764216
-MAK16	-0,627148096
-FRY	-0,626684765
-UBE2V2	-0,626378865
-RWDD2B	-0,626170788
-FBXO9	-0,62572532
-FLJ41278	-0,6251633
-SLC30A9	-0,624759053
-LOC100132015	-0,623179237
-EXOG	-0,622056922
-RAP1GAP	-0,618803848
-DYNC1LI1	-0,618641756
-HARS	-0,618639749
-NDUFA5	-0,618245275
-SPCS1	-0,618130333
-PSMB7	-0,618122572
-NETO2	-0,618103081
-ATP5G3	-0,617855025
-UCHL1	-0,617452524
-FAM127A	-0,616124191
-TSSC1	-0,615619431
-CBLN1	-0,615519237
-CYB5R1	-0,615294192
-PSMG1	-0,61487171
-AKAP12	-0,614821543
-CYB561	-0,614281499
-KCND3	-0,613554227
-GABRB1	-0,613364723
-SLIT1	-0,613251897
-HN1	-0,612796898
-F8	-0,612749576
-VSNL1	-0,611517123
-ATP5A1	-0,611141848
-ARMCX5	-0,610703909
-AI097640	-0,610659067
-CERK	-0,610508368
-TMX4	-0,610174408
-TSPAN13	-0,609932725
-CAMLG	-0,609409157
-NDUFA7	-0,609351405
-STRAP	-0,609237631
-RTCD1	-0,607502869
-ORC5L	-0,606910471
-SCG5	-0,606870723
-HSPA12A	-0,606863939
-VAV3	-0,606070683
-TUBB2C	-0,60582666
-DCTN2	-0,605238426
-OCRL	-0,604661192
-HPCAL4	-0,604023171
-ARL1	-0,604008234
-CDK14	-0,603712397
-TLK1	-0,603591955
-BLVRA	-0,603201697
-NEFL	-0,602887281
-SLC25A32	-0,602708801
-ATXN10	-0,602624835
-UQCRC2	-0,601726567
-SLC25A3	-0,601470752
-MYL12B	-0,601373186
-CDS2	-0,601292766
-DDC	-0,601079077
-BSCL2	-0,6009448
-CACNB3	-0,598982611
-RIMS3	-0,598771066
-LASS6	-0,598387226
-FIBP	-0,598382328
-LRPPRC	-0,598144321
-PYROXD1	-0,598012671
-MAP3K9	-0,597438703
-CHL1	-0,5969101
-FJX1	-0,596748319
-PFN2	-0,596551333
-ATMIN	-0,59649395
-LIN7B	-0,596058244
-AV704232	-0,595274626
-PPP2R5C	-0,594797769
-SNAP91	-0,59414072
-AKT3	-0,593859242
-NDUFAB1	-0,593111219
-CCDC28A	-0,59307395
-GLOD4	-0,592429097
-STXBP1	-0,591440124
-HLTF	-0,591296161
-CRMP1	-0,590916915
-KIAA0513	-0,590696005
-GHITM	-0,590624599
-ATP6V1B2	-0,590367192
-USP14	-0,589739205
-RNFT2	-0,589705749
-SCG3	-0,589375952
-ATP5B	-0,588999541
-FAM136A	-0,588982627
-UBE2N	-0,588308222
-ANXA6	-0,588071667
-MRTO4	-0,58799806
-SNRK	-0,587183425
-CACNA2D2	-0,587134808
-IFT57	-0,586933566
-PPP3CB	-0,586906049
-RICH2	-0,586554767
-ME3	-0,586514247
-THOC7	-0,585617181
-FAM188A	-0,584083221
-EIF2B3	-0,582997986
-CNTNAP1	-0,582856877
-SCRN1	-0,582791752
-ACAT1	-0,582760841
-IDI1	-0,582694626
-PBX1	-0,582658829
-CDC42	-0,582658446
-NBEA	-0,582614884
-PPP1R2	-0,581839918
-ACTR6	-0,581817384
-TAF9	-0,581794162
-NIPSNAP1	-0,581711722
-SEC61A2	-0,58139821
-WDR37	-0,581272248
-VWA5A	-0,581248993
-CDC27	-0,580500838
-MYT1L	-0,580491453
-PSMC1	-0,580473356
-KATNB1	-0,578133005
-ZWINT	-0,577661475
-C12orf24	-0,577181135
-SLC25A46	-0,577144749
-DOLK	-0,576794187
-APOO	-0,576716633
-GCH1	-0,576494714
-TBC1D30	-0,575582077
-DCTN3	-0,575526778
-FBXL2	-0,575141782
-KIFAP3	-0,574923419
-CMAS	-0,574834972
-C18orf10	-0,574780811
-PNMA2	-0,574504978
-PDHX	-0,574434123
-SAMM50	-0,574204311
-NDUFA2	-0,574087728
-NPTN	-0,573534504
-HIGD1A	-0,573110642
-CYC1	-0,573010558
-HMGCR	-0,572959475
-TRAPPC2L	-0,572517332
-IMPA1	-0,572397104
-IMPACT	-0,572070372
-KIAA0802	-0,572067617
-DSTN	-0,571964512
-C5orf44	-0,571958339
-CCK	-0,571148184
-OGDHL	-0,571078621
-TCP11L1	-0,570951095
-RNF14	-0,569913578
-IARS	-0,569079443
-CDH8	-0,569072707
-RNF41	-0,568830451
-SCN3A	-0,568276898
-PSMD12	-0,567936617
-TNFRSF21	-0,567631199
-FIG4	-0,566751868
-DDX24	-0,566446037
-MARK1	-0,566206858
-ATP8A2	-0,565754513
-ACLY	-0,565055263
-DDX42	-0,564984354
-KIF3C	-0,564949485
-PIN1	-0,564290859
-PSEN2	-0,564206755
-TERF2IP	-0,564084181
-VDAC3	-0,563895581
-B3GNT1	-0,563686309
-CHN1	-0,563660153
-GLO1	-0,561564055
-RAB11A	-0,561549092
-PRPS1	-0,561391557
-MAP2	-0,561080301
-NHP2	-0,56096586
-DNAJA2	-0,560780556
-NDRG4	-0,560771764
-HNRNPA0	-0,560406816
-NDUFV2	-0,559975953
-ADH5	-0,559909821
-FAM3C	-0,559672666
-COPS7A	-0,559265307
-SULT4A1	-0,558733244
-MATN3	-0,558346148
-TMEM14A	-0,557817575
-HRASLS	-0,557799459
-TMEM14B	-0,557593404
-TTC1	-0,557573183
-R3HDM1	-0,557428266
-AUH	-0,55725646
-C5orf22	-0,55714645
-TUBB	-0,557095971
-C5orf13	-0,55663948
-COX7A2L	-0,556219721
-POMP	-0,556110434
-ATP5J2	-0,555267292
-ZNF204P	-0,555121445
-INA	-0,554984251
-NUP93	-0,55488654
-STAU2	-0,55454534
-VAT1	-0,554180752
-DDB1	-0,554146967
-THY1	-0,554057809
-SRPRB	-0,553818923
-IMP4	-0,553554219
-SRP19	-0,552319097
-FUCA1	-0,551919323
-PRKCZ	-0,551777138
-CD2BP2	-0,55167071
-C12orf43	-0,551436389
-SUSD4	-0,55137396
-W88821	-0,551080268
-LSM4	-0,550328209
-SNAP25	-0,550276399
-ACSL6	-0,549806401
-MYH10	-0,549550685
-DDHD2	-0,548942799
-PRKACA	-0,548422775
-CHRNB3	-0,547701041
-NEFM	-0,547618123
-PLD3	-0,547495065
-GSPT2	-0,547329995
-ATP6V1E1	-0,546911033
-GABBR2	-0,546899558
-IPW	-0,546596796
-SCAMP5	-0,546380917
-RFPL1S	-0,545994554
-BSN	-0,545979557
-MAGI1	-0,54490486
-DRG1	-0,544733954
-PITPNB	-0,544704547
-LETMD1	-0,544636809
-AI263044	-0,544470885
-STOML1	-0,544383238
-GBAS	-0,544103215
-RAB3GAP1	-0,543092086
-ACTG1	-0,54300405
-PPME1	-0,542943175
-AFG3L2	-0,542490245
-DNAJC6	-0,541912283
-TUBA1B	-0,541625287
-ABCE1	-0,541581351
-ARF3	-0,541401116
-SRSF3	-0,54134715
-NEFH	-0,540578844
-ADK	-0,540377244
-TIMM17A	-0,540158649
-ELOVL6	-0,540054201
-FAM189A1	-0,539987546
-ATP6V1A	-0,539816156
-OAT	-0,53960074
-KIAA0284	-0,539436564
-SLC25A12	-0,538986194
-AP3D1	-0,538816413
-ISCU	-0,53848727
-CDH10	-0,538458105
-APEH	-0,538385859
-TMEM35	-0,537944022
-NDFIP1	-0,537769873
-U79277	-0,537586945
-SYNGR1	-0,53757151
-MEAF6	-0,537175986
-DNM1	-0,536361784
-DEF8	-0,536162488
-PDXK	-0,536128962
-RIT2	-0,536060129
-AACS	-0,535868362
-RAB3A	-0,535840143
-LXN	-0,535676847
-CCBL2	-0,53559953
-ATXN7L3B	-0,535570224
-RCN2	-0,535264733
-SDC2	-0,535187449
-NRXN3	-0,534911729
-SDC1	-0,534748047
-PSMD1	-0,534162775
-UBA5	-0,534098166
-PEX11B	-0,533915774
-RAP1GDS1	-0,533764019
-NUPL1	-0,533680375
-ARMCX1	-0,533607326
-SDHAP1	-0,533209621
-PJA2	-0,532853246
-ACOT7	-0,532662038
-SEZ6L	-0,532618647
-CELF2	-0,532603645
-CXorf40A	-0,532513065
-NDUFB5	-0,532279155
-GARS	-0,532224902
-NRG1	-0,532009485
-SEC31B	-0,53180843
-ME1	-0,531466374
-PSMD8	-0,531445018
-MSL1	-0,531268404
-PCLO	-0,531166247
-RAB14	-0,531006634
-MAGED2	-0,530858407
-EIF3K	-0,530846086
-MMD	-0,530845303
-MYO5A	-0,530805656
-NCRNA00094	-0,530597959
-KIAA1107	-0,53057188
-KIAA0564	-0,530294183
-PSMB2	-0,530140819
-C1orf114	-0,530111522
-GCLM	-0,529867963
-NDN	-0,529086871
-SRD5A1	-0,528786683
-DNAJB9	-0,528374918
-SLC7A8	-0,528181836
-CLIP3	-0,527794519
-NDUFB1	-0,527724864
-CLSTN2	-0,52726691
-C14orf156	-0,527148764
-CIAPIN1	-0,527136633
-ATP5F1	-0,527047789
-PSMB5	-0,526841307
-FAM32A	-0,526499611
-KIAA1644	-0,526147045
-RTN1	-0,526062751
-EXOSC9	-0,525622526
-PFKM	-0,525053758
-TCF25	-0,524910517
-ATP5O	-0,524889972
-PTPRN2	-0,524794642
-SNX4	-0,524373257
-ATP6V1G2	-0,524016622
-SLC35E3	-0,523930118
-SLC2A6	-0,52364368
-SUCLA2	-0,523588063
-PLCB1	-0,523263994
-TMEM30A	-0,521872901
-PDE4D	-0,521870014
-RAB5A	-0,521632556
-MAPK9	-0,521572661
-CAP2	-0,521120749
-RPS6KA3	-0,520660932
-GNAO1	-0,520506337
-PSMD6	-0,520132666
-TBCE	-0,519679173
-C9orf125	-0,519623009
-MN1	-0,51937171
-MFSD1	-0,51842841
-KIF3A	-0,518357676
-SHFM1	-0,517546292
-NRIP3	-0,516545986
-ANKMY2	-0,516365077
-CDK5	-0,516196782
-REEP5	-0,516165841
-SLC1A1	-0,516141732
-UBE2K	-0,516036367
-SMEK2	-0,515537555
-PI4K2A	-0,515462049
-TTC39A	-0,514924765
-GUCY1B3	-0,514788287
-QPCT	-0,514170797
-ST6GALNAC5	-0,514077764
-ATP6V1F	-0,513941613
-HSD17B12	-0,513489073
-PPFIA2	-0,51321383
-PLCH1	-0,512855521
-CNTN6	-0,512564243
-ENTPD6	-0,512350634
-ALAS1	-0,512141897
-RUNDC3A	-0,511994377
-PCMT1	-0,511547085
-IDS	-0,511290223
-PLEKHB2	-0,510964275
-CDO1	-0,510668427
-NDUFB6	-0,510219117
-COX6C	-0,509869079
-OPTN	-0,509603205
-PSMA1	-0,509510596
-STS	-0,509361214
-TIMM10	-0,509318807
-C1D	-0,509252454
-GAP43	-0,509215292
-CCDC6	-0,509150548
-TRIM37	-0,509012308
-ATP2B2	-0,508803511
-PGAM1	-0,50863259
-GGNBP2	-0,508616013
-SRP72	-0,508482078
-TCEAL2	-0,508464868
-SV2A	-0,508330914
-CDK5R2	-0,508227652
-FHOD3	-0,508155146
-FECH	-0,508046235
-ATP2A3	-0,507932978
-SUB1	-0,507787459
-ACO2	-0,507726776
-C20orf3	-0,507526055
-SEC22B	-0,507453281
-VPS35	-0,507278509
-MRPS33	-0,507141908
-TXNL4A	-0,50704416
-ARHGEF9	-0,506224253
-RBM9	-0,506096633
-TMEM135	-0,506088817
-UHRF1BP1L	-0,505757524
-ME2	-0,505446593
-BZRAP1	-0,505378895
-MCAT	-0,50534007
-AKAP6	-0,505213579
-COPS3	-0,505110121
-MRPS35	-0,505107922
-YWHAB	-0,505015581
-PEX7	-0,504955276
-COPS8	-0,504746043
-OXCT1	-0,504643125
-MAD2L1	-0,504589351
-MCTS1	-0,504510155
-LGALS8	-0,50448664
-ACP1	-0,504339709
-MX1	-0,50393674
-NCALD	-0,50389725
-TASP1	-0,503797818
-AGTPBP1	-0,503605082
-RNF128	-0,503554068
-PSMD13	-0,503503704
-TXN	-0,50336484
-NHLH2	-0,50325399
-USP12	-0,503149229
-PFDN4	-0,502988386
-NAP1L3	-0,502893901
-MRPL20	-0,502624211
-ACSL3	-0,502355771
-MTPAP	-0,502307088
-PMPCB	-0,502239978
-SH3GL3	-0,502227406
-API5	-0,502196949
-CAPNS1	-0,5020898
-YWHAZ	-0,501747483
-TOMM70A	-0,501591565
-STX18	-0,501503813
-HNRNPK	-0,501464694
-LRP1B	-0,501433491
-CDC123	-0,500993468
-DCTN6	-0,500740808
-VAPB	-0,500599356
-CCDC56	-0,499906136
-GOT2	-0,499477446
-RHEB	-0,499343134
-PSMD2	-0,499333749
-YPEL5	-0,49910251
-ATP5G1	-0,499077107
-TUBA1A	-0,498949544
-GSTM3	-0,498766376
-EPB41L1	-0,498605796
-EPS15	-0,498447403
-ENO2	-0,498261848
-ASMTL	-0,498100631
-FH	-0,498098378
-CLTC	-0,497596743
-PSMA3	-0,497405846
-UROS	-0,497291028
-OLFM1	-0,496832922
-ATP6V1G1	-0,496818916
-B3GALNT1	-0,496135395
-PHLPP2	-0,496077027
-TSPYL1	-0,495383913
-SERINC1	-0,49538338
-RPL15	-0,495355843
-ITFG1	-0,495195881
-PDHB	-0,494999933
-RABL3	-0,494855325
-TMEM22	-0,49462563
-MCFD2	-0,494506103
-GABARAPL1	-0,494373853
-MAGEL2	-0,493987847
-VPS33B	-0,493750355
-CDIPT	-0,493440531
-ATP6V0B	-0,493438352
-CLGN	-0,493358721
-SEC23A	-0,493255831
-C7orf43	-0,49286586
-ARL3	-0,492481932
-SLC12A5	-0,492392187
-LAPTM4B	-0,492348426
-LOC285359	-0,492290998
-LARP1	-0,49192011
-YME1L1	-0,491725992
-RAB2A	-0,491586306
-SPATA20	-0,490991626
-ASH2L	-0,490785052
-PTBP2	-0,490747846
-WTAP	-0,490599757
-NANS	-0,490410248
-SCFD1	-0,490269997
-EPB49	-0,489916122
-TUFT1	-0,489843226
-POP4	-0,489594415
-CACNA1G	-0,489236615
-PRPF19	-0,48917604
-NCOA4	-0,488872014
-C1orf216	-0,488856307
-TXNL1	-0,488777426
-AMPD2	-0,48875487
-ASL	-0,488300478
-PFDN1	-0,48807629
-EXTL2	-0,488020888
-RPA3	-0,48773487
-ACVR1B	-0,487609726
-ANKRD46	-0,487476076
-GRIA1	-0,48726366
-PSMB6	-0,487099126
-CAPRIN2	-0,486969775
-SRGAP3	-0,48684289
-ARPC5L	-0,486786621
-PSME3	-0,486309204
-NME2	-0,486066455
-ISCA1	-0,485683262
-ZNF365	-0,485504618
-PINK1	-0,485341061
-RWDD2A	-0,48504437
-EXOC1	-0,484927354
-ECE2	-0,484617735
-WDR77	-0,484600271
-AI890972	-0,484490353
-ERBB4	-0,484253264
-PSMD4	-0,483962197
-RAB6C	-0,483864006
-CSTF3	-0,483798153
-NIPA2	-0,483638091
-AK5	-0,483482302
-C17orf91	-0,483141592
-INPP4B	-0,482534933
-PJA1	-0,482372063
-BE551361	-0,482367089
-B4GALT5	-0,48224903
-MTX2	-0,481915827
-MGST3	-0,481667788
-TRMT11	-0,481613419
-PTPRN	-0,481522612
-DNAJC12	-0,48150495
-FTSJ2	-0,481162212
-CCT8	-0,48112028
-PGAP1	-0,481030935
-SLC25A44	-0,480898127
-AMIGO2	-0,480319409
-SCAMP1	-0,480275681
-RBKS	-0,480222
-SYN1	-0,48014199
-APEX1	-0,479680328
-AL157484	-0,4790893
-PAK3	-0,479026618
-SLC25A13	-0,478484409
-EIF1B	-0,478403329
-DLAT	-0,478235597
-AI375694	-0,47804406
-PMS2L1	-0,477748782
-DYNC2LI1	-0,477528415
-RANBP9	-0,477445784
-PTPN20A	-0,476653786
-ZMYM4	-0,476508652
-UQCRQ	-0,476353248
-EXOSC7	-0,476299374
-NDUFB3	-0,476207507
-LCMT1	-0,476121484
-ZNF547	-0,47597802
-TBCA	-0,475802982
-MAPK8IP3	-0,475554385
-N80935	-0,475378775
-SLC4A3	-0,475327531
-AASDHPPT	-0,475086681
-CAND2	-0,475049952
-CXorf40B	-0,474988185
-FXYD6	-0,47456179
-RNF10	-0,474499733
-ELOVL4	-0,474412575
-AAK1	-0,474378982
-SEH1L	-0,474159291
-PTPRU	-0,473978747
-LPGAT1	-0,473432618
-VPS24	-0,473360696
-MCF2	-0,473341916
-FAR2	-0,473007144
-CKMT1A	-0,472884518
-TMED3	-0,472883274
-RNASEH1	-0,47283341
-NDUFA3	-0,472657747
-GLS	-0,472644869
-FAM168A	-0,472617309
-KLHDC10	-0,472577269
-GLRX5	-0,472478522
-SYT17	-0,472292582
-PAM	-0,472018566
-CLTB	-0,471770785
-COPS2	-0,470912718
-DDA1	-0,470419616
-PCSK2	-0,470372976
-SLC25A6	-0,470332168
-TPI1	-0,470300584
-MECR	-0,47026417
-ORC4L	-0,47025895
-ITPR1	-0,470228063
-HMG20A	-0,470060529
-GNB5	-0,470039178
-TMEM208	-0,469963608
-NCAPG	-0,469752447
-GLRB	-0,469638821
-ATP6V1D	-0,469577982
-AKAP11	-0,469501191
-SH3GL2	-0,46948768
-NISCH	-0,469445416
-SIPA1L1	-0,469275377
-PFKP	-0,469125064
-LYRM4	-0,469088537
-SLC4A1AP	-0,46898494
-AP2A2	-0,468669242
-CX3CL1	-0,46850557
-WBP11	-0,468444743
-LASP1	-0,468444317
-GOT1	-0,468375399
-C6orf120	-0,468133996
-SPAG7	-0,468070563
-SERGEF	-0,467688975
-TFB2M	-0,4675501
-AP3B2	-0,467537408
-PAFAH1B1	-0,467362101
-BPGM	-0,467130793
-CRAT	-0,466839519
-DDX1	-0,466770911
-ADAM23	-0,46652833
-ASB6	-0,466473575
-PCDHA1	-0,466456945
-TUSC3	-0,465574044
-TCEA2	-0,465512943
-SMARCA4	-0,4653413
-DAPK1	-0,465142929
-DBNDD1	-0,464965333
-NDUFC2	-0,464959656
-IDH3B	-0,464778307
-CDC37L1	-0,464692992
-WDR11	-0,464429092
-CD200	-0,464378251
-TUSC2	-0,464289641
-IRGQ	-0,464009317
-CALY	-0,463919598
-NNT	-0,463872117
-MSH2	-0,463745236
-GYG1	-0,463657489
-FAM134C	-0,463380379
-RTN2	-0,463379977
-RBM12	-0,463289569
-SYNJ1	-0,463207762
-ABCA5	-0,462881594
-ENTPD4	-0,462777994
-MAP2K4	-0,462732144
-AIMP2	-0,46256199
-PITPNA	-0,462484131
-BNIP3	-0,461982272
-COPS5	-0,461956463
-BRE	-0,461910476
-MIR21	-0,461667267
-ATP5S	-0,46152488
-SIN3B	-0,461515059
-NAT10	-0,461457105
-MTCH2	-0,461117099
-ACHE	-0,461032229
-PSD3	-0,46079613
-UCHL3	-0,460466303
-SMPX	-0,459975528
-USP11	-0,459753441
-RNF187	-0,459566796
-AAGAB	-0,458932639
-ENY2	-0,458770966
-NDEL1	-0,458614173
-FAM184A	-0,458384449
-TOX4	-0,458204483
-SLC25A15	-0,458110832
-SACM1L	-0,458050139
-ADARB1	-0,458034616
-SPHK2	-0,457781426
-CES2	-0,457687554
-CYFIP2	-0,457201169
-KPNA2	-0,457034156
-ACTR1A	-0,456856222
-SLC25A22	-0,456321526
-DPYSL3	-0,456025294
-PRKAR1A	-0,455984698
-SIDT1	-0,455560984
-TIPRL	-0,455474112
-EIF5	-0,455347544
-C16orf58	-0,455176502
-RAB7A	-0,454946879
-MFSD6	-0,454914435
-NDUFS2	-0,454605666
-APOOL	-0,454580027
-GNB1	-0,454284789
-SARS	-0,454282127
-PIK3R3	-0,454240907
-SERINC3	-0,454097365
-ST3GAL5	-0,45407104
-DHRS11	-0,453695947
-NEDD8	-0,45367218
-RAB15	-0,453664346
-HSPA13	-0,453577406
-OLA1	-0,453153228
-C3orf18	-0,45312023
-AF131844	-0,453027105
-C12orf52	-0,452914604
-ACBD3	-0,452894377
-PCIF1	-0,452240197
-BMP2K	-0,451224584
-TSPYL5	-0,450674174
-SEC63	-0,450642641
-C7orf44	-0,450408444
-PWP1	-0,450360796
-SLC25A14	-0,45012674
-SYP	-0,449768016
-PRKCB	-0,449564151
-KIF2A	-0,449276369
-PEX26	-0,449100108
-SDHA	-0,448617251
-PITRM1	-0,448602767
-PPA2	-0,448269554
-MAN2A2	-0,448177121
-FAM49A	-0,448170721
-KCTD9	-0,448062861
-REEP2	-0,44801948
-NDUFS3	-0,447803075
-CHGA	-0,447356315
-UBE2E3	-0,447311178
-LOC595101	-0,447006376
-RNF170	-0,446698112
-TMCO1	-0,446651514
-PCCB	-0,446640741
-RAB1A	-0,44645249
-ATP1A1	-0,446309137
-KIAA1045	-0,446174802
-CASD1	-0,445992918
-C3orf37	-0,445975885
-RAD17	-0,445659766
-BBS4	-0,445631347
-TBC1D19	-0,445509157
-TSG101	-0,445289202
-DKK3	-0,445181251
-KCNQ2	-0,444911548
-EIF4E	-0,44477948
-LOC100134209	-0,444742688
-OSTF1	-0,444651424
-PPCS	-0,444330494
-ATP13A2	-0,443924538
-DHRS7B	-0,443866868
-TSN	-0,443785273
-AI201594	-0,443780197
-UBE2J1	-0,443536878
-C12orf51	-0,443320039
-INPP5F	-0,44324612
-KIAA0391	-0,443138749
-NDUFB8	-0,442168118
-COX8A	-0,442151263
-PLCB4	-0,442128902
-UQCRC1	-0,442055114
-RNMT	-0,442010619
-PSMB4	-0,441631296
-ATP9A	-0,441570839
-COMMD8	-0,441419712
-STX7	-0,441415012
-UQCRFS1	-0,441387219
-ARMC8	-0,441335025
-USP33	-0,441131902
-SC4MOL	-0,441051846
-AVL9	-0,440604375
-CORO1C	-0,440555184
-ATP6V0A1	-0,440500219
-AKTIP	-0,440321706
-C11orf49	-0,440065839
-ACCN1	-0,439959618
-DYNC1H1	-0,439954428
-RTN4	-0,439926435
-IFT52	-0,439664934
-ARIH1	-0,439616652
-SLC23A2	-0,439279622
-FDPS	-0,439263979
-ZW10	-0,439088192
-C6orf211	-0,438493952
-CAPZA2	-0,438442617
-TRIM9	-0,43841496
-PANK2	-0,438226487
-SLC25A36	-0,437878589
-TM7SF2	-0,437751686
-GPD1L	-0,437274057
-TM2D3	-0,437156245
-TBC1D22A	-0,436837159
-AFF2	-0,436678505
-PSMA4	-0,43652406
-SCAPER	-0,436328183
-KPNB1	-0,43624217
-C8orf33	-0,436164892
-RRAS2	-0,435924543
-PNMA1	-0,435862986
-DRD2	-0,435854058
-CCDC92	-0,435740221
-CYB5B	-0,435703661
-DNM1L	-0,435497666
-FAM98A	-0,435109538
-CYCS	-0,43500707
-UBE2B	-0,434857087
-DCTPP1	-0,434751269
-ENC1	-0,434576571
-SAP18	-0,434463135
-MED7	-0,43446171
-UBXN6	-0,433506891
-MAEA	-0,433493136
-C20orf27	-0,433220759
-ARFGEF2	-0,4331108
-FKBP9	-0,433030189
-COQ10B	-0,432955202
-SNRNP25	-0,432902395
-PHKB	-0,432809153
-CETN2	-0,432732838
-PIK3R4	-0,432641256
-EFR3A	-0,432263211
-FAM162A	-0,432255742
-LOC732160	-0,432226821
-SRPK2	-0,432044566
-USP9X	-0,431489845
-DENND2A	-0,431031563
-PPP2CA	-0,430950806
-CHST1	-0,430892555
-OSBPL9	-0,430720865
-TPM3	-0,430527364
-UGP2	-0,430314768
-AL049387	-0,430134526
-ARHGDIG	-0,429952838
-GPR161	-0,429932801
-HGSNAT	-0,429440496
-TCEAL4	-0,429402449
-KHDC1	-0,429285977
-SPATA7	-0,428924113
-NIPSNAP3B	-0,428922472
-NHP2L1	-0,42870798
-BZW2	-0,428685674
-BZW1	-0,428658261
-ABCF3	-0,428526247
-PEX19	-0,428349422
-POLR2K	-0,42820853
-FAM134B	-0,428156057
-TUBGCP4	-0,428150919
-CSNK2A1	-0,427824997
-PPP2R5D	-0,427719013
-CEND1	-0,427667723
-RNF11	-0,427514623
-EBNA1BP2	-0,427275229
-SDHC	-0,42690156
-ATP6AP2	-0,426823582
-MAPK1	-0,426681157
-YTHDC2	-0,425950246
-ACTR3B	-0,425721173
-LRRC47	-0,424928312
-ANO10	-0,424906321
-MORF4L2	-0,424702281
-NAE1	-0,424669605
-GRSF1	-0,424576498
-UBE3C	-0,42455123
-RRM1	-0,424268285
-IARS2	-0,424201991
-HINT1	-0,423973896
-B4GALT7	-0,423964657
-OBSL1	-0,423852756
-RPH3A	-0,423713255
-PTPRM	-0,423526608
-TRAP1	-0,423405292
-GSTO1	-0,423136683
-PGK1	-0,423107749
-KCTD2	-0,423033005
-AKAP9	-0,423014145
-KIAA0090	-0,422971022
-NIF3L1	-0,422805913
-SAE1	-0,422487927
-TRAPPC4	-0,422454822
-UBE3B	-0,422322842
-MRPL13	-0,422291395
-ARF1	-0,422218883
-NCKAP1	-0,421739152
-COX11	-0,421717769
-XPA	-0,421552598
-FKBP11	-0,421544606
-ZFAND1	-0,42136139
-RUSC1	-0,421250909
-PSMC2	-0,42099626
-MCM4	-0,420976269
-HEXA	-0,420954607
-PDE4A	-0,420795908
-VPS45	-0,420785909
-OGFOD1	-0,420640442
-ADPGK	-0,420505817
-AP2M1	-0,420467875
-PSMD5	-0,420139323
-PGRMC1	-0,420109613
-CLASP2	-0,419942702
-CAMTA1	-0,419843296
-COX5A	-0,419753275
-BCAP29	-0,419678508
-C21orf59	-0,419586484
-INSIG1	-0,419347593
-NDUFAF1	-0,419256514
-SNCG	-0,419205938
-NCAN	-0,418993508
-SLC24A3	-0,418714364
-MAP2K1	-0,418679322
-BRCC3	-0,418660516
-MYCBP2	-0,418420128
-PREPL	-0,41818051
-TUFM	-0,418149804
-LYRM2	-0,41810337
-ORC3L	-0,417994092
-TSR2	-0,417894679
-SLC41A3	-0,41774061
-DZIP3	-0,417712026
-MRPS11	-0,417644175
-B4GALT6	-0,41761846
-CHD5	-0,417472
-TUBA1C	-0,417351982
-OTUB1	-0,41729395
-DCAF6	-0,417154254
-UQCR10	-0,417021115
-BEX4	-0,416948363
-RTN3	-0,416868526
-GOLT1B	-0,416408995
-MRPL3	-0,416396676
-DDX19A	-0,416375948
-C4orf41	-0,416356919
-SEMA3G	-0,416349944
-TUBA3D	-0,416216957
-B4GALNT1	-0,415958605
-TOR1A	-0,415819164
-SUPT16H	-0,415597727
-ACTR3	-0,415469056
-ABCB9	-0,415410201
-SERF1B	-0,415262572
-PSMC6	-0,415072747
-GALNT2	-0,414525722
-ARF5	-0,414370994
-TCEB1	-0,414262524
-FEN1	-0,414164817
-HS2ST1	-0,413801139
-FBXL15	-0,413238338
-ANAPC10	-0,413161353
-MAPK10	-0,413048251
-FGF12	-0,412576909
-GTF2B	-0,412561968
-CALM3	-0,412474461
-C12orf5	-0,412385409
-BTRC	-0,412323302
-UBXN8	-0,411884422
-G6PC3	-0,411853401
-MARK4	-0,411850043
-SDHB	-0,411814414
-FXC1	-0,411804756
-KIAA1467	-0,411406746
-COL4A3BP	-0,411372338
-MADD	-0,411317373
-SLC25A11	-0,411257994
-APBB3	-0,411242683
-LDHB	-0,411172229
-ENTPD3	-0,410988615
-CAMK2B	-0,410817586
-C15orf24	-0,410807275
-RAB11FIP5	-0,410722406
-C18orf1	-0,410410534
-IL13RA2	-0,410393436
-TMEFF1	-0,40994415
-TAX1BP1	-0,409905258
-ABHD11	-0,409662969
-SETD4	-0,409479623
-NARS	-0,409352949
-LOC441259	-0,409193342
-SMAD2	-0,408937637
-MAGEH1	-0,408820062
-LPIN2	-0,408744346
-WRB	-0,408371938
-HSPB11	-0,408269901
-COMMD9	-0,407620354
-RMND1	-0,407542555
-RBP1	-0,407484296
-TSPAN7	-0,407465467
-YKT6	-0,407243851
-ATP5L	-0,407238078
-STAT1	-0,407123963
-SPTAN1	-0,407085674
-SLBP	-0,407034029
-FAM115A	-0,407018502
-ATP1B1	-0,407007242
-GIN1	-0,406994648
-SLC25A4	-0,406703055
-RPAP3	-0,40653888
-ELAVL4	-0,406510215
-LDHA	-0,406394191
-GABRG2	-0,406143723
-ACOT1	-0,406088493
-LZTFL1	-0,406077259
-LARP4	-0,406073312
-PTPRG	-0,405852123
-DIRAS2	-0,405793372
-SNCB	-0,405789504
-CDS1	-0,405765281
-ARL2BP	-0,405758176
-BCL2L13	-0,405729545
-STAT4	-0,405634359
-C17orf75	-0,405632179
-ELAVL2	-0,405590653
-DNM3	-0,405342092
-SNX16	-0,404866663
-TACO1	-0,40485549
-HPGD	-0,404805074
-CHMP2B	-0,404775945
-DPP8	-0,404495701
-SYBU	-0,403649563
-CHP	-0,403478973
-GTF2H5	-0,403475179
-PPP2R5B	-0,403191055
-TRAK1	-0,402996995
-ACSL4	-0,402921692
-RABGAP1L	-0,402883713
-PSMB3	-0,402864552
-ASTN1	-0,402784524
-TIMM23B	-0,402679864
-NDUFC1	-0,402669713
-GPM6A	-0,402645229
-NCDN	-0,402391637
-TMEM183A	-0,402206694
-LACTB2	-0,402125728
-SFPQ	-0,401934429
-SLC1A4	-0,401903736
-LOC731884	-0,401617561
-TTC3	-0,401599425
-APBA1	-0,401587582
-FAM20B	-0,401527926
-ISOC1	-0,401479145
-TMEM70	-0,401425176
-GLUD1	-0,401204073
-NDUFA4	-0,401152135
-SHANK2	-0,401076931
-NDUFA6	-0,400922451
-FAM128A	-0,400907344
-TSNAX	-0,400758374
-BLCAP	-0,400561763
-WASF3	-0,400514139
-MTMR6	-0,400412018
-CBARA1	-0,399961135
-SMCR7L	-0,399645568
-REXO2	-0,399637796
-ASTN2	-0,399013865
-FBXO31	-0,398919379
-MRPS10	-0,398754479
-GNAL	-0,398117434
-RDH11	-0,398104472
-ANKH	-0,398086916
-EPHA5	-0,397910595
-DPY19L2P2	-0,397861593
-NRXN1	-0,39777997
-FOXA1	-0,397622781
-AGGF1	-0,397583973
-CLCN6	-0,397581706
-PRKAG1	-0,397496639
-GRM5	-0,397456403
-BCAT1	-0,397331444
-MAP1LC3B	-0,397317027
-HMGCL	-0,397130437
-IFIT5	-0,397045055
-FAM82B	-0,397007464
-TMEM189-UBE2V1	-0,39671729
-TMEM160	-0,396535704
-PIGZ	-0,396390486
-VDAC2	-0,3962914
-BCAP31	-0,396227306
-CUL2	-0,395939867
-C5orf30	-0,395902062
-VAMP4	-0,395520757
-CLTA	-0,395495699
-NOS1AP	-0,395452681
-YWHAH	-0,395414553
-AGL	-0,39537715
-PPIA	-0,395286888
-POLR2E	-0,395239973
-FAM190B	-0,395231307
-CAND1	-0,395218949
-DIABLO	-0,395167608
-FAM155A	-0,395099838
-FAM174B	-0,394929763
-ABCA11P	-0,394841999
-LMF1	-0,394801997
-EIF3I	-0,394774336
-RRAGA	-0,39363313
-SLC25A5	-0,39336993
-BTBD3	-0,393323586
-SLC38A6	-0,393193457
-TSPYL4	-0,39289974
-NDUFA8	-0,392898828
-ERI3	-0,392853573
-CDH11	-0,392815946
-VPS11	-0,392712183
-RPP40	-0,39270293
-SMS	-0,392616216
-USP4	-0,39251437
-RAN	-0,392486577
-SYT11	-0,392234251
-SEC23IP	-0,392233152
-SUPV3L1	-0,392124663
-TOX3	-0,392048323
-OSBPL3	-0,391742979
-ATP5J	-0,391738382
-APC	-0,391687772
-EIF2AK2	-0,391678642
-MPPE1	-0,391534871
-CHD3	-0,391021702
-BE858194	-0,390954653
-GPN2	-0,390821549
-TMEM97	-0,39059622
-BRF2	-0,390477924
-NSDHL	-0,390017568
-LOC654342	-0,389476483
-SATB1	-0,389035394
-RPP14	-0,388984247
-C16orf68	-0,388858051
-PHF14	-0,388842446
-CKAP5	-0,388699527
-MMADHC	-0,388406258
-MEST	-0,388313548
-UQCRH	-0,387974488
-GBAP1	-0,387823169
-PMPCA	-0,387778282
-TMEM41B	-0,387668262
-SCLY	-0,387620138
-OXA1L	-0,387520115
-CLPX	-0,387517816
-EML1	-0,387443167
-DPP6	-0,387318033
-FBXO3	-0,387294212
-GAPDH	-0,386769027
-ATP6V1C1	-0,386766958
-PRAF2	-0,386484628
-NAA35	-0,386425969
-EIF4H	-0,386302469
-SGSH	-0,386196526
-CLCN3	-0,386084887
-SMARCA1	-0,385880429
-FAM158A	-0,385760557
-AP3S2	-0,385712457
-EIF1AX	-0,385367803
-RNF115	-0,385287305
-GPI	-0,385266179
-SEC62	-0,385020013
-G3BP2	-0,384968143
-NDUFV1	-0,38487232
-C19orf42	-0,384758261
-BEND5	-0,384699839
-KCNAB2	-0,384620267
-EVL	-0,384619104
-MTMR9	-0,384460721
-SIRT3	-0,384239932
-CNIH	-0,383916854
-TOLLIP	-0,383913386
-C11orf2	-0,383735535
-NUDCD3	-0,383703548
-MED4	-0,383545823
-RABGEF1	-0,38353381
-PTN	-0,383407974
-GBF1	-0,383365739
-C1orf163	-0,383317238
-LOC100129361	-0,383315417
-CUL4B	-0,383032231
-OXR1	-0,382758654
-TRIM33	-0,382726006
-GPC5	-0,382713696
-C11orf51	-0,382673891
-MAN1C1	-0,382595078
-FGF9	-0,382294616
-SPOCK2	-0,382267861
-GLMN	-0,382038722
-MPP1	-0,381567886
-KIF21B	-0,381555674
-RND1	-0,381481938
-PEX1	-0,381462705
-C2orf34	-0,381417191
-OTUD3	-0,381344145
-MSRB2	-0,381206334
-CCDC85B	-0,38118283
-RGS3	-0,380621769
-SERPINI1	-0,380596066
-C14orf2	-0,380470075
-IDH3G	-0,380458518
-POLR2C	-0,380378788
-CTNNA2	-0,380377628
-XRCC6	-0,380295972
-EIF3A	-0,380281294
-CRBN	-0,380214781
-RPS6KC1	-0,3801397
-NUDT2	-0,380057201
-GOLPH3L	-0,379823471
-CSNK1A1	-0,379812095
-NDUFB2	-0,379757693
-FTO	-0,37940886
-SLC6A15	-0,379271656
-PCP4	-0,379256762
-NIT1	-0,37912136
-CCNC	-0,378699092
-DGKB	-0,378485235
-RANBP6	-0,377965444
-DNAJC8	-0,377764456
-MAPRE2	-0,377675379
-ARFGAP2	-0,377574006
-BDNF	-0,377511436
-HSD17B10	-0,376728332
-AKAP7	-0,376531212
-EHD1	-0,376479944
-PSMD10	-0,376243528
-FABP5L2	-0,376090187
-VAMP7	-0,376017526
-WBP4	-0,375749974
-MAP1B	-0,375485017
-SMPDL3A	-0,375390185
-GPR89C	-0,375362209
-SEPT2	-0,37512019
-GPX3	-0,374915078
-AARSD1	-0,374664572
-HSPA9	-0,37466397
-MAP1A	-0,374598439
-C16orf62	-0,374459363
-CARKD	-0,374388504
-ASS1	-0,374197776
-WDR12	-0,374046313
-ABHD14A	-0,37397421
-SPIN2B	-0,373568971
-RAB6A	-0,373528481
-PTPRF	-0,373483075
-RRAGB	-0,373427062
-STK39	-0,373365187
-COX7B	-0,373307822
-PDCL	-0,373110957
-ATP2A2	-0,373066228
-PPM1E	-0,37285382
-TRMT61B	-0,372798595
-C21orf33	-0,372766056
-MGMT	-0,372730061
-LPHN3	-0,372647138
-WBP2	-0,372385809
-ACSBG1	-0,372296169
-PGRMC2	-0,372287654
-LRRC20	-0,372239514
-AGA	-0,372171162
-NRCAM	-0,372117405
-FUT9	-0,372053568
-C22orf28	-0,371916518
-MRPS15	-0,371914782
-UFM1	-0,371876489
-CAMK2G	-0,371790847
-AVPI1	-0,371692415
-MAST2	-0,371637676
-PPP1R7	-0,371553142
-EEF1A2	-0,371514176
-ATP5D	-0,371416456
-EEF1E1	-0,37139203
-NLRP1	-0,371368381
-PMS2CL	-0,371209965
-CDK5R1	-0,371120209
-C2orf72	-0,371108998
-OAZ2	-0,3710748
-AL109698	-0,37073584
-INPP4A	-0,370700597
-ERH	-0,370513944
-CAMK1G	-0,370474818
-MED24	-0,370430566
-DMXL1	-0,370287216
-COMMD4	-0,370258812
-NOMO3	-0,370043447
-MORF4	-0,369691968
-ZNHIT3	-0,369651044
-GDPD5	-0,369635923
-CUL5	-0,369519961
-AP1B1	-0,369511443
-YARS	-0,369387873
-ABHD10	-0,36913324
-KCNB1	-0,369083149
-SKP1	-0,369015624
-FBXO28	-0,368924883
-ATR	-0,368436696
-TMED2	-0,368132686
-ARPC1A	-0,367983188
-PHYH	-0,367958422
-MRPL22	-0,367879083
-SRRD	-0,367868238
-WDYHV1	-0,367821841
-EIF3CL	-0,367732775
-HMGB3	-0,367450086
-DENND1B	-0,36732795
-ALDH5A1	-0,367318431
-CCNA1	-0,367103911
-FAM134A	-0,367014983
-DZIP1	-0,366778091
-WASF1	-0,366602553
-ATXN3	-0,366426778
-CCDC25	-0,3658102
-ERP29	-0,365799413
-IVD	-0,365499555
-SNX24	-0,365222253
-CDK20	-0,365176415
-TTC9	-0,365148586
-RBM8A	-0,36488846
-AMACR	-0,364562114
-TBPL1	-0,364450426
-PTPMT1	-0,364434415
-CANX	-0,364232908
-ELAC2	-0,364131757
-EIF2S1	-0,364109368
-AKR1B1	-0,363915593
-ACADM	-0,363858719
-RGS16	-0,363795844
-SLC20A1	-0,363602798
-MTUS2	-0,363384151
-ZMIZ2	-0,363364816
-NDUFS4	-0,363146027
-AW242701	-0,363104323
-SNAPC3	-0,363053639
-ENOPH1	-0,362868334
-LYRM1	-0,362706602
-TRMT12	-0,362561085
-BAALC	-0,362539013
-CHMP1B	-0,362404908
-ATP1A3	-0,362300724
-TOMM20	-0,362192747
-PEX14	-0,362047536
-EIF2AK1	-0,361934247
-CNNM2	-0,361790716
-PPOX	-0,361753445
-TAC1	-0,361655557
-GLRX3	-0,361266708
-OBFC1	-0,360197329
-MFN2	-0,360036589
-DGCR14	-0,359808857
-FAM175B	-0,359691136
-PARP2	-0,359639462
-GPR107	-0,359495249
-TUBGCP5	-0,35920098
-ENSA	-0,359186957
-UMPS	-0,358973056
-SSBP1	-0,358916914
-PFDN2	-0,358707301
-IFFO1	-0,35859667
-CCT2	-0,358497035
-PSMA5	-0,358414139
-ZC3H15	-0,358397302
-EPHX2	-0,358269729
-CALB1	-0,358259257
-POP7	-0,358253841
-MRPL12	-0,357874032
-DFNA5	-0,357815106
-PIAS1	-0,357740062
-ARL4C	-0,35770713
-HRAS	-0,357592893
-CEP68	-0,35754909
-SNRPA1	-0,357535253
-SCP2	-0,357518758
-C4orf27	-0,356816465
-TMEM185B	-0,35662055
-SPAG16	-0,356585241
-ESYT1	-0,356493695
-PTP4A1	-0,356347412
-PDLIM2	-0,356333479
-MSRA	-0,355999453
-UAP1	-0,355870622
-CDK16	-0,355785531
-MBOAT7	-0,355761708
-FARSA	-0,355610517
-MRPS7	-0,355424517
-EPHB2	-0,355389176
-LOC729991-MEF2B	-0,355378273
-PDHA1	-0,355252318
-ACTL6B	-0,355166654
-SAR1A	-0,355144478
-KDM1A	-0,355067715
-PRDX3	-0,354963773
-ETF1	-0,354759299
-ARMCX2	-0,354758912
-IQSEC1	-0,35395949
-TIMM13	-0,353925241
-AP2B1	-0,353904118
-STYK1	-0,353863363
-CDK7	-0,353806664
-DLG3	-0,353783905
-SEPHS2	-0,353722454
-MTOR	-0,353463273
-PPIH	-0,353351383
-GRPEL1	-0,353254529
-C9orf91	-0,353075824
-RGS17	-0,353023569
-NTSR1	-0,352789658
-HNRNPH2	-0,352751195
-HCCS	-0,3526918
-C2orf3	-0,352661516
-TFDP2	-0,352647453
-GOSR2	-0,352396188
-PSMB1	-0,352279045
-MPI	-0,35224609
-DUSP26	-0,351953212
-HERC1	-0,351631367
-SORD	-0,351295095
-TUBB2B	-0,351140866
-LPCAT4	-0,351128323
-CFL1	-0,351124653
-ARPP19	-0,350935095
-MTMR4	-0,350923479
-COX7A2	-0,350878835
-PGM1	-0,350865278
-RHOQ	-0,350802567
-CCDC53	-0,350756677
-UQCRB	-0,350742301
-NAPA	-0,350657124
-CSDC2	-0,35061274
-BECN1	-0,350596093
-GYG2	-0,350535323
-GPKOW	-0,35045328
-FXYD7	-0,350387292
-CYLD	-0,349973469
-CSPG5	-0,349825086
-TTC15	-0,349816074
-ILF2	-0,349761198
-STOML2	-0,349586681
-CACNB2	-0,349516102
-VARS	-0,349372141
-ZSCAN18	-0,349241937
-PTRH2	-0,349224021
-P2RX5	-0,349175679
-RALB	-0,349042784
-NUBPL	-0,348899542
-NCBP2	-0,348786336
-DKFZp434H1419	-0,348772873
-UFSP2	-0,348370783
-ARHGEF17	-0,348050229
-FXR2	-0,34801331
-INSIG2	-0,347755165
-XRCC5	-0,347746659
-CLTCL1	-0,34759935
-TMEM177	-0,347585446
-VAMP2	-0,347189398
-EML2	-0,347084746
-SNUPN	-0,346850632
-GPX4	-0,346688538
-RASA1	-0,346685342
-USP46	-0,346590476
-LSM5	-0,346546029
-SEC31A	-0,34652486
-PALM2-AKAP2	-0,346447335
-CKAP2	-0,346385113
-ELOVL5	-0,346375127
-PMS2L3	-0,346133275
-PAQR3	-0,346117871
-ST8SIA3	-0,34604187
-FDX1	-0,34603415
-C12orf4	-0,345989709
-COQ7	-0,345988262
-UROD	-0,345987158
-RPE65	-0,345902642
-DCK	-0,345889475
-RARS	-0,345819092
-CAPZA1	-0,345775372
-NRN1	-0,345693574
-RNF7	-0,345545425
-ABAT	-0,345474072
-CRY2	-0,345467057
-HR	-0,345290796
-CACNA2D3	-0,345213407
-TWIST1	-0,345148814
-P4HTM	-0,345112277
-GDI1	-0,344731063
-GRIA3	-0,344721718
-D4S234E	-0,344715573
-TMEM151B	-0,344385728
-MPHOSPH6	-0,344298044
-PYGB	-0,344201683
-MARCH6	-0,344086188
-AL050136	-0,343680587
-NDUFS6	-0,343667551
-TRAPPC9	-0,343555476
-PYGL	-0,343533875
-EFNB3	-0,343417492
-SCD	-0,343398039
-TFG	-0,342863204
-PPFIA3	-0,342761025
-SENP6	-0,342750174
-KCMF1	-0,342689973
-GNAS	-0,342684217
-MAPK6	-0,342588157
-PRMT5	-0,34246621
-SEPT11	-0,342460355
-MEIS3P1	-0,342265108
-FABP3	-0,3421554
-YIPF6	-0,3420929
-FABP6	-0,342074193
-SRSF9	-0,341825092
-AP1AR	-0,341737984
-PKNOX2	-0,341609179
-PAK6	-0,341535575
-PRKAA1	-0,341378959
-UBA3	-0,34130955
-OAZ1	-0,341251276
-EID1	-0,340941987
-MRPS28	-0,340842312
-AA890010	-0,340724739
-OSBP	-0,340497775
-ATP6V0C	-0,34047911
-ARHGAP24	-0,340414643
-PNKP	-0,340118439
-PSMD7	-0,340085658
-IPO9	-0,340071575
-ARF4	-0,339993296
-TERF2	-0,339818219
-SRSF2	-0,339525933
-PSMC5	-0,33950993
-TM9SF1	-0,339389717
-ACAT2	-0,339093022
-CDK8	-0,33909169
-KIAA0196	-0,338987444
-TFPT	-0,338941882
-TRPC4AP	-0,338718194
-TUBG1	-0,338211067
-SCN2B	-0,338080627
-MTHFD1	-0,338071854
-ATPAF2	-0,338050158
-IGSF1	-0,337997383
-RGPD6	-0,337877048
-C16orf45	-0,33773508
-C10orf76	-0,337659307
-UBE2A	-0,33762595
-PQLC1	-0,337612976
-SOD1	-0,337454918
-ARPC2	-0,337418781
-MEMO1	-0,33728488
-CSDE1	-0,337036578
-PHYHIP	-0,336992273
-LYPLA1	-0,33698776
-NDUFA1	-0,336883322
-MARCKSL1	-0,336747008
-DCTN1	-0,336745427
-COX6A1	-0,336728807
-DPM1	-0,336614034
-ELP3	-0,336602956
-LOC653566	-0,336555692
-COX7BP1	-0,336528019
-CAPZB	-0,336348777
-DCUN1D4	-0,335942405
-UCHL5	-0,335933871
-PSIP1	-0,335684272
-MRS2	-0,335589123
-RABGAP1	-0,335570544
-KCNA6	-0,335454989
-RAC1	-0,335429141
-ZMYM2	-0,33542626
-MRPL17	-0,335371398
-MLF1	-0,335274724
-RFC3	-0,33507418
-ARMCX3	-0,335005795
-GMDS	-0,334931775
-KIAA0317	-0,334922749
-CAMSAP1	-0,334678333
-LSG1	-0,334628714
-PNPO	-0,334625052
-THOC5	-0,334532053
-C11orf58	-0,334154436
-MTCH1	-0,334038037
-KAL1	-0,333848755
-OMG	-0,333590731
-KLHL7	-0,333537148
-TTPAL	-0,333489991
-GLA	-0,333336937
-SEZ6L2	-0,333262252
-SNURF	-0,333035272
-ARL6IP1	-0,332988884
-BFSP1	-0,332976059
-MAPKSP1	-0,332894473
-HABP4	-0,332672498
-SLC8A2	-0,332645114
-CKAP4	-0,332543738
-NPM1	-0,332250102
-CLSTN3	-0,332157745
-RUSC2	-0,33210981
-RCHY1	-0,331805148
-CACNA1D	-0,331681156
-ZFAND5	-0,331302172
-TACC2	-0,331046487
-CHCHD3	-0,331008486
-RGS2	-0,330792786
-LDOC1	-0,330775706
-BTN2A1	-0,33075204
-WDR45	-0,330593865
-W87688	-0,330499179
-YWHAQ	-0,330473094
-RAB3GAP2	-0,33029144
-HTRA2	-0,330240669
-SNRPD1	-0,330240562
-ANXA7	-0,330030639
-KIAA1024	-0,329770804
-RAD51C	-0,329735785
-PRPF18	-0,329474331
-CCT6B	-0,329361737
-ABCD3	-0,329205796
-PARN	-0,329139621
-APOL2	-0,328983174
-MRPS18A	-0,32863432
-RASL10A	-0,328581006
-COG8	-0,328398026
-ZNF512B	-0,327877848
-ATP5H	-0,327758416
-PRDM4	-0,327710757
-TSPAN3	-0,327644045
-EPB41L3	-0,327416874
-APLNR	-0,327394979
-TFR2	-0,327337619
-GADD45A	-0,327012981
-POLR3F	-0,326871651
-FASTKD3	-0,326789822
-TCERG1	-0,326746174
-VPS41	-0,326459968
-C17orf101	-0,325979143
-EXOC3	-0,325763291
-SLC25A17	-0,325666279
-GDAP1L1	-0,325526797
-HCFC1R1	-0,325022815
-SF3B5	-0,324878766
-TEX10	-0,324812522
-PSMA7	-0,324673715
-TCTN3	-0,324389244
-NOVA1	-0,32437578
-RABEPK	-0,324366299
-ALG5	-0,324335095
-ENOSF1	-0,32427768
-SH3BGRL3	-0,32409913
-CTNND2	-0,324002004
-NKRF	-0,323983769
-SLC6A1	-0,323833407
-MAPK1IP1L	-0,323722226
-RAB22A	-0,323713658
-GRP	-0,323354345
-SDS	-0,323335387
-IBTK	-0,323304602
-CARS	-0,322679359
-WWP1	-0,322463311
-ARL8B	-0,322442301
-SLC19A2	-0,322361872
-F8A3	-0,322202521
-LPHN1	-0,322183082
-SMARCD3	-0,322148361
-GPN1	-0,322024809
-FAF2	-0,322014431
-SLC35B1	-0,321878066
-MPV17	-0,321698226
-TOM1	-0,321634922
-NEDD4L	-0,321518057
-MRFAP1L1	-0,321393672
-C6orf62	-0,321303598
-POLR3B	-0,321247444
-HTR2A	-0,321189596
-CUL3	-0,321141566
-PSMD9	-0,321108014
-LRP3	-0,32099653
-TMEM62	-0,320873847
-PLS3	-0,320803014
-SUMO1	-0,32076762
-DLG4	-0,320617015
-ANKRD17	-0,320557554
-ARFIP2	-0,320500236
-HMGN4	-0,320196335
-PRKAG2	-0,319945607
-STAR	-0,319749743
-NF1	-0,319726773
-ATOX1	-0,31967306
-UBE2M	-0,319629201
-NDRG3	-0,319446308
-SNPH	-0,319396594
-TPD52	-0,319178712
-PLK2	-0,319120325
-C1QBP	-0,318975829
-SRSF8	-0,318843616
-USP22	-0,318806098
-GPD1	-0,318728943
-MAPK8IP2	-0,318691894
-USP20	-0,318610382
-RPA2	-0,31845096
-CCPG1	-0,318358561
-NQO2	-0,318256129
-POLR3C	-0,318231923
-HBXIP	-0,318079181
-MRPS31	-0,318018334
-SNRPB2	-0,31801084
-CACNG3	-0,317104885
-CCNE1	-0,316783937
-NDUFAF4	-0,316755785
-GRK6	-0,316405946
-ZER1	-0,316363024
-CHCHD7	-0,316179658
-C20orf29	-0,315860291
-AI693193	-0,315746456
-TPMT	-0,315745725
-TPPP3	-0,315557058
-CTH	-0,315210231
-HSDL2	-0,31516145
-MAPRE3	-0,314964867
-NLE1	-0,314918022
-ARHGEF4	-0,314777145
-STK19	-0,314737564
-AW503390	-0,314280211
-KIAA1279	-0,314104435
-CA14	-0,313849822
-CYP2E1	-0,313441486
-FHL1	-0,313417456
-MYL6B	-0,313075964
-PACRG	-0,3129322
-SCN2A	-0,312912414
-POLR3G	-0,312898745
-MED6	-0,312862133
-PCSK1N	-0,312861133
-FLJ10038	-0,312756044
-PHTF1	-0,312716368
-PRPF4	-0,312654478
-RPRD1A	-0,312642779
-HLF	-0,312545473
-MTMR1	-0,312535102
-MFN1	-0,312461722
-C1orf50	-0,312398425
-QPRT	-0,312349796
-ZDHHC6	-0,31229266
-ITGAE	-0,311863717
-SLC18A1	-0,311739998
-CD83	-0,311711539
-GGCT	-0,311631664
-KIAA0100	-0,311503156
-OPN3	-0,311374884
-SSX2IP	-0,311111099
-NUCB2	-0,31105706
-UTP11L	-0,311015852
-GOLGA8B	-0,310924837
-UST	-0,310734373
-PRKCI	-0,310493775
-AP2S1	-0,310480065
-WBSCR22	-0,310476192
-PPP3CA	-0,310434457
-PDSS2	-0,310396648
-PEG3	-0,310335546
-ATP5E	-0,310319916
-GABRA5	-0,310200087
-AGPAT4	-0,310173061
-PDCD10	-0,310157516
-DDOST	-0,310094837
-RPL23	-0,309992315
-HOMER1	-0,309485866
-C1orf123	-0,309187816
-POLE3	-0,309012195
-DDX41	-0,308923345
-HSD17B8	-0,308824584
-GMPR2	-0,308792858
-SCARB2	-0,308695909
-DGUOK	-0,308606021
-MAGEF1	-0,308535371
-FOXA2	-0,308348483
-GLS2	-0,308287643
-TBCC	-0,308286536
-FBXO41	-0,308255485
-SLC12A1	-0,308214984
-PELO	-0,308137793
-KCNE1L	-0,30811412
-RBBP4	-0,308007454
-UBL5	-0,307720013
-KLHL12	-0,307571676
-FTSJ1	-0,307464516
-ZFYVE16	-0,307366442
-PPT1	-0,3073579
-ZC3H13	-0,307293327
-DYRK1A	-0,307183877
-PHACTR2	-0,306935621
-SLITRK3	-0,306872073
-PI4KA	-0,306770561
-RNPS1	-0,306364972
-RALGAPB	-0,306086767
-BRP44	-0,305953308
-BNIP1	-0,305883874
-SUPT4H1	-0,305675152
-BCKDK	-0,30566687
-PLAA	-0,305619464
-ACTR2	-0,305363631
-PION	-0,305054773
-NFU1	-0,305010295
-CCT6A	-0,304801168
-KIAA0427	-0,304585348
-EHD3	-0,304533089
-FAM63B	-0,304437794
-STK25	-0,304425083
-POLB	-0,304419007
-MRPL35	-0,304416576
-UBE2Z	-0,3043165
-GSTZ1	-0,304133065
-AP3S1	-0,30395899
-SPATS2L	-0,303776395
-LOC729580	-0,303766036
-RALGAPA1	-0,303697943
-PUF60	-0,303647762
-DAP3	-0,303640732
-AHI1	-0,303570806
-UBE2NL	-0,303361552
-TMEM164	-0,303165514
-DOCK3	-0,303099341
-CADM3	-0,303050893
-ZNF219	-0,302968533
-PRKAR1B	-0,302898104
-DOK5	-0,302798088
-ORMDL2	-0,302372011
-ACVR2A	-0,302331205
-ALDOA	-0,30171568
-ATRN	-0,301666345
-COX7C	-0,301597748
-PRKDC	-0,301229867
-GNG10	-0,300757182
-SNX17	-0,300752701
-RBMS1	-0,300466996
-AJAP1	-0,300458474
-PREP	-0,300414848
-ALDOC	-0,300361514
-LAMA4	-0,300246196
-PI4KAP1	-0,300223018
-TMEM222	-0,30010369
-PIGB	-0,299980372
-SSSCA1	-0,29997354
-DCUN1D1	-0,299517655
-DLSTP1	-0,299414392
-ITM2B	-0,299325985
-AK025651	-0,299260618
-ACOT13	-0,299073057
-ZNF593	-0,298588283
-LOC100129250	-0,298385026
-H2AFY	-0,298292243
-IGF1	-0,298232454
-KIAA0368	-0,29819687
-FKBP3	-0,298122528
-C12orf49	-0,297820161
-PRKRIR	-0,297808472
-GLUD2	-0,297805688
-NBL1	-0,297799978
-PTPN4	-0,297657679
-LOC644617	-0,297586698
-IL33	-0,297538719
-CUL4A	-0,29730361
-SIP1	-0,297199387
-POLDIP2	-0,297140479
-EBP	-0,297109427
-FASTKD2	-0,296665172
-SMPD1	-0,296658212
-FAM55C	-0,296650198
-TRPV2	-0,296465177
-DOPEY1	-0,29633822
-SCYL3	-0,296201386
-UBL3	-0,296188632
-STK38L	-0,296164266
-APITD1	-0,296017845
-SFXN1	-0,295918484
-CPT1A	-0,295754312
-USP8	-0,29570338
-MRPS30	-0,295702739
-ATG7	-0,295335659
-C10orf88	-0,29514056
-PIPOX	-0,295018193
-RAC3	-0,294600261
-CIAO1	-0,294564961
-KLC2	-0,294523931
-LEPROTL1	-0,29448316
-ENDOD1	-0,294147277
-FEM1B	-0,294007766
-IRS1	-0,293342341
-CYP51A1	-0,293155923
-DYNLRB1	-0,292974645
-TOM1L2	-0,292906836
-TDP2	-0,292808809
-MRPL49	-0,292778686
-LRP8	-0,292767989
-MOSPD1	-0,292730297
-C6orf134	-0,29255632
-TRPC1	-0,29249815
-RASL11B	-0,292459191
-AL109671	-0,292334441
-TTC37	-0,292136499
-ODZ4	-0,292070818
-KIN	-0,291741417
-KPNA1	-0,291721639
-CAST	-0,291558763
-NDUFA13	-0,291524477
-AKR1A1	-0,29149158
-QARS	-0,29146477
-MRPS22	-0,29145846
-MMACHC	-0,291414294
-UBQLN2	-0,291358191
-PIK3CB	-0,291242041
-COX6B1	-0,291081182
-PDK2	-0,290962723
-RABGGTB	-0,290962562
-SR140	-0,290943983
-ATF2	-0,290881352
-FADS1	-0,290820194
-SRP14	-0,290691218
-RAD23B	-0,290632171
-AHCY	-0,290521401
-RINT1	-0,290502144
-SRP54	-0,290224786
-COX5B	-0,289972152
-NBN	-0,289962803
-DDX50	-0,289845246
-NUFIP1	-0,289611609
-HDGFRP3	-0,289540354
-HBA2	-0,289412602
-SRP9L1	-0,289377441
-ARFGEF1	-0,289327503
-FAM13B	-0,289118442
-DIMT1L	-0,288943725
-LPO	-0,28888192
-VPS28	-0,288730564
-SSR3	-0,28867602
-SEPT7	-0,288663677
-NARS2	-0,288651232
-EMG1	-0,288493971
-HSPA8	-0,288488899
-TBC1D13	-0,288209587
-TTC35	-0,288076299
-GTPBP4	-0,287916733
-SPG7	-0,287774853
-PAFAH1B3	-0,28772138
-MAPT	-0,28765216
-RERGL	-0,287509361
-HNRNPD	-0,287438947
-PLCL2	-0,287391702
-HLA-DPA1	-0,287200849
-CD55	-0,286966384
-IDH3A	-0,286870398
-STXBP5L	-0,286801199
-MAP3K12	-0,286334641
-PPP2R1A	-0,286259611
-TMEM126B	-0,286136364
-CDKN3	-0,286064506
-ABCC5	-0,286013319
-TMEM127	-0,285913561
-DNAJC2	-0,285585137
-SEC61G	-0,285583827
-SSR1	-0,285489405
-AIMP1	-0,285281231
-YTHDF2	-0,285194578
-FAM86B1	-0,285046154
-CTBP1	-0,285027477
-CHRFAM7A	-0,285001423
-SSBP3	-0,284934817
-MRPL46	-0,284930449
-TSPAN6	-0,284861931
-MYST2	-0,284824247
-GGH	-0,284817124
-PRKACB	-0,2847024
-C2orf47	-0,284692381
-NLK	-0,284579832
-ASNS	-0,28445955
-EXOC5	-0,28439526
-OAZ3	-0,284379411
-CTNNBIP1	-0,284364924
-PVR	-0,284070802
-C16orf80	-0,284019987
-UBE3A	-0,283816198
-EAPP	-0,28376748
-IGSF3	-0,283764031
-KCND2	-0,283569047
-FOXK2	-0,283286684
-SLC35A2	-0,283204451
-TBCB	-0,283168385
-SLC38A1	-0,283158141
-ACCN2	-0,283147998
-FAM149A	-0,283126904
-TIMM22	-0,283102824
-EIF4ENIF1	-0,28310048
-THSD1P1	-0,282819454
-MAGED4	-0,282562753
-CLASP1	-0,282510547
-C1orf61	-0,282424601
-C6orf106	-0,282397365
-WDR44	-0,282155933
-GNL3	-0,282115302
-RCBTB1	-0,28192202
-OSTM1	-0,281535242
-AGPAT5	-0,281510168
-PRNP	-0,281405094
-APPBP2	-0,281330465
-GAD1	-0,281295305
-NECAB3	-0,281056363
-ABCF1	-0,280961256
-DNAJC7	-0,280750506
-EPHB1	-0,280596899
-GPRC5A	-0,280368026
-HSPA14	-0,280049432
-CLPTM1	-0,280042656
-SGPP1	-0,27999737
-ABCG4	-0,279891909
-GFRA1	-0,279146972
-ATP5SL	-0,278849245
-CTSO	-0,278677227
-DCTN4	-0,278556645
-MAP2K2	-0,278535478
-ZNF423	-0,278503712
-FUS	-0,278285124
-ACTR8	-0,278282163
-PRR13	-0,278189761
-ZNF329	-0,278179162
-RNASEH2B	-0,278151755
-LOC284244	-0,278099761
-FAM117A	-0,277715513
-MREG	-0,277651168
-C2orf18	-0,277609469
-AW612311	-0,277599115
-SYNRG	-0,277434047
-SMARCE1	-0,277346186
-DNAJA3	-0,277188103
-PPP2R5E	-0,2770317
-TMCO6	-0,276951805
-C6orf35	-0,276886272
-DDX18	-0,276619655
-TTLL1	-0,276373935
-LANCL1	-0,276361838
-SNRPE	-0,276287655
-DTX4	-0,276233703
-IDH2	-0,276017451
-SACS	-0,275814599
-ABHD2	-0,275491786
-VAMP1	-0,275092752
-AGPAT1	-0,27504004
-TYMS	-0,274913065
-ZDHHC3	-0,27479568
-LMO1	-0,274566957
-UVRAG	-0,274559415
-HBB	-0,274385467
-PSMA2	-0,274273938
-CD24	-0,27422103
-GRAMD1B	-0,27394685
-PRC1	-0,27393137
-YARS2	-0,27376193
-SIGMAR1	-0,273597834
-CPEB3	-0,273534888
-ARMC9	-0,273442678
-DNAJC10	-0,273369377
-TM9SF4	-0,27326642
-RBX1	-0,273166064
-C13orf1	-0,273151402
-PDCD4	-0,273130523
-LUZP2	-0,272843047
-APLP2	-0,272609838
-USO1	-0,272598741
-SH3BP5	-0,272512602
-PPP1R11	-0,272494252
-PEMT	-0,272485616
-CDC16	-0,272287144
-LCMT2	-0,272235596
-DCX	-0,271983078
-DDAH1	-0,271924121
-UBE2D2	-0,271815552
-TANK	-0,271664689
-AW974666	-0,271662837
-USH1C	-0,271630244
-BDH1	-0,271624449
-B9D1	-0,271589518
-BRD9	-0,271105209
-USP7	-0,271052865
-TRIM2	-0,270764995
-PARK7	-0,270634786
-NSFL1C	-0,270597248
-COQ2	-0,269953826
-HNRPDL	-0,269787459
-NOV	-0,269731303
-SLC25A28	-0,269706278
-EXT2	-0,26958066
-VLDLR	-0,269148459
-SLC4A4	-0,268895862
-SMURF1	-0,268798637
-ORC2L	-0,268275919
-ZC4H2	-0,268056536
-SDHAF1	-0,267985583
-VDAC1	-0,267895013
-ALDH1A3	-0,267738476
-PNPLA4	-0,267586498
-HAGH	-0,267406111
-CNTNAP2	-0,267355858
-KPNA3	-0,267278305
-LRBA	-0,267216793
-DPYSL4	-0,267150239
-MCCC2	-0,26714725
-KBTBD4	-0,267031071
-DCTD	-0,267005887
-C1orf21	-0,266982234
-C2orf43	-0,26679916
-SF3A3	-0,266732334
-PTPN3	-0,266674559
-FBXO21	-0,26664933
-CCT7	-0,266615147
-CLNS1A	-0,266539743
-HAPLN1	-0,266160364
-SYT13	-0,26591944
-SENP5	-0,265695364
-HMGB2	-0,265556554
-CANT1	-0,265168032
-CGREF1	-0,265157579
-GRM1	-0,26510368
-ZFHX4	-0,265049797
-PVRL3	-0,264999073
-ADAR	-0,264636454
-TRIM3	-0,264561355
-ANP32E	-0,264413865
-PDLIM7	-0,264406742
-MLH1	-0,264377914
-PRKCA	-0,264376056
-CYB5R3	-0,264120933
-PDE1A	-0,263919942
-LOC100127998	-0,263915362
-WSB2	-0,263691169
-RPF1	-0,263404659
-CXCL12	-0,26333499
-TMEM66	-0,263285506
-EIF6	-0,263232223
-NFE2L1	-0,262789646
-KLHL20	-0,262772392
-PPM1H	-0,262689193
-PIN4	-0,262483899
-TUBA4B	-0,26241982
-ECT2	-0,262276809
-MGC5566	-0,261888759
-C9orf116	-0,261830489
-ASB1	-0,261751394
-ABCC8	-0,261735107
-ELOVL2	-0,261638578
-PHB2	-0,261466477
-ZNF580	-0,261379751
-DNAJC24	-0,261364702
-PSMB10	-0,261344946
-CSE1L	-0,261292597
-ANKRD27	-0,261154598
-TUBG2	-0,261047779
-C6orf162	-0,261001828
-AL034399	-0,260886813
-GLT8D1	-0,26052144
-SRR	-0,260520305
-MCC	-0,260395686
-COX4I1	-0,260324715
-SEP15	-0,260222524
-RNF103	-0,260210477
-ZNF576	-0,260159221
-MGEA5	-0,260092677
-RSL24D1	-0,259958151
-USP13	-0,25969613
-MLLT3	-0,259631882
-SRI	-0,259268888
-NCS1	-0,259133737
-MAPKAPK5	-0,259103348
-IQCG	-0,25908825
-FN3KRP	-0,258914892
-BCKDHB	-0,258870249
-GOLGA5	-0,258736414
-RDBP	-0,258483881
-SUPT7L	-0,258355414
-METTL1	-0,258206012
-CREB3	-0,258159408
-TMEM111	-0,258136123
-NRSN2	-0,257397396
-CNTN1	-0,257314074
-COX10	-0,257277055
-SERPINB9	-0,257269621
-MTF2	-0,256976969
-EDNRB	-0,25676028
-HSF2	-0,25652969
-POLR2L	-0,256424652
-TRIM58	-0,256294322
-DACH1	-0,256241463
-UEVLD	-0,256239024
-ATP1B3	-0,256215499
-SAP130	-0,256053262
-TRPC6	-0,255890704
-HERC6	-0,255794959
-NAV3	-0,255707496
-GOSR1	-0,25567987
-CNR1	-0,255506006
-PSME4	-0,25522233
-CAMKV	-0,254605479
-ADSL	-0,254512794
-BCS1L	-0,254298738
-CCNB1	-0,253924801
-SNX2	-0,253887319
-ASAP2	-0,25387509
-WDR70	-0,253565737
-PTPRE	-0,253309549
-SEPT5	-0,253058348
-SCML1	-0,253051964
-BCR	-0,252946659
-MAGOH	-0,252829021
-SEMA4F	-0,25277628
-CLIP1	-0,252764211
-JMJD4	-0,252747043
-ZMYND11	-0,25273006
-CPSF6	-0,252574141
-PTPRA	-0,252430519
-PLA2G12A	-0,252393049
-MXRA5	-0,252290125
-RFX5	-0,252264534
-WARS	-0,252174212
-HUS1	-0,252166663
-VCAM1	-0,251733145
-CEACAM21	-0,25171453
-RHOT1	-0,251514974
-EMD	-0,251327933
-TSPYL2	-0,251307071
-THNSL1	-0,25130438
-NDUFB4	-0,251250318
-CHMP5	-0,251232028
-SKAP2	-0,251185084
-LRPAP1	-0,251070101
-COMMD3	-0,251069448
-ROGDI	-0,250917557
-PPAP2B	-0,25089017
-ADSS	-0,250852878
-LGI2	-0,250809779
-CBX6	-0,250671998
-NELF	-0,250584567
-DENND5B	-0,250357567
-ATP2C1	-0,239139672
-SUMO2	-0,233193565
-KRAS	-0,208565613
-PEX3	-0,200767265
-PRDX2	-0,195371323
-PDCD2	-0,194653063
-TM2D1	-0,189207426
-KHDRBS1	-0,16653347
-KLC1	-0,156510024
-ANK2	-0,155852142
-HBS1L	-0,155006259
-NTRK3	-0,121314135
-PTPRO	-0,110200451
-PLEKHA5	-0,10184855
-GCOM1	-0,091608137
-TIMM8A	-0,084179504
-MKRN1	-0,074942655
-PLA2G4B	-0,068760926
-RUFY3	-0,059042335
-RIMS2	-0,057507607
-C21orf2	-0,054091983
-METAP2	-0,053236401
-LRRC40	-0,040678287
-RPL10	-0,034862755
-RIOK3	-0,033313025
-SYNCRIP	-0,027340658
-UNC45A	-0,021866459
-MPZL1	-0,020796077
-RANBP1	-0,01610173
-ITGB1BP1	-0,011025016
-UBC	-0,009666523
-RER1	-0,007044099
-PDS5B	-0,005231512
-NCAM1	-0,004638056
-LIMCH1	0,003894784
-VPS13D	0,014841215
-WDFY3	0,017457694
-MRP63	0,023151675
-TSR1	0,064261585
-GRB10	0,066410415
-FAM128B	0,074972161
-PAK2	0,079518764
-PKP4	0,080237181
-TMEM144	0,083124821
-C3orf63	0,086752023
-DDAH2	0,250378216
-AF238870	0,250544885
-PTMS	0,250667518
-JAG1	0,250675664
-RPL32	0,25075902
-UXT	0,250812127
-HSP90B1	0,250888984
-SS18	0,250904748
-RND2	0,250918958
-CLEC4M	0,250931594
-AU147194	0,251115897
-IL1RAPL1	0,251119435
-EPB41L2	0,251131328
-TFDP3	0,251241244
-GAL3ST4	0,251281983
-EDN2	0,251371356
-SFTPC	0,251372616
-TRMT61A	0,251534845
-GPR4	0,251535902
-KEAP1	0,251692277
-RNF122	0,251718243
-NOTCH2	0,251745042
-WDR1	0,251871256
-NFX1	0,252023298
-DOHH	0,252100123
-NES	0,252167647
-SRSF10	0,252172984
-AQP3	0,252182392
-LOC728412	0,252404082
-RCN3	0,252455902
-CSNK1G1	0,252462493
-KCNS1	0,252601737
-CCDC71	0,252614101
-JUND	0,252645305
-LYST	0,252718314
-TPCN1	0,252770336
-MTA1	0,252823052
-RIN1	0,252841454
-ATHL1	0,252944239
-FTSJ3	0,253136044
-SERPINA1	0,253202139
-STARD7	0,2533744
-MRPL34	0,253425868
-PPID	0,25344089
-SH3PXD2A	0,253534644
-UBA7	0,253547625
-RUNX1	0,253686159
-ARNTL	0,253823553
-STAT6	0,253840779
-CASKIN2	0,25393147
-NFATC4	0,253965486
-LILRB2	0,254041373
-PPP1R13L	0,254173566
-RAP1A	0,254249533
-OTUD4	0,254380531
-ZNF516	0,254390037
-ZC3H14	0,254430628
-BTD	0,254441889
-ABHD4	0,254494909
-MT3	0,254554667
-PTCH1	0,254572046
-CDC42EP3	0,254591236
-LOC150776	0,254715807
-PTGES	0,254816225
-TPM2	0,254867646
-TAGLN	0,254960085
-AL050032	0,254984309
-HPN	0,25500915
-FLNC	0,255046574
-GJB3	0,255060346
-RAB40B	0,255071999
-CST1	0,255226531
-FGF21	0,255229382
-AW574933	0,255334628
-FGF5	0,255461872
-CLCN7	0,2555275
-BAHCC1	0,255618646
-FANCA	0,255627746
-CYBA	0,255682121
-TIE1	0,255683605
-ANKHD1-EIF4EBP3	0,255707685
-CDV3	0,255740411
-COL9A1	0,255878907
-TTC31	0,256049153
-ZIC1	0,256075896
-CCDC121	0,256090992
-FUT4	0,256155794
-UCP3	0,256197327
-AU146391	0,25625958
-MMP2	0,256269664
-STXBP2	0,256386629
-TMEM87A	0,2564575
-FXR1	0,256493521
-RDX	0,256507051
-HPS1	0,256516919
-TRAM2	0,256517872
-HYAL2	0,256778041
-TNFRSF14	0,256783849
-NEK7	0,256861333
-AGRN	0,256876471
-SMC4	0,256895131
-GAS7	0,256949822
-PDE4B	0,256950938
-CHD4	0,256970114
-SPP1	0,257084517
-HECA	0,257172806
-NXF2B	0,257181225
-LILRA5	0,257188463
-SCAP	0,257267679
-SNX1	0,257354288
-GIGYF2	0,257400552
-CELF1	0,257407908
-HSD17B14	0,257420303
-DUOX1	0,25770603
-MRM1	0,257826185
-NBR2	0,257852879
-FAM176B	0,257955278
-SYNPO	0,257997864
-GPRIN2	0,258040238
-IER3	0,25816919
-ZNF506	0,258198461
-NM_016414	0,25824817
-VPS53	0,258358594
-PGPEP1	0,258378109
-GNL1	0,25847832
-OGFR	0,258496938
-CXCR2	0,258632799
-C1orf38	0,258857462
-RPL22	0,258901214
-NM_018041	0,259005358
-MYOF	0,259133176
-NGB	0,259197495
-CLIC4	0,259260666
-TBC1D9B	0,259295717
-KCND1	0,259337213
-RNASET2	0,259420675
-EXT1	0,259568659
-AQR	0,259572114
-VWA1	0,259618684
-MUC3A	0,259647513
-CAV1	0,259682957
-IRF4	0,259719685
-OR7C1	0,259728956
-SETDB1	0,259737838
-E2F6	0,259867146
-TFEB	0,259924981
-CPSF3L	0,26005015
-MARCH8	0,260576922
-MFSD11	0,260945964
-ETAA1	0,260954881
-SMARCD2	0,260999203
-RGS12	0,261024661
-CCNG2	0,261112401
-RPS8	0,261183649
-IL17RA	0,261275371
-NUDC	0,261284708
-ZNF133	0,261329337
-ATP13A1	0,261543252
-PICK1	0,26166607
-C20orf117	0,261682534
-GIPR	0,261728602
-HIST2H4B	0,261730186
-S100A11P1	0,261732522
-MARCH3	0,26174629
-ZBED4	0,261794357
-KHK	0,261822851
-SCAMP2	0,26194666
-AF070579	0,261954742
-TECR	0,261998101
-AK024915	0,262016665
-CASP7	0,262240261
-PDK4	0,262293861
-MYO7A	0,262479993
-TUBBP5	0,262483574
-TMEM143	0,262491406
-NAP1L1	0,262524812
-PLEKHB1	0,262542861
-ING1	0,262679424
-SPSB3	0,262786186
-C9orf167	0,262955615
-NTM	0,262977412
-FIP1L1	0,263199662
-FYCO1	0,26321575
-GGT1	0,263227324
-ALG12	0,263240056
-IGL@	0,263282588
-PPBP	0,263290228
-SNX13	0,263292989
-SRSF4	0,263309909
-CYTH1	0,263721364
-AL050035	0,263831657
-TRMU	0,263920451
-TIMP1	0,263959235
-RFNG	0,263965598
-HIP1R	0,264033626
-NR1H3	0,264039538
-NT5C2	0,264091319
-FNTB	0,264115077
-SAR1B	0,264175117
-GIT1	0,26420824
-RRAGD	0,264311012
-HAP1	0,26435511
-FLT3LG	0,264378926
-NM_018612	0,264421364
-SLC7A9	0,26447762
-GLTSCR2	0,264541217
-SUN1	0,264635751
-CEP152	0,264663399
-MBTD1	0,264688291
-SYT12	0,264690461
-ACTR5	0,264835312
-EIF4A1	0,264933012
-COX7A1	0,26511391
-CMTM6	0,265385079
-FAM102A	0,265449454
-AW970584	0,265532869
-FMO5	0,265619005
-N4BP2L1	0,26587536
-SPAG11A	0,265939376
-TGFBI	0,265987004
-RYK	0,266131346
-SERBP1	0,266135884
-AK021988	0,266152576
-NCAM2	0,266199101
-AK024995	0,266233606
-RAB9A	0,266259326
-SYNJ2	0,266313048
-PHLDB1	0,266315252
-PKN1	0,266439146
-MFAP3L	0,266558078
-PPFIBP2	0,266640652
-WBP5	0,266861878
-TMX1	0,266949292
-SLC6A12	0,267009029
-C3AR1	0,267017849
-CSRP2	0,267020264
-SP3	0,267034674
-ATN1	0,267069634
-GNB3	0,267107148
-TIAL1	0,267113358
-GPATCH8	0,267177985
-PMEPA1	0,267182372
-MAP2K3	0,267199274
-NM_018033	0,267304029
-WWTR1	0,267350058
-SEMA6A	0,267400431
-RBPJ	0,267426168
-AL049279	0,267438916
-IL1RN	0,267473934
-QKI	0,267577841
-SOX15	0,267588393
-DMTF1	0,267672579
-RPL19	0,267821304
-TRIM39R	0,267839755
-SLC26A6	0,267879749
-NM_025056	0,267969441
-BBS9	0,267969882
-M85256	0,26799656
-ADORA3	0,268097905
-TMEM176B	0,268515164
-SECTM1	0,268600799
-ST14	0,268612452
-ARHGEF18	0,268652414
-SIRT5	0,268726991
-MYBPC1	0,268763379
-RPL15P22	0,268793196
-SIGLEC15	0,268860828
-DNAJA1	0,26890035
-LMBR1L	0,269042598
-GIMAP4	0,269074847
-MFAP3	0,269075993
-ABCA6	0,269120338
-AW836210	0,26919833
-LOC100133772	0,269228182
-CHST4	0,269387102
-RNASEH2A	0,269387986
-RPL18	0,269450865
-RPLP2	0,269486597
-MEPE	0,269489799
-FAM106A	0,269545639
-GATAD1	0,269621956
-PPP2R3A	0,269725552
-MASP2	0,269836416
-MYO10	0,26992164
-PIGG	0,269941407
-SMG5	0,269952017
-IFI30	0,269956381
-AK025180	0,269971157
-AMD1	0,269982316
-LMOD1	0,270125966
-SNX15	0,270191178
-SCARB1	0,270338985
-SERTAD3	0,270373355
-MBD5	0,270430073
-SLC2A5	0,270454389
-ITCH	0,270468949
-ADA	0,270490353
-PWP2	0,270541137
-ARHGEF1	0,270572389
-C2CD2	0,270675538
-EIF1	0,27071329
-C1orf35	0,270772513
-IFI16	0,270855012
-LOC285830	0,270905428
-IL10	0,271025993
-MORC4	0,2712707
-CA11	0,271346355
-C5orf54	0,271348162
-C14orf93	0,271428228
-RPL17P7	0,271481741
-TMEM161A	0,271564557
-LRCH3	0,271627825
-DFFB	0,271779652
-BAZ1B	0,271859723
-DKFZp547G183	0,271894591
-RAB11FIP2	0,271895928
-PCK1	0,27194659
-TMPRSS5	0,27195628
-TIPARP	0,272078235
-UBE2L3	0,272125747
-ZNF672	0,272142507
-GALNT10	0,272151507
-EXD2	0,272173543
-KAT2B	0,272322281
-RPS11	0,27237174
-POLR2H	0,272422791
-IGLL3	0,272574443
-AA554430	0,272578205
-DOCK10	0,272578712
-DMC1	0,272606886
-CD40	0,272762332
-CDK11A	0,272811711
-UCKL1	0,272898303
-FAM125B	0,273084179
-UBXN7	0,273084433
-SMA4	0,273204796
-DYNLT1	0,273349219
-CTTNBP2NL	0,273380758
-HSPH1	0,273396703
-CYP39A1	0,273418193
-HOMER3	0,273432217
-RRBP1	0,273480926
-ATAD2B	0,27361049
-LGALS3	0,273847411
-LASS2	0,273913098
-ZNF451	0,273935073
-NXPH4	0,27404559
-C22orf46	0,274118605
-KDM4B	0,27422483
-GPNMB	0,274363725
-CYHR1	0,274415705
-CCDC9	0,274487483
-WWC2	0,274522318
-ZNF652	0,274533788
-ILK	0,274538403
-CTDP1	0,27455992
-LOC51152	0,274810051
-AL442084	0,274963062
-CPNE7	0,275259638
-CENPB	0,275294531
-TCIRG1	0,275300556
-PRPF40A	0,275423637
-ARHGAP17	0,27552534
-LOC100133811	0,275961848
-ADAM17	0,276019886
-CRISPLD2	0,276144309
-IFIH1	0,276175289
-LOC440434	0,276293985
-DCLK2	0,276369722
-MS4A6A	0,276482788
-VASH1	0,276499979
-SRSF7	0,276513035
-B3GAT3	0,276752575
-CALHM2	0,276762436
-MAP4	0,276867434
-DULLARD	0,27687625
-CTSS	0,276943812
-BAG3	0,277040195
-KRT8P12	0,277155277
-POLR2F	0,277193722
-CD14	0,277207134
-SF3B1	0,277255775
-EZH1	0,277320185
-MBD1	0,277342685
-MITF	0,277407356
-BAIAP2	0,277445862
-FCGR2B	0,277531437
-PAQR4	0,277547889
-NFATC2IP	0,277597337
-CAT	0,277600148
-TJP2	0,277610024
-CCNA2	0,277687494
-GEM	0,277887602
-C2orf54	0,277935237
-HIRIP3	0,278018588
-MCM3APAS	0,278082892
-CFB	0,278130274
-TAGLN2	0,278365668
-AK024851	0,278382784
-HGD	0,278585783
-NR2E1	0,278716062
-SEC61A1	0,278797194
-PDE4DIP	0,278806635
-FRMD4A	0,278822955
-RHOC	0,278842121
-UBTF	0,278963815
-NCOR2	0,279024257
-PPP6R3	0,279218049
-ALAS2	0,279327775
-SPSB1	0,279537438
-SGMS1	0,279545277
-TEAD4	0,279565374
-AK024897	0,27961031
-IRS2	0,279708094
-TRIM62	0,279977776
-AF308291	0,279984986
-AK022362	0,280079092
-KIAA0495	0,280115197
-CUL7	0,280170918
-PARD3	0,280192562
-NUP98	0,280376383
-DHRS4L2	0,280391865
-AK024093	0,280444114
-VEGFB	0,280560816
-PTEN	0,280592383
-NBPF10	0,280620974
-CASP1	0,280699269
-AK2	0,280734467
-MLX	0,280792537
-GNG11	0,280826824
-HNRNPM	0,280968313
-IL12RB2	0,28098376
-CDK18	0,28098866
-RARA	0,280998983
-GYPC	0,281028129
-PAK4	0,28104576
-SEMA3F	0,281239182
-BAT2L2	0,281335934
-BRD4	0,28139016
-PAOX	0,281415979
-SMAD3	0,281446531
-PIK3R2	0,281480063
-IFT122	0,281682471
-IRAK4	0,281825175
-RASSF2	0,281825652
-RPL13A	0,282085077
-ZNF22	0,282127023
-KDM4A	0,282136199
-CPM	0,282150511
-EIF2S2	0,282316006
-USP48	0,282335945
-CLCNKB	0,282422648
-C11orf61	0,282474246
-ANKRD11	0,282516441
-PTTG1IP	0,282619596
-SEC14L1	0,282620994
-DOCK6	0,282646645
-CARHSP1	0,28271852
-RRAS	0,282814195
-TRIM38	0,283129972
-PLA1A	0,283206252
-GAB1	0,283220235
-PDLIM1	0,283254227
-SSH3	0,283308195
-KLF9	0,283315657
-N4BP2L2	0,283629404
-TNS4	0,283667599
-C15orf28	0,28383226
-ANXA11	0,283988681
-TAF12	0,283993401
-SLC39A1	0,284190806
-SAP30	0,284320416
-RNASE4	0,284337811
-RPS28P6	0,28438483
-DDR2	0,284449824
-BMP4	0,284614799
-CEPT1	0,284615091
-ITPKB	0,284650775
-PLEKHF2	0,284678379
-AW974812	0,284683098
-PTCRA	0,284827371
-SETMAR	0,2848555
-SOCS3	0,284925858
-NM_014129	0,284930906
-MYO1D	0,285094554
-RBL1	0,28514691
-HN1L	0,285254673
-LASS4	0,285307965
-RPS21	0,285547221
-PPP2R1B	0,285765143
-NEO1	0,285937917
-SEC24C	0,286013109
-BCL3	0,286014454
-KCNMA1	0,286080656
-AL137590	0,286198689
-EDIL3	0,286207431
-ARHGEF16	0,286210956
-HCK	0,286227266
-GSTA1	0,286246055
-SLA	0,286356975
-UNG	0,286379363
-SP100	0,286388329
-PRSS53	0,28642638
-MYL6	0,286728542
-CDH5	0,286728949
-C10orf116	0,286730624
-GTF2IRD1	0,286882519
-POLH	0,286995879
-SFRS16	0,287066034
-TPM4	0,28709233
-ABCD4	0,287100216
-GLT25D2	0,287127854
-COL18A1	0,287131911
-NPIPL3	0,287424398
-C1orf69	0,287453135
-MTF1	0,287488427
-IGF2BP2	0,287555495
-PALLD	0,287872078
-RPS16	0,287887395
-CYP2C9	0,287955438
-SC65	0,288029122
-CRYBG3	0,288096904
-SHC2	0,288312879
-FLNA	0,288339801
-NM_014486	0,288348194
-ISYNA1	0,288383809
-PNO1	0,288506351
-GZMK	0,2886543
-ATG13	0,288748426
-NCOR1	0,288772721
-ZSWIM1	0,288892162
-GPM6B	0,28893274
-SNTA1	0,289049438
-RHOBTB1	0,289064808
-GGA1	0,289073087
-ATXN2L	0,289088819
-FAM46A	0,289172187
-ZNF532	0,289393934
-CD40LG	0,289400418
-ZCCHC11	0,289421485
-WDR5B	0,289498086
-EPN2	0,289629137
-WNK1	0,289684816
-ZNF408	0,289721753
-LHFPL2	0,290003635
-NARG2	0,290029081
-STYXL1	0,29008917
-YY1AP1	0,290249669
-CPOX	0,290281635
-IL11RA	0,290333682
-PAXIP1	0,290387596
-ZNF282	0,290414378
-C11orf95	0,290643441
-MERTK	0,290681835
-VPS13C	0,29069039
-RPS17	0,290756898
-NEIL1	0,290762184
-ZNF292	0,290850132
-NOSIP	0,290873511
-DNAJB2	0,290950763
-INPPL1	0,29102828
-ZFX	0,29106383
-SETX	0,291138151
-SLC25A37	0,291207794
-PCDHGA8	0,291472818
-TXNIP	0,291962928
-DDX27	0,291971417
-BG389073	0,29216848
-JTB	0,292275569
-RBM10	0,292352574
-RASGRF1	0,29242252
-SYNM	0,292474024
-EXPH5	0,292481151
-NPL	0,292494012
-CHKA	0,292519533
-MGA	0,292564204
-SOX10	0,292580481
-AK024185	0,292975066
-FAM120A	0,292996604
-PLXNB1	0,293000141
-BDH2	0,293071563
-JRK	0,293136106
-SLC11A1	0,293139917
-TM4SF1	0,293242649
-EDA	0,293286441
-CDK10	0,293299298
-HLA-E	0,293305618
-LOC642846	0,293349826
-GFPT2	0,293396887
-SENP3	0,293408144
-RPS3AP44	0,293415546
-C16orf88	0,293431615
-FAM60A	0,293472328
-RPL36A	0,293501288
-SERPINA5	0,293547044
-CNOT8	0,293568161
-KDM4C	0,293620372
-POU2F2	0,293815578
-C14orf139	0,293870806
-ZNF217	0,293937173
-NM_025042	0,294034268
-NNMT	0,294200775
-VEZT	0,294224684
-KIAA0754	0,294307773
-RBM28	0,294637248
-ITPR2	0,294711729
-PPPDE1	0,294796015
-KLHL28	0,294874305
-MGP	0,294956866
-LOC729602	0,295016892
-SRSF5	0,295036903
-ROCK1	0,295267164
-SS18L2	0,295271871
-LMNA	0,29532356
-ESRRA	0,295387708
-SNHG3-RCC1	0,295411716
-TAL1	0,295434654
-SQRDL	0,295470062
-TARDBP	0,295665655
-LMAN2L	0,295705138
-RIN3	0,295771443
-PSPH	0,29602696
-DGKD	0,296027908
-WHSC1	0,296067068
-SPRY4	0,296068122
-ADARB2	0,296162399
-ELF3	0,296200778
-TLE1	0,296292637
-ACAN	0,296375799
-AK022038	0,296556116
-IL1RL1	0,296721787
-OR2A9P	0,296898432
-NCRNA00260	0,296954725
-CAD	0,296976627
-PNRC2	0,297129071
-IQCK	0,297134521
-ACOX2	0,297377087
-APOC4	0,297497329
-DGKA	0,297541846
-ZBTB1	0,297547513
-PUS1	0,297622568
-C7orf64	0,297653213
-FBLN1	0,297723957
-SBF1	0,297752819
-TMF1	0,298582891
-IL1R1	0,298701666
-LILRB3	0,298823808
-FLAD1	0,298825369
-CD163	0,299040686
-TCL6	0,299056301
-FADS3	0,299096634
-LBR	0,299180453
-AL162044	0,299184427
-ZNF337	0,299271736
-AHNAK	0,299352615
-YY1	0,299417937
-HIPK2	0,299439852
-NAT15	0,299519834
-ANKZF1	0,299817611
-NECAP2	0,299838267
-MAP3K7	0,299838407
-SAMD4A	0,299863792
-WDR8	0,300094232
-ZNF24	0,300179611
-NR3C1	0,300200063
-FGF1	0,300357727
-NPC1	0,300564708
-LMO4	0,300573598
-TTLL5	0,300853453
-AL050053	0,300945526
-RSU1	0,300958049
-C15orf39	0,301123219
-SLC14A1	0,301147038
-ELAVL1	0,301190126
-SLC17A4	0,301215925
-FANCC	0,301274346
-LRCH4	0,301338927
-EGFL7	0,301340052
-C9orf3	0,301357727
-SRGN	0,301411135
-PLCL1	0,301576339
-MAN1A1	0,301613058
-S100A8	0,301917937
-W86781	0,301984854
-HIP1	0,302012828
-OR7A5	0,302027387
-PPP1CC	0,3020408
-CGGBP1	0,302058231
-CYP3A4	0,302333153
-GALNS	0,302376776
-NR0B1	0,302394827
-SMNDC1	0,302468654
-MGST2	0,302482901
-RPL12	0,302658969
-DMPK	0,302955014
-TNRC6B	0,30299615
-PPM1D	0,303104009
-EED	0,303134999
-STAG3L1	0,3031801
-TMCC1	0,303195736
-RPL13	0,303245467
-RBPMS	0,30326423
-ARHGAP10	0,303298204
-PLCB3	0,303300054
-XPO1	0,303410309
-MYO1F	0,30341788
-SRPK1	0,303531642
-ZCWPW1	0,303562617
-MTHFD2L	0,303678034
-FAM111A	0,303798707
-TTC38	0,304186409
-COL7A1	0,304295553
-C4orf19	0,304312458
-NGLY1	0,304332742
-HTATIP2	0,304339936
-IFNAR2	0,304414877
-CXorf1	0,304737703
-UNC5B	0,304789798
-YAP1	0,30479215
-PHC2	0,30485466
-FBL	0,304914384
-CDH2	0,304939032
-FXYD2	0,304942957
-ANKRD36	0,305000603
-KRT8	0,305028726
-DSCAM	0,30505625
-SMO	0,305151387
-FCGRT	0,305420183
-PAIP2B	0,305483478
-PABPC1	0,305528523
-PIGV	0,305604211
-BACH2	0,305697602
-PLGLA	0,305722503
-MORC3	0,305845022
-DIDO1	0,305996983
-PRPF38B	0,306041882
-TRMT1	0,306054262
-NFATC1	0,306233076
-AK021495	0,306242002
-GPR1	0,306335484
-STARD13	0,306369109
-CELSR2	0,306371185
-ZNF193	0,306396574
-ABHD6	0,306458055
-PLCXD1	0,306486283
-RPAP1	0,306695411
-AL050122	0,306737964
-DHRS3	0,306750918
-C1QA	0,306800137
-AF009267	0,30681596
-SETD2	0,307047565
-STX6	0,307184977
-TMEM204	0,307304516
-SMYD2	0,307490131
-BF942161	0,307560212
-SLC44A1	0,307685609
-ELF2	0,307698089
-AATF	0,307770923
-AV761453	0,307800442
-ACTN1	0,307927265
-AI523613	0,307943372
-SOLH	0,307971092
-ZNF410	0,308222237
-GOLGA4	0,308250269
-FLJ21369	0,308352331
-FCGR2A	0,308469725
-BRD7	0,308638563
-TLR2	0,308769609
-FTHL5	0,308790654
-SPOCK1	0,308861441
-LSM14A	0,308907157
-USF2	0,309161806
-TENC1	0,309220224
-EMP2	0,309252571
-BSDC1	0,309299474
-ZNF701	0,309462113
-PLIN3	0,309516744
-SORBS1	0,309562012
-FTL	0,309588981
-AGFG2	0,309634949
-UBR5	0,309647344
-MMP14	0,30965745
-SFRS8	0,309923113
-ITPR3	0,309975876
-PLK3	0,310097184
-NUP188	0,310124261
-CROCC	0,310245563
-CHSY1	0,310328559
-CTCF	0,310675097
-EDC4	0,310685915
-NFE2L2	0,31069885
-LILRA6	0,311008878
-SATB2	0,311055754
-GTPBP6	0,311254994
-TSPAN14	0,311316513
-C10orf18	0,31133762
-SECISBP2	0,311419174
-DHX34	0,311443077
-LSS	0,311450185
-CHI3L1	0,311532669
-PDGFC	0,311715929
-BMP7	0,311741682
-MBNL1	0,311755686
-DNA2	0,311841432
-COMT	0,312081286
-LOC100133005	0,312165679
-PTOV1	0,312192713
-LCAT	0,312407744
-LRRFIP2	0,312480817
-UCN	0,312589312
-AK024606	0,312655002
-MICAL3	0,312700621
-ROM1	0,31291043
-MED12	0,312925796
-CPNE1	0,313173908
-GBP2	0,313262095
-PELI2	0,313279559
-MLL	0,313398121
-HIF3A	0,313438743
-ST18	0,313449639
-AF131777	0,313643716
-CATSPER2P1	0,313785721
-ZNF302	0,314066212
-APBB2	0,314110219
-KIAA0907	0,31421022
-ZNF592	0,314679884
-HNRNPA1	0,314773035
-TSC2	0,314882123
-SFRS15	0,314884343
-ZNF835	0,314920694
-WDR6	0,314979423
-LOC729143	0,315037798
-PPARD	0,315048839
-U2AF2	0,315118843
-MGAT1	0,315269456
-ZNF44	0,315270856
-RPL36	0,315475789
-GRAMD3	0,315513449
-PTPN2	0,315554784
-AL080072	0,315635626
-C19orf2	0,315918303
-DNAH3	0,315930745
-ZNF146	0,316341954
-SMEK1	0,316538461
-MLXIP	0,31681421
-NMT2	0,316848231
-G3BP1	0,316864559
-DDX3Y	0,316997159
-STEAP1	0,317082981
-BC002629	0,317231764
-KDM2A	0,317406731
-TMEM39A	0,317430306
-C15orf29	0,317437851
-MACF1	0,317513626
-LOC391020	0,317572673
-SETD1A	0,317586539
-KTN1	0,317889697
-RUNX3	0,31809511
-NINJ1	0,318107478
-ARMC7	0,318150459
-BMP1	0,318194029
-DKFZP586I1420	0,318199121
-JARID2	0,318226296
-AW972351	0,318303541
-PAPSS2	0,31841091
-ELTD1	0,31845583
-ETS2	0,318667898
-CREB3L2	0,318705762
-DFNB31	0,31892768
-SERHL2	0,318966243
-C10orf26	0,319058163
-NM_030892	0,319421731
-WRAP53	0,319795295
-UBQLN4	0,319828198
-RALGDS	0,319938162
-PRKCH	0,320101043
-AU146983	0,320105843
-SLC5A3	0,32021553
-DUSP1	0,320239212
-NKX2-2	0,320312108
-C1orf183	0,320387827
-PCM1	0,320482282
-THRA	0,320531901
-NM_025028	0,320726138
-SIVA1	0,320736787
-TTR	0,320757249
-IKBKB	0,320778441
-ARID1A	0,321020715
-HDAC4	0,321059842
-ZFP36L2	0,321167918
-TMEM212	0,321179342
-AA443771	0,321214505
-AGAP5	0,32125931
-PIGA	0,3216713
-SFRS12	0,321704401
-LDLRAP1	0,321832456
-CCDC21	0,321857948
-SSFA2	0,321990716
-RAMP1	0,322050077
-FLJ10357	0,322160744
-LAD1	0,322322766
-RACGAP1	0,322340831
-NPIPL2	0,322616655
-CEP350	0,322648588
-CRLF1	0,322735059
-IGSF9B	0,322744338
-PLXND1	0,322801951
-MCL1	0,322913781
-ALMS1	0,32297709
-ZNF768	0,323059066
-RSL1D1	0,323228527
-C4orf34	0,323582139
-PNPLA6	0,323738553
-MAST4	0,323801655
-NME3	0,323835175
-SNHG3	0,32391938
-S100A12	0,324014586
-PPP4R1	0,32409634
-PLD1	0,324165096
-POLG	0,324186823
-NKTR	0,324203565
-ST3GAL4	0,324231325
-TMEM63A	0,324243134
-ST20	0,32438459
-RNF114	0,324406844
-HYI	0,324468621
-DUSP6	0,324699964
-NR1H2	0,324884332
-DVL2	0,324900869
-SRSF11	0,324979841
-CLK2	0,325170283
-MKLN1	0,325287178
-SCRIB	0,325320413
-KIAA0467	0,325541973
-DMWD	0,325745064
-KLHL23	0,32579572
-RPS6	0,325948088
-ZBTB17	0,326014408
-RAI14	0,326038467
-UBE2G2	0,326143089
-ZNF562	0,326186073
-EZR	0,326282578
-TRPS1	0,326283144
-HFE	0,326390644
-MED23	0,32658232
-DDX11	0,326766632
-SHMT2	0,326784725
-LRP5	0,326954416
-PTH1R	0,327100265
-LOC731602	0,327131294
-AA401963	0,327241371
-CDK5RAP2	0,327276136
-SERP1	0,327279991
-SLC1A5	0,327303416
-BGN	0,327370767
-HSD17B1	0,327475971
-AL390143	0,327497051
-DIAPH2	0,327617697
-PITPNC1	0,327719899
-SPRY2	0,327767132
-FZD7	0,327974293
-MAP4K4	0,328171238
-TNS1	0,328369107
-ZNF783	0,328517049
-M78162	0,328518574
-ADAMTS1	0,32853944
-FKBP5	0,328911405
-AGAP8	0,329115979
-PLEKHF1	0,329179433
-DNAJB1	0,329339376
-RBMS2	0,329438459
-HNRNPH1	0,329454824
-ULK2	0,329496298
-PAPD7	0,329501864
-SURF1	0,329547559
-W61005	0,329673439
-ZNF862	0,330131081
-GNA15	0,330266409
-CHD9	0,330273108
-DLC1	0,330294104
-TMEM2	0,330321664
-AK024879	0,330353812
-N4BP1	0,330435804
-SERF2	0,330633507
-SNRPA	0,330957742
-IRF8	0,33098543
-ABCA2	0,331251046
-NPFF	0,331328402
-CP	0,331565597
-AU144887	0,331713137
-AW851559	0,33185735
-TCF4	0,332062967
-ZNF354A	0,332076549
-TMEM92	0,332352956
-NFATC3	0,332386137
-SSRP1	0,332529738
-TCF7L2	0,332651908
-PIM1	0,332716071
-PIP4K2A	0,332914219
-EIF4EBP1	0,332959146
-LOC100132863	0,333054912
-MMRN2	0,333075923
-AU147295	0,333342973
-VIM	0,333356286
-C2orf67	0,333469715
-DNMT1	0,333550022
-CEP110	0,333679402
-BAZ2B	0,33371151
-KDELR2	0,333939841
-L3MBTL	0,334448273
-CDK19	0,334505985
-CYorf15B	0,334832089
-DDX17	0,334839203
-FKBP4	0,335166906
-STOM	0,335173644
-U82303	0,335241438
-LOC202181	0,335841121
-ATM	0,335893127
-STK3	0,335957389
-MID1	0,336166241
-IGFBP5	0,336454348
-PARP4	0,336459483
-EXOC7	0,336479503
-FANCG	0,336652927
-PHF2	0,336678654
-FBRS	0,33674511
-ANP32B	0,336836072
-NCK2	0,336876937
-CASP6	0,336920233
-ZBTB3	0,337122586
-DHFR	0,337448147
-APOLD1	0,337464001
-STAG1	0,337490482
-NM_024305	0,337551103
-SIGLEC8	0,337608204
-ERLIN1	0,337809212
-POLDIP3	0,337889824
-SPTLC2	0,33799094
-C7orf26	0,338204972
-UBE2D4	0,338265561
-MAP2K7	0,3384787
-MECOM	0,338508564
-DOCK1	0,339029429
-HS1BP3	0,339148762
-PRKY	0,339216015
-GOLGA1	0,33927478
-XPC	0,339433169
-PHF3	0,33953002
-HIC2	0,339768003
-C9orf7	0,340519877
-CTDSPL	0,340591645
-ZNF83	0,34077157
-PHGDH	0,340889735
-TMEM165	0,340978736
-CLN3	0,341078466
-AU147983	0,34113627
-PATZ1	0,341151411
-DIP2C	0,341390806
-RECK	0,341533646
-EWSR1	0,342003886
-SMAD7	0,342182186
-MTRF1L	0,34225773
-TJAP1	0,342452426
-PRKD2	0,342725824
-SPOP	0,343019265
-HLA-J	0,343028528
-PLXNB2	0,343103735
-FBXL14	0,343454364
-LAMA2	0,343637649
-RNF220	0,343845541
-CLK3	0,344164444
-STARD3	0,344187457
-OGT	0,345118989
-IFITM3	0,345141829
-HMOX1	0,345196784
-EIF2C2	0,34557825
-CCND3	0,345663426
-TGFBR3	0,345676022
-POLR2J3	0,345712548
-BCAR3	0,345713549
-C14orf147	0,34610842
-CLDN15	0,34616346
-TOP1	0,346179876
-RASL12	0,346286134
-MED13L	0,346369067
-SOS2	0,346799305
-SERPING1	0,347144597
-IER5	0,347279068
-TLE2	0,347426427
-LLGL2	0,347448236
-TMCC2	0,347500013
-PHF20	0,347602909
-SIRT4	0,347862165
-OSGIN1	0,348060574
-H2BFS	0,348076316
-NM_017756	0,348230007
-NCRNA00115	0,348422218
-MT1E	0,348733923
-NACC2	0,3488369
-NFIB	0,348943619
-AKR1C3	0,349206923
-ARPC1B	0,349407208
-NIPBL	0,349628117
-RPL11	0,349803207
-MSH6	0,350014407
-PTDSS2	0,350073646
-AL050145	0,350120404
-FAM107A	0,350271118
-CHN2	0,350358174
-DAPK2	0,350378033
-DLG5	0,350436992
-OPHN1	0,350596034
-C20orf11	0,351010126
-SLC35D1	0,35135795
-SELL	0,35142274
-FAM193B	0,351790995
-NM_024880	0,352020901
-RASGRP2	0,352114346
-CAPN3	0,352194849
-THOC1	0,352289646
-TAOK3	0,352396226
-FBXO42	0,352613215
-LARP6	0,352692849
-KLKB1	0,352702835
-METTL7A	0,352961228
-STIP1	0,352968743
-WIPF2	0,353085817
-FOXD1	0,353404764
-HSPB2	0,35378232
-ENGASE	0,353978221
-LAT2	0,354239264
-HIST1H2AH	0,354250391
-GSDMD	0,354483715
-TRA2A	0,354674037
-C19orf29	0,354762053
-BRPF1	0,355002213
-NUMA1	0,355146564
-SNW1	0,355320637
-SMARCC1	0,355374541
-ZNF175	0,35555253
-BATF3	0,355680727
-HIST1H2BC	0,35575565
-ERN2	0,356098991
-ZFR	0,356185362
-AW301806	0,356253591
-SMTN	0,356289422
-RPS6KA2	0,356774064
-MIIP	0,35685635
-ARGLU1	0,356919378
-CTNNAL1	0,357152141
-PCDH9	0,357228835
-LAS1L	0,357263917
-DOK1	0,358029668
-AFTPH	0,35852635
-ZNF143	0,358674337
-C11orf71	0,35888557
-MICALL2	0,359221642
-KDM6A	0,359260932
-CFH	0,359284568
-CEBPB	0,359516672
-MTUS1	0,359547348
-AW973791	0,359548173
-SERTAD2	0,359684853
-FGFR1	0,359721729
-KPTN	0,360479451
-NR2F2	0,361169645
-RGL2	0,361384531
-NM_014120	0,361482036
-TAF5	0,361611903
-ZC3HAV1	0,362177526
-BEST1	0,362248528
-TNFRSF1A	0,362724804
-CLIP2	0,363062238
-EHMT2	0,363078239
-IFITM1	0,363162265
-GCFC1	0,363190607
-PECAM1	0,363227012
-YES1	0,363556218
-ZFP36L1	0,363744573
-SBNO2	0,364095165
-RMND5A	0,364201024
-IL10RB	0,364481295
-CBS	0,364486163
-TBC1D2B	0,364503601
-C10orf10	0,36458821
-AU144530	0,365137826
-ZNF500	0,365202134
-ATP6V0E1	0,36527949
-SEPT8	0,365711052
-VCAN	0,365762437
-RPL36AP51	0,366073863
-RPL31	0,36613283
-TAOK1	0,36613666
-GCN1L1	0,366181489
-CALCOCO1	0,366300689
-GNA11	0,366387362
-SH2B2	0,366425408
-RREB1	0,367259867
-SLC35E1	0,3672965
-GPRC5B	0,367311931
-TCF7	0,367371063
-PDIA4	0,367810651
-ZNF34	0,367845233
-MBD3	0,36793004
-CXCR4	0,368041224
-C9orf114	0,368120984
-IFITM2	0,368313531
-ZNF665	0,368328536
-ZCCHC24	0,368368275
-LOC100133944	0,369022431
-CSDA	0,369150342
-AU148255	0,369666508
-CIZ1	0,369704457
-CRTC3	0,369792369
-CTNNA1	0,369962411
-RARRES2	0,37011032
-NM_025033	0,370246707
-VSIG4	0,370274949
-FAM48A	0,370421427
-ZDHHC11	0,370675656
-NPAS2	0,370715345
-ADH1B	0,370935809
-ACSL1	0,371025369
-C1orf63	0,371083889
-TYMP	0,371266716
-LEPREL1	0,371463494
-LAMB2	0,371472469
-MAFB	0,371542293
-AW971248	0,371589606
-BC003629	0,371603781
-FAM63A	0,371786321
-ABCA1	0,371992682
-IGF2R	0,37211512
-SOX13	0,372131188
-WAPAL	0,372391179
-ZFC3H1	0,372437982
-ZNF710	0,372493324
-HSPA6	0,37258644
-CCDC101	0,372823539
-BAZ1A	0,372824952
-AXL	0,372842922
-NPIPL1	0,372916072
-HDGF	0,372923023
-KHDRBS3	0,373093219
-MT1X	0,373144553
-MTMR15	0,373164421
-AF257099	0,373262757
-AEBP1	0,37342966
-KLHL25	0,373672957
-GJB4	0,37372121
-LUC7L3	0,374023648
-U79248	0,374142769
-LOC653562	0,374188384
-RBM4	0,374375075
-ABCC10	0,374890625
-CXorf21	0,374896996
-DAXX	0,374917403
-C1R	0,375063944
-TPST2	0,375279072
-KLHL24	0,375307199
-C7orf68	0,375539219
-ZCCHC8	0,375600764
-CASP4	0,375605037
-ETV1	0,37597402
-BIN1	0,376340315
-RGS19	0,376617752
-PKNOX1	0,377091746
-CTTN	0,377173864
-TRIP10	0,377452782
-ANGEL1	0,377498562
-PLIN2	0,377879768
-NM_025007	0,377942771
-PTMA	0,378229214
-S100A11	0,378255627
-AXIN1	0,378580893
-NPRL3	0,378633074
-PNN	0,378695864
-AV727934	0,378843386
-ANGPT2	0,37912784
-AK023918	0,379250766
-CNPY3	0,37927474
-AF130051	0,37947818
-TLE4	0,379880985
-PAPOLA	0,379974199
-ITGB5	0,380683545
-FAM38B	0,380693638
-PABPN1	0,380909515
-SLC6A8	0,38116858
-RYBP	0,38121367
-NASP	0,381229843
-FGR	0,381246748
-PER1	0,381695992
-CDR2L	0,381867955
-LRRFIP1	0,382075479
-HMHA1	0,382282948
-KIAA0485	0,382313718
-GUSB	0,38235255
-RPS17P5	0,38240934
-FXYD5	0,382563723
-RBL2	0,382697586
-RANBP10	0,382980904
-NEDD9	0,383084673
-MSL2	0,383144236
-FAM50A	0,383317183
-AL080232	0,383323554
-SPG21	0,383712061
-TPD52L1	0,384098652
-H2AFX	0,384141378
-SWAP70	0,384225003
-IVNS1ABP	0,384369268
-KDELC1	0,384542393
-MYL12A	0,384757468
-FOXO3	0,384856157
-MED13	0,385128516
-AL049252	0,38560217
-AF007147	0,385820993
-PAX6	0,385884587
-DNASE2	0,38591545
-SLC12A9	0,386200858
-SIRT1	0,38637719
-ARID5B	0,386492868
-MT2A	0,38656824
-SLC38A2	0,386710042
-GNG5	0,386756333
-SRRM2	0,386841072
-SERPINB6	0,386985458
-CC2D1A	0,387023088
-LRRC37A2	0,387067777
-CSF1	0,387071999
-RPL29P11	0,38708859
-SFRS14	0,387094074
-MYO9B	0,387103012
-AW972855	0,387241981
-TRIP4	0,387728627
-ZBTB40	0,387827711
-STARD8	0,387863703
-WBSCR16	0,387992811
-NXF1	0,388021286
-CTDSP1	0,38803541
-RSAD1	0,388042285
-SUV420H1	0,38833134
-CDKN1C	0,388508896
-NM_016415	0,388588403
-E2F4	0,388673603
-KANK2	0,388702219
-ZC3H7B	0,388980025
-ANGPTL4	0,389035415
-CRY1	0,389801967
-KIAA0556	0,389845114
-TBC1D16	0,390016803
-TCOF1	0,390109025
-ZFYVE26	0,390278079
-IFRD1	0,39034324
-EIF4B	0,390385914
-SMC1A	0,390525141
-SCIN	0,3907272
-MARS	0,391061966
-PTRF	0,391089965
-POLR2J	0,391514571
-APAF1	0,391530483
-ITPK1	0,3915415
-PNRC1	0,392133859
-CLIC2	0,392140808
-KIAA0913	0,392243895
-PRKAR2A	0,392619325
-PRKX	0,392750502
-SYDE1	0,392957216
-ACSL5	0,393140899
-LRP10	0,393162277
-LPP	0,393214983
-SNTB2	0,393383504
-NADK	0,393882671
-PCBP2	0,394206896
-N51370	0,394562467
-CLIC1	0,394663761
-CTBP2	0,394785714
-PHB	0,394929787
-BCL2	0,395102709
-TAF4	0,395492947
-LOC652607	0,395562084
-YBX1	0,396079328
-PRPF3	0,396609142
-SLC38A10	0,396741732
-ERBB2IP	0,396808535
-CFLAR	0,396840203
-TNFRSF10B	0,397091951
-PHC1B	0,397196351
-ARL17A	0,397406114
-ZBTB20	0,397424403
-REPIN1	0,397830532
-BE466926	0,397930108
-MT1P2	0,398055653
-ZNF778	0,398225613
-DICER1	0,398300689
-NM_018603	0,398329284
-RAF1	0,398631868
-MXD4	0,398685167
-FBXL7	0,398770393
-CALD1	0,399121196
-GSDMB	0,399246982
-ZCCHC2	0,399293751
-PODXL	0,399691684
-ACACB	0,400136922
-VEZF1	0,400413083
-PLEKHM1	0,401187317
-CSPG4	0,401646086
-ID3	0,40170175
-RBM41	0,401719975
-KDM6B	0,401885964
-PHF15	0,402522419
-LAMP2	0,402538077
-CDC14B	0,402583482
-HNRNPL	0,403044314
-SLC4A2	0,403448509
-DDX23	0,403953946
-TUBD1	0,40407115
-SLC16A3	0,404204458
-CAPN2	0,405022548
-CBFA2T2	0,40560438
-TCEB2	0,405769952
-HNRNPF	0,406126644
-MORC2	0,406182732
-FOXO1	0,406430281
-AI962978	0,406538883
-HP1BP3	0,406567553
-CBFB	0,406789498
-RBM14	0,406886421
-SFI1	0,407058786
-ZHX3	0,407089165
-KDM3A	0,407233406
-SIRT2	0,407341821
-ANKS1A	0,407373917
-TCF3	0,407442968
-NOTCH2NL	0,407672378
-EEF1D	0,407830724
-SOX12	0,408065349
-SLCO1A2	0,40820492
-HNRNPA3	0,408299868
-GTF2H3	0,408624789
-FZD9	0,408729069
-SAFB2	0,408755308
-APBA3	0,408834306
-ASCL1	0,409161488
-CG012	0,409559201
-WDR59	0,409606436
-LAMA5	0,409632505
-ZNF276	0,409730125
-ZNF395	0,410080702
-TIMM44	0,410223052
-BGLAP	0,410749324
-ZHX2	0,411039562
-CARS2	0,411302016
-SLCO3A1	0,411338796
-LOC442497	0,411765627
-FRYL	0,411842495
-CYP2J2	0,412070197
-ABL1	0,412522321
-INF2	0,412975218
-SGK1	0,413352645
-SFTPB	0,413789208
-TIGD1L	0,41383023
-RBCK1	0,414019825
-TRAPPC10	0,414285862
-DUSP7	0,414641136
-WSCD1	0,415016303
-DCP1A	0,415308358
-LPAR1	0,415365439
-RBBP6	0,415730871
-DONSON	0,416255506
-C16orf5	0,416258918
-NCOA1	0,416350707
-CFHR1	0,416440287
-AA126763	0,416566153
-LRRC32	0,416765832
-CP110	0,41732481
-LTBP3	0,417338221
-TDRD3	0,417356196
-HMG20B	0,417456909
-CDC42EP2	0,417645635
-TAF1C	0,417736819
-NM_013344	0,41778911
-VGLL4	0,417820331
-PHKA2	0,417904785
-KDSR	0,418009802
-RELA	0,418064238
-TBL1X	0,41814877
-SIAH2	0,418727849
-MYO1E	0,418747589
-HIST1H2BD	0,419127582
-AI744451	0,419208355
-PTMAP7	0,419537834
-ARID5A	0,419593497
-CYP27A1	0,420064872
-RAB13	0,420441013
-CPSF7	0,420526378
-CPT1B	0,420770156
-LRDD	0,420794327
-PILRB	0,421599366
-STAB1	0,421733406
-FCHO1	0,422126906
-ZNF32	0,422311821
-TBC1D3H	0,422328806
-C1orf66	0,42292679
-NM_025032	0,423323973
-AI732802	0,423584905
-PCID2	0,423787762
-POGK	0,423912669
-TMEM140	0,424587207
-TMC6	0,424604298
-AL080160	0,42490597
-AK021505	0,425024442
-SCD5	0,425610027
-RAD52	0,425956612
-AF116715	0,425960499
-DCI	0,425967692
-SFRS18	0,426091505
-HCG2P7	0,426136765
-ADORA2A	0,426366158
-NM_021651	0,426442506
-MID1IP1	0,426940092
-HNRNPC	0,427103695
-NM_025024	0,427155973
-AK024315	0,427460397
-AK021514	0,427966252
-SLC29A3	0,428138792
-NSUN5	0,428255135
-PHF10	0,428599049
-DAPP1	0,428626141
-TMEM109	0,428647746
-LOC91316	0,428742129
-ITGB4	0,42956266
-SLC30A1	0,429998682
-AW150065	0,430129937
-ZCCHC6	0,430267528
-ARHGEF2	0,430371137
-AK027193	0,43049002
-TRIM52	0,430535815
-MT1G	0,430767233
-NOTCH1	0,430849119
-ZRSR2	0,43114681
-RPS6KA1	0,43184981
-KANK1	0,432456197
-FURIN	0,432618855
-APOBEC3C	0,432749845
-ANKRD40	0,432772877
-TRIOBP	0,432900403
-ZNF384	0,433116555
-CDKN1A	0,43319672
-BTG1	0,433570541
-EPHX1	0,433658916
-CNOT6	0,434207544
-HSPA1L	0,434322364
-PKD1	0,434547199
-WAS	0,434717417
-RPL23AP32	0,434993767
-P4HA1	0,434997425
-MAX	0,435160002
-UIMC1	0,435278167
-NM_025120	0,435322168
-NCOA6	0,435700178
-TPD52L2	0,435768747
-BCL6	0,435938226
-AK024108	0,436355329
-C7orf23	0,436800978
-CDC42BPA	0,437074951
-CD59	0,437137855
-POLR1B	0,437227618
-TLR5	0,437498143
-HDAC1	0,437993569
-ARHGEF7	0,438071237
-AA045174	0,438161955
-TBC1D17	0,438488128
-PRELP	0,438518539
-GTF2H2B	0,438525643
-HIST1H2BK	0,43866778
-AU147851	0,438979485
-RBM39	0,439661925
-IQGAP1	0,439786742
-RPL18AP3	0,440613252
-LTBR	0,440721546
-RPL35A	0,441136859
-ARAP2	0,441441928
-ARAF	0,441560027
-MT1H	0,441587824
-LOC441258	0,442117007
-ZCCHC14	0,442132801
-IRF7	0,442147625
-NOL12	0,442203671
-PTPLB	0,442541309
-AI683552	0,442752948
-MYST1	0,442881562
-MXI1	0,443040642
-AW974910	0,443299524
-C1orf144	0,443500279
-KRCC1	0,444417306
-PIAS4	0,444438643
-SRSF1	0,444637015
-LRP2	0,444740953
-ZDHHC18	0,445392541
-SPN	0,445443935
-ST13	0,446667878
-PHF17	0,446746739
-NACA2	0,446876872
-SASH1	0,447285208
-CD22	0,44772036
-CSNK1E	0,447902552
-COL5A3	0,447933631
-MAT2A	0,448695587
-EFHD1	0,448820126
-MAP3K3	0,448963961
-BIN3	0,449317201
-LUC7L	0,449469644
-KIF1C	0,449622117
-RNF144A	0,450034368
-TULP3	0,450626451
-CDKN2C	0,450879897
-HSD17B7	0,451226227
-ACIN1	0,451331774
-PABPC3	0,451363083
-PHF21A	0,45139036
-HNRNPH3	0,451480034
-HIST2H2BE	0,452219911
-RRP1B	0,452597128
-SOX2	0,453132172
-ZNF444	0,453296716
-FAM13A	0,453547738
-JUP	0,453753674
-PODNL1	0,453854292
-MAML1	0,453885
-SNRNP70	0,45408945
-SDCCAG3	0,45464357
-PLGLB1	0,454722494
-CDH19	0,454754165
-HSPA1B	0,455063205
-ARHGEF10	0,455229121
-NFIL3	0,455469821
-NFKBIA	0,455577982
-XRCC2	0,455670024
-ACTN4	0,455764555
-PDS5A	0,456071133
-POU2F1	0,456120351
-VPS54	0,456318614
-BANF1	0,456451252
-PGCP	0,456765652
-RPL28	0,456867479
-ICAM2	0,457066169
-SNAP23	0,457069788
-SART1	0,457941993
-AK023891	0,458253977
-BANP	0,458588544
-MAP3K11	0,458968207
-EPOR	0,459463669
-FKSG49	0,459538011
-MT1F	0,459638951
-NM_014128	0,460468204
-AP1G2	0,460676306
-GAS2L1	0,461632768
-PHIP	0,462053958
-NOL8	0,462387404
-NM_017932	0,462395281
-RNF130	0,462894529
-ZMYND8	0,463309493
-AK024525	0,463401166
-TRIM28	0,463454342
-BCAT2	0,463509769
-TYRO3	0,463574548
-PHLPP1	0,463738295
-BST2	0,465024297
-PDGFRB	0,465034704
-AL049987	0,465336929
-AKAP8L	0,466278804
-TGM2	0,467555999
-CREBBP	0,467899354
-KIAA0894	0,468325808
-DDX39	0,468959477
-NCAPD2	0,468959537
-ALPK1	0,469621875
-TGIF1	0,469902489
-PPP1R14B	0,470121069
-PNMT	0,470291567
-NAA16	0,470467422
-ZNF611	0,470526774
-ZRSR1	0,470857426
-NPIP	0,472818474
-RBM38	0,473036567
-USP34	0,473278809
-TGFB3	0,474067001
-ITSN2	0,475328182
-CEBPD	0,475754278
-MCM3AP	0,476296498
-HAPLN2	0,476718109
-POGZ	0,477224004
-NR2F1	0,477556735
-GAS1	0,478628972
-SLTM	0,478903701
-ECE1	0,479007813
-CALCOCO2	0,47910558
-RXRA	0,479821295
-MEIS2	0,480178943
-CLEC2B	0,481843785
-AL049260	0,482481089
-CHST3	0,48259726
-COL16A1	0,483094975
-SLC25A16	0,483255606
-LHPP	0,48421483
-AF010144	0,484619234
-GTSE1	0,484629217
-MUM1	0,484956644
-TNXB	0,485246904
-PRINS	0,486032909
-ANKRD49	0,486282532
-PTPRK	0,486899575
-PPAP2C	0,487395433
-C22orf9	0,488987561
-KHNYN	0,489026627
-RAPGEF3	0,489474077
-AF078844	0,489716822
-MAN2A1	0,489875474
-IFT20	0,490824284
-USP21	0,490859618
-NOP2	0,491526918
-LOC440248	0,491905455
-LOC647070	0,493492979
-MAFF	0,494072026
-BG251521	0,495196452
-C6orf145	0,496322836
-MLL4	0,496324893
-ATF4	0,49676781
-RELN	0,497310216
-PELI1	0,497491599
-P2RX7	0,497499324
-CNOT2	0,498172475
-FAM38A	0,498599859
-DCLRE1C	0,498693515
-INSR	0,502304787
-MAPKAPK2	0,502573806
-NDE1	0,50267356
-MT1M	0,502716901
-CDK5RAP3	0,504041432
-SULT1A4	0,504805398
-NSUN5P2	0,505093708
-ANKRD10	0,505841449
-LOC339047	0,506042447
-LRRC1	0,506594446
-CUX1	0,507257715
-SRRT	0,508240438
-MAF	0,508625791
-EBLN2	0,509549245
-NM_017618	0,510705903
-RBM4B	0,51138423
-FBXW12	0,511744983
-ATP8B1	0,511969804
-NM_024978	0,512045897
-KCNMB4	0,512142959
-CLMN	0,512461537
-LOC100132540	0,512589899
-SERPINH1	0,513136463
-RHBDF2	0,513703735
-PCF11	0,514081494
-HAUS2	0,514694211
-TECPR2	0,514970535
-TNIP2	0,515014912
-AUP1	0,516155581
-KIAA0101	0,516801916
-N35922	0,51703624
-STK38	0,517483454
-AZGP1P1	0,518047589
-C13orf15	0,518310047
-PRR11	0,518691616
-PDCD6	0,51972326
-AFF1	0,520716014
-AF222691	0,521107674
-BE045142	0,521502008
-PACS2	0,521749261
-PSRC1	0,522634606
-ZNF358	0,523463012
-MAPKBP1	0,523696079
-S100A4	0,524041412
-MYO1C	0,524902669
-IRF3	0,52538788
-TOB2	0,526119659
-KLHL21	0,527145117
-PGF	0,527713686
-LOC399491	0,528407104
-ARAP1	0,528556373
-AZGP1	0,528659072
-SIRT7	0,528927974
-C16orf53	0,529668261
-KLHL2	0,533153888
-AK022213	0,533802801
-ANKRD28	0,534099367
-TF	0,536170201
-MAVS	0,53636005
-MSX1	0,536723495
-C12orf35	0,537890473
-AA554945	0,538449904
-SUN2	0,539191173
-RBM6	0,54218394
-AL080112	0,542349721
-SORT1	0,542569398
-AL049285	0,542660805
-FOXO4	0,542834527
-ABCA8	0,543725594
-RING1	0,54468938
-KCNE4	0,546337688
-TAZ	0,546506594
-DIP2A	0,546907877
-CLK4	0,548788669
-ZNF277	0,549312201
-MUS81	0,551193399
-DBT	0,556696292
-EMP3	0,557013195
-DDIT4	0,557077384
-RUFY1	0,557170712
-MYST3	0,559285285
-PRPF4B	0,559881298
-LOC100132247	0,562956585
-HSPB1	0,56508456
-CHD7	0,566776564
-CHORDC1	0,566831861
-COBL	0,569205746
-STAG2	0,569603186
-CTDSP2	0,570069613
-ZNF160	0,572703009
-PDE4C	0,574535337
-WWC3	0,575159977
-BMI1	0,576213767
-CRYAB	0,577245348
-AHCTF1	0,577515066
-ADIPOR2	0,5780263
-CASC3	0,57815663
-MUTYH	0,579456271
-AK023783	0,580340854
-HIGD1B	0,583663012
-PLOD1	0,587347495
-PRR14	0,587364521
-SH3BP4	0,58788373
-C19orf28	0,587956493
-NDRG1	0,588555643
-HIST1H1C	0,591446402
-TCF12	0,592176798
-MPST	0,593408757
-SEPP1	0,593935425
-DNAJB6	0,595685757
-SIRPA	0,596218961
-FLT1	0,597923318
-MYOT	0,598968138
-HIST1H2AC	0,600586387
-HBP1	0,600714263
-KAZ	0,601415288
-PTBP1	0,602313539
-NSUN5P1	0,603090503
-GUSBP3	0,604393039
-KCNJ2	0,616084197
-KAT2A	0,620256502
-MCM7	0,622618327
-FBXW4	0,627081137
-MKNK2	0,628440154
-IL17RB	0,631530593
-CLK1	0,632420317
-LRP4	0,632833859
-FAM53B	0,641895571
-JMJD6	0,64411039
-TYK2	0,644727629
-PLOD3	0,644893842
-CXXC1	0,650530485
-AK024136	0,659066605
-PAN2	0,66036619
-NPTX2	0,665210794
-SPEN	0,669461617
-SETD5	0,670191692
-STX10	0,674048462
-CDK2AP2	0,67411425
-PPM1B	0,68382966
-SLCO4A1	0,685048974
-GLT25D1	0,706365388
-ZC3H11A	0,716021559
-ZBTB16	0,720405109
-ZNF692	0,720940567
-NUPR1	0,724120307
-FLCN	0,747339708
-NFASC	0,755177517
+name	value
+GBE1	-0,943978048
+SLC18A2	-0,941309505
+KCNJ6	-0,894120983
+DLK1	-0,887122171
+PTDSS1	-0,851959645
+FGF13	-0,842876271
+PCDH8	-0,83524894
+ZNF226	-0,82900335
+SLC6A3	-0,824713365
+PIP5K1B	-0,812285785
+DENR	-0,81101551
+TPBG	-0,806963209
+PRKAR2B	-0,805288865
+OSBPL10	-0,80406299
+ALDH1A1	-0,795042129
+GGCX	-0,795035797
+ACP2	-0,794853979
+SLITRK5	-0,793842132
+FAM70A	-0,793715412
+HPRT1	-0,792370336
+CCNH	-0,790971864
+MYRIP	-0,78490295
+TUBB2A	-0,783142444
+ACTR10	-0,782043082
+BASP1	-0,778702387
+CADPS2	-0,777552826
+PID1	-0,775106213
+SV2C	-0,774895093
+RBM3	-0,77091551
+REEP1	-0,770000111
+RIMBP2	-0,766421185
+CNIH3	-0,765790316
+DMXL2	-0,765309344
+LOC10431	-0,762992699
+SV2B	-0,759985564
+AGK	-0,756506198
+RCAN2	-0,753762002
+LPPR4	-0,753018962
+RALYL	-0,75270126
+L1CAM	-0,751978689
+BCAS2	-0,751241508
+LOC100131795	-0,750350108
+TH	-0,748260596
+AV756161	-0,747351587
+TRIM36	-0,746057792
+MPPED2	-0,743864716
+NELL2	-0,742513977
+MAGED1	-0,739190733
+LRRC49	-0,738776851
+SYNGR3	-0,734846774
+ERC2	-0,734619705
+VBP1	-0,73223558
+UQCC	-0,729749962
+DCLK1	-0,725139215
+GSS	-0,724321987
+OPA1	-0,723790592
+PPP2R2B	-0,720892147
+COPS4	-0,720599852
+NSF	-0,720580224
+DLD	-0,72035948
+DYNC1I1	-0,719837984
+GABARAPL3	-0,717235008
+GPRASP1	-0,71302626
+NAP1L2	-0,712876929
+AMPH	-0,711957162
+PNMAL1	-0,70952389
+RGS6	-0,706463
+LDB2	-0,704777497
+TTC19	-0,704232585
+SCN3B	-0,703738866
+ATPIF1	-0,702603531
+BEX1	-0,700382911
+LMO3	-0,699029823
+TBC1D9	-0,698189481
+NDUFS1	-0,697230219
+INSM1	-0,696524737
+PARL	-0,696362568
+MRPL15	-0,688780959
+C3orf14	-0,687875821
+C19orf62	-0,687403479
+PCYOX1L	-0,686812669
+VRK1	-0,685016241
+MDH2	-0,684889561
+SMYD3	-0,684642724
+ASAH1	-0,68459801
+GSTA4	-0,684021936
+NDUFA9	-0,683116722
+ATP5C1	-0,682289667
+DDX25	-0,681511867
+GNG3	-0,681122999
+MUDENG	-0,67996077
+SCG2	-0,679728044
+MOAP1	-0,679575281
+SYT1	-0,678979261
+ATP6V1H	-0,6786546
+SHOC2	-0,677754756
+PCSK1	-0,677441918
+LBH	-0,67710638
+HK1	-0,676818391
+KIAA0319	-0,676346138
+SMAP1	-0,67618103
+EHBP1	-0,675429621
+RAP1GAP2	-0,673705297
+FABP7	-0,673485271
+LRRN3	-0,6731503
+AHNAK2	-0,672875949
+DHDDS	-0,671959403
+SNAPC5	-0,670824633
+C17orf108	-0,670563093
+AL390170	-0,67026906
+PTS	-0,669577055
+NUDT11	-0,668061506
+HMP19	-0,66794356
+IMMT	-0,667541939
+RGS4	-0,667109174
+RET	-0,667088994
+PBLD	-0,666164981
+AP3M2	-0,666056972
+WDR7	-0,665751643
+ATP6V0D1	-0,665487037
+RTF1	-0,664652469
+TUBB3	-0,664644351
+CHCHD2	-0,664529051
+DYNLT3	-0,663584428
+RAB6B	-0,662755469
+CHGB	-0,661865706
+NGFRAP1	-0,659441958
+AZIN1	-0,659394366
+EN1	-0,659313013
+SNX10	-0,659251628
+MIA3	-0,65882244
+ANK1	-0,657621479
+NR4A2	-0,65598531
+ANAPC13	-0,655864214
+RGS7	-0,654445938
+NME5	-0,652754395
+TXNDC9	-0,652019899
+PPIP5K2	-0,651763237
+RFK	-0,651442652
+BE674466	-0,651048329
+PEG10	-0,650932122
+PIAS2	-0,650823358
+CUX2	-0,649970555
+SEPT6	-0,649422911
+FKBP1B	-0,649416387
+C12orf10	-0,648407487
+HMGCS1	-0,648164918
+WDR61	-0,648133373
+GFPT1	-0,647751981
+MLLT11	-0,647471245
+AGTR1	-0,645674318
+CSNK1D	-0,645408463
+WDR47	-0,64495088
+PSMD14	-0,644669314
+CISD1	-0,643780748
+PSMD11	-0,642982055
+KCNS3	-0,642919136
+TIMM8B	-0,642730563
+RUNDC3B	-0,641744336
+ANKRD6	-0,640032629
+MDH1	-0,639623665
+STMN2	-0,639070421
+BAI3	-0,638894116
+STX12	-0,638382169
+NECAP1	-0,638376593
+NIT2	-0,638223243
+CIRBP	-0,637859912
+XK	-0,636787355
+KIAA1797	-0,636384728
+ICMT	-0,636379567
+GALT	-0,636138691
+SPINT2	-0,635454321
+PAIP1	-0,634724103
+TAGLN3	-0,63459569
+CADPS	-0,634245008
+GALNT11	-0,634168707
+SLC9A6	-0,632805526
+ANKRD34C	-0,63217094
+COPG2IT1	-0,63213856
+VPS4B	-0,63135628
+ATP6V0E2	-0,631164455
+SC5DL	-0,631137699
+CNPY2	-0,630875303
+GCC2	-0,630691438
+CRYZL1	-0,63015348
+MOBKL3	-0,630076244
+SNCA	-0,629316875
+STAM	-0,628134338
+TUBA4A	-0,627764216
+MAK16	-0,627148096
+FRY	-0,626684765
+UBE2V2	-0,626378865
+RWDD2B	-0,626170788
+FBXO9	-0,62572532
+FLJ41278	-0,6251633
+SLC30A9	-0,624759053
+LOC100132015	-0,623179237
+EXOG	-0,622056922
+RAP1GAP	-0,618803848
+DYNC1LI1	-0,618641756
+HARS	-0,618639749
+NDUFA5	-0,618245275
+SPCS1	-0,618130333
+PSMB7	-0,618122572
+NETO2	-0,618103081
+ATP5G3	-0,617855025
+UCHL1	-0,617452524
+FAM127A	-0,616124191
+TSSC1	-0,615619431
+CBLN1	-0,615519237
+CYB5R1	-0,615294192
+PSMG1	-0,61487171
+AKAP12	-0,614821543
+CYB561	-0,614281499
+KCND3	-0,613554227
+GABRB1	-0,613364723
+SLIT1	-0,613251897
+HN1	-0,612796898
+F8	-0,612749576
+VSNL1	-0,611517123
+ATP5A1	-0,611141848
+ARMCX5	-0,610703909
+AI097640	-0,610659067
+CERK	-0,610508368
+TMX4	-0,610174408
+TSPAN13	-0,609932725
+CAMLG	-0,609409157
+NDUFA7	-0,609351405
+STRAP	-0,609237631
+RTCD1	-0,607502869
+ORC5L	-0,606910471
+SCG5	-0,606870723
+HSPA12A	-0,606863939
+VAV3	-0,606070683
+TUBB2C	-0,60582666
+DCTN2	-0,605238426
+OCRL	-0,604661192
+HPCAL4	-0,604023171
+ARL1	-0,604008234
+CDK14	-0,603712397
+TLK1	-0,603591955
+BLVRA	-0,603201697
+NEFL	-0,602887281
+SLC25A32	-0,602708801
+ATXN10	-0,602624835
+UQCRC2	-0,601726567
+SLC25A3	-0,601470752
+MYL12B	-0,601373186
+CDS2	-0,601292766
+DDC	-0,601079077
+BSCL2	-0,6009448
+CACNB3	-0,598982611
+RIMS3	-0,598771066
+LASS6	-0,598387226
+FIBP	-0,598382328
+LRPPRC	-0,598144321
+PYROXD1	-0,598012671
+MAP3K9	-0,597438703
+CHL1	-0,5969101
+FJX1	-0,596748319
+PFN2	-0,596551333
+ATMIN	-0,59649395
+LIN7B	-0,596058244
+AV704232	-0,595274626
+PPP2R5C	-0,594797769
+SNAP91	-0,59414072
+AKT3	-0,593859242
+NDUFAB1	-0,593111219
+CCDC28A	-0,59307395
+GLOD4	-0,592429097
+STXBP1	-0,591440124
+HLTF	-0,591296161
+CRMP1	-0,590916915
+KIAA0513	-0,590696005
+GHITM	-0,590624599
+ATP6V1B2	-0,590367192
+USP14	-0,589739205
+RNFT2	-0,589705749
+SCG3	-0,589375952
+ATP5B	-0,588999541
+FAM136A	-0,588982627
+UBE2N	-0,588308222
+ANXA6	-0,588071667
+MRTO4	-0,58799806
+SNRK	-0,587183425
+CACNA2D2	-0,587134808
+IFT57	-0,586933566
+PPP3CB	-0,586906049
+RICH2	-0,586554767
+ME3	-0,586514247
+THOC7	-0,585617181
+FAM188A	-0,584083221
+EIF2B3	-0,582997986
+CNTNAP1	-0,582856877
+SCRN1	-0,582791752
+ACAT1	-0,582760841
+IDI1	-0,582694626
+PBX1	-0,582658829
+CDC42	-0,582658446
+NBEA	-0,582614884
+PPP1R2	-0,581839918
+ACTR6	-0,581817384
+TAF9	-0,581794162
+NIPSNAP1	-0,581711722
+SEC61A2	-0,58139821
+WDR37	-0,581272248
+VWA5A	-0,581248993
+CDC27	-0,580500838
+MYT1L	-0,580491453
+PSMC1	-0,580473356
+KATNB1	-0,578133005
+ZWINT	-0,577661475
+C12orf24	-0,577181135
+SLC25A46	-0,577144749
+DOLK	-0,576794187
+APOO	-0,576716633
+GCH1	-0,576494714
+TBC1D30	-0,575582077
+DCTN3	-0,575526778
+FBXL2	-0,575141782
+KIFAP3	-0,574923419
+CMAS	-0,574834972
+C18orf10	-0,574780811
+PNMA2	-0,574504978
+PDHX	-0,574434123
+SAMM50	-0,574204311
+NDUFA2	-0,574087728
+NPTN	-0,573534504
+HIGD1A	-0,573110642
+CYC1	-0,573010558
+HMGCR	-0,572959475
+TRAPPC2L	-0,572517332
+IMPA1	-0,572397104
+IMPACT	-0,572070372
+KIAA0802	-0,572067617
+DSTN	-0,571964512
+C5orf44	-0,571958339
+CCK	-0,571148184
+OGDHL	-0,571078621
+TCP11L1	-0,570951095
+RNF14	-0,569913578
+IARS	-0,569079443
+CDH8	-0,569072707
+RNF41	-0,568830451
+SCN3A	-0,568276898
+PSMD12	-0,567936617
+TNFRSF21	-0,567631199
+FIG4	-0,566751868
+DDX24	-0,566446037
+MARK1	-0,566206858
+ATP8A2	-0,565754513
+ACLY	-0,565055263
+DDX42	-0,564984354
+KIF3C	-0,564949485
+PIN1	-0,564290859
+PSEN2	-0,564206755
+TERF2IP	-0,564084181
+VDAC3	-0,563895581
+B3GNT1	-0,563686309
+CHN1	-0,563660153
+GLO1	-0,561564055
+RAB11A	-0,561549092
+PRPS1	-0,561391557
+MAP2	-0,561080301
+NHP2	-0,56096586
+DNAJA2	-0,560780556
+NDRG4	-0,560771764
+HNRNPA0	-0,560406816
+NDUFV2	-0,559975953
+ADH5	-0,559909821
+FAM3C	-0,559672666
+COPS7A	-0,559265307
+SULT4A1	-0,558733244
+MATN3	-0,558346148
+TMEM14A	-0,557817575
+HRASLS	-0,557799459
+TMEM14B	-0,557593404
+TTC1	-0,557573183
+R3HDM1	-0,557428266
+AUH	-0,55725646
+C5orf22	-0,55714645
+TUBB	-0,557095971
+C5orf13	-0,55663948
+COX7A2L	-0,556219721
+POMP	-0,556110434
+ATP5J2	-0,555267292
+ZNF204P	-0,555121445
+INA	-0,554984251
+NUP93	-0,55488654
+STAU2	-0,55454534
+VAT1	-0,554180752
+DDB1	-0,554146967
+THY1	-0,554057809
+SRPRB	-0,553818923
+IMP4	-0,553554219
+SRP19	-0,552319097
+FUCA1	-0,551919323
+PRKCZ	-0,551777138
+CD2BP2	-0,55167071
+C12orf43	-0,551436389
+SUSD4	-0,55137396
+W88821	-0,551080268
+LSM4	-0,550328209
+SNAP25	-0,550276399
+ACSL6	-0,549806401
+MYH10	-0,549550685
+DDHD2	-0,548942799
+PRKACA	-0,548422775
+CHRNB3	-0,547701041
+NEFM	-0,547618123
+PLD3	-0,547495065
+GSPT2	-0,547329995
+ATP6V1E1	-0,546911033
+GABBR2	-0,546899558
+IPW	-0,546596796
+SCAMP5	-0,546380917
+RFPL1S	-0,545994554
+BSN	-0,545979557
+MAGI1	-0,54490486
+DRG1	-0,544733954
+PITPNB	-0,544704547
+LETMD1	-0,544636809
+AI263044	-0,544470885
+STOML1	-0,544383238
+GBAS	-0,544103215
+RAB3GAP1	-0,543092086
+ACTG1	-0,54300405
+PPME1	-0,542943175
+AFG3L2	-0,542490245
+DNAJC6	-0,541912283
+TUBA1B	-0,541625287
+ABCE1	-0,541581351
+ARF3	-0,541401116
+SRSF3	-0,54134715
+NEFH	-0,540578844
+ADK	-0,540377244
+TIMM17A	-0,540158649
+ELOVL6	-0,540054201
+FAM189A1	-0,539987546
+ATP6V1A	-0,539816156
+OAT	-0,53960074
+KIAA0284	-0,539436564
+SLC25A12	-0,538986194
+AP3D1	-0,538816413
+ISCU	-0,53848727
+CDH10	-0,538458105
+APEH	-0,538385859
+TMEM35	-0,537944022
+NDFIP1	-0,537769873
+U79277	-0,537586945
+SYNGR1	-0,53757151
+MEAF6	-0,537175986
+DNM1	-0,536361784
+DEF8	-0,536162488
+PDXK	-0,536128962
+RIT2	-0,536060129
+AACS	-0,535868362
+RAB3A	-0,535840143
+LXN	-0,535676847
+CCBL2	-0,53559953
+ATXN7L3B	-0,535570224
+RCN2	-0,535264733
+SDC2	-0,535187449
+NRXN3	-0,534911729
+SDC1	-0,534748047
+PSMD1	-0,534162775
+UBA5	-0,534098166
+PEX11B	-0,533915774
+RAP1GDS1	-0,533764019
+NUPL1	-0,533680375
+ARMCX1	-0,533607326
+SDHAP1	-0,533209621
+PJA2	-0,532853246
+ACOT7	-0,532662038
+SEZ6L	-0,532618647
+CELF2	-0,532603645
+CXorf40A	-0,532513065
+NDUFB5	-0,532279155
+GARS	-0,532224902
+NRG1	-0,532009485
+SEC31B	-0,53180843
+ME1	-0,531466374
+PSMD8	-0,531445018
+MSL1	-0,531268404
+PCLO	-0,531166247
+RAB14	-0,531006634
+MAGED2	-0,530858407
+EIF3K	-0,530846086
+MMD	-0,530845303
+MYO5A	-0,530805656
+NCRNA00094	-0,530597959
+KIAA1107	-0,53057188
+KIAA0564	-0,530294183
+PSMB2	-0,530140819
+C1orf114	-0,530111522
+GCLM	-0,529867963
+NDN	-0,529086871
+SRD5A1	-0,528786683
+DNAJB9	-0,528374918
+SLC7A8	-0,528181836
+CLIP3	-0,527794519
+NDUFB1	-0,527724864
+CLSTN2	-0,52726691
+C14orf156	-0,527148764
+CIAPIN1	-0,527136633
+ATP5F1	-0,527047789
+PSMB5	-0,526841307
+FAM32A	-0,526499611
+KIAA1644	-0,526147045
+RTN1	-0,526062751
+EXOSC9	-0,525622526
+PFKM	-0,525053758
+TCF25	-0,524910517
+ATP5O	-0,524889972
+PTPRN2	-0,524794642
+SNX4	-0,524373257
+ATP6V1G2	-0,524016622
+SLC35E3	-0,523930118
+SLC2A6	-0,52364368
+SUCLA2	-0,523588063
+PLCB1	-0,523263994
+TMEM30A	-0,521872901
+PDE4D	-0,521870014
+RAB5A	-0,521632556
+MAPK9	-0,521572661
+CAP2	-0,521120749
+RPS6KA3	-0,520660932
+GNAO1	-0,520506337
+PSMD6	-0,520132666
+TBCE	-0,519679173
+C9orf125	-0,519623009
+MN1	-0,51937171
+MFSD1	-0,51842841
+KIF3A	-0,518357676
+SHFM1	-0,517546292
+NRIP3	-0,516545986
+ANKMY2	-0,516365077
+CDK5	-0,516196782
+REEP5	-0,516165841
+SLC1A1	-0,516141732
+UBE2K	-0,516036367
+SMEK2	-0,515537555
+PI4K2A	-0,515462049
+TTC39A	-0,514924765
+GUCY1B3	-0,514788287
+QPCT	-0,514170797
+ST6GALNAC5	-0,514077764
+ATP6V1F	-0,513941613
+HSD17B12	-0,513489073
+PPFIA2	-0,51321383
+PLCH1	-0,512855521
+CNTN6	-0,512564243
+ENTPD6	-0,512350634
+ALAS1	-0,512141897
+RUNDC3A	-0,511994377
+PCMT1	-0,511547085
+IDS	-0,511290223
+PLEKHB2	-0,510964275
+CDO1	-0,510668427
+NDUFB6	-0,510219117
+COX6C	-0,509869079
+OPTN	-0,509603205
+PSMA1	-0,509510596
+STS	-0,509361214
+TIMM10	-0,509318807
+C1D	-0,509252454
+GAP43	-0,509215292
+CCDC6	-0,509150548
+TRIM37	-0,509012308
+ATP2B2	-0,508803511
+PGAM1	-0,50863259
+GGNBP2	-0,508616013
+SRP72	-0,508482078
+TCEAL2	-0,508464868
+SV2A	-0,508330914
+CDK5R2	-0,508227652
+FHOD3	-0,508155146
+FECH	-0,508046235
+ATP2A3	-0,507932978
+SUB1	-0,507787459
+ACO2	-0,507726776
+C20orf3	-0,507526055
+SEC22B	-0,507453281
+VPS35	-0,507278509
+MRPS33	-0,507141908
+TXNL4A	-0,50704416
+ARHGEF9	-0,506224253
+RBM9	-0,506096633
+TMEM135	-0,506088817
+UHRF1BP1L	-0,505757524
+ME2	-0,505446593
+BZRAP1	-0,505378895
+MCAT	-0,50534007
+AKAP6	-0,505213579
+COPS3	-0,505110121
+MRPS35	-0,505107922
+YWHAB	-0,505015581
+PEX7	-0,504955276
+COPS8	-0,504746043
+OXCT1	-0,504643125
+MAD2L1	-0,504589351
+MCTS1	-0,504510155
+LGALS8	-0,50448664
+ACP1	-0,504339709
+MX1	-0,50393674
+NCALD	-0,50389725
+TASP1	-0,503797818
+AGTPBP1	-0,503605082
+RNF128	-0,503554068
+PSMD13	-0,503503704
+TXN	-0,50336484
+NHLH2	-0,50325399
+USP12	-0,503149229
+PFDN4	-0,502988386
+NAP1L3	-0,502893901
+MRPL20	-0,502624211
+ACSL3	-0,502355771
+MTPAP	-0,502307088
+PMPCB	-0,502239978
+SH3GL3	-0,502227406
+API5	-0,502196949
+CAPNS1	-0,5020898
+YWHAZ	-0,501747483
+TOMM70A	-0,501591565
+STX18	-0,501503813
+HNRNPK	-0,501464694
+LRP1B	-0,501433491
+CDC123	-0,500993468
+DCTN6	-0,500740808
+VAPB	-0,500599356
+CCDC56	-0,499906136
+GOT2	-0,499477446
+RHEB	-0,499343134
+PSMD2	-0,499333749
+YPEL5	-0,49910251
+ATP5G1	-0,499077107
+TUBA1A	-0,498949544
+GSTM3	-0,498766376
+EPB41L1	-0,498605796
+EPS15	-0,498447403
+ENO2	-0,498261848
+ASMTL	-0,498100631
+FH	-0,498098378
+CLTC	-0,497596743
+PSMA3	-0,497405846
+UROS	-0,497291028
+OLFM1	-0,496832922
+ATP6V1G1	-0,496818916
+B3GALNT1	-0,496135395
+PHLPP2	-0,496077027
+TSPYL1	-0,495383913
+SERINC1	-0,49538338
+RPL15	-0,495355843
+ITFG1	-0,495195881
+PDHB	-0,494999933
+RABL3	-0,494855325
+TMEM22	-0,49462563
+MCFD2	-0,494506103
+GABARAPL1	-0,494373853
+MAGEL2	-0,493987847
+VPS33B	-0,493750355
+CDIPT	-0,493440531
+ATP6V0B	-0,493438352
+CLGN	-0,493358721
+SEC23A	-0,493255831
+C7orf43	-0,49286586
+ARL3	-0,492481932
+SLC12A5	-0,492392187
+LAPTM4B	-0,492348426
+LOC285359	-0,492290998
+LARP1	-0,49192011
+YME1L1	-0,491725992
+RAB2A	-0,491586306
+SPATA20	-0,490991626
+ASH2L	-0,490785052
+PTBP2	-0,490747846
+WTAP	-0,490599757
+NANS	-0,490410248
+SCFD1	-0,490269997
+EPB49	-0,489916122
+TUFT1	-0,489843226
+POP4	-0,489594415
+CACNA1G	-0,489236615
+PRPF19	-0,48917604
+NCOA4	-0,488872014
+C1orf216	-0,488856307
+TXNL1	-0,488777426
+AMPD2	-0,48875487
+ASL	-0,488300478
+PFDN1	-0,48807629
+EXTL2	-0,488020888
+RPA3	-0,48773487
+ACVR1B	-0,487609726
+ANKRD46	-0,487476076
+GRIA1	-0,48726366
+PSMB6	-0,487099126
+CAPRIN2	-0,486969775
+SRGAP3	-0,48684289
+ARPC5L	-0,486786621
+PSME3	-0,486309204
+NME2	-0,486066455
+ISCA1	-0,485683262
+ZNF365	-0,485504618
+PINK1	-0,485341061
+RWDD2A	-0,48504437
+EXOC1	-0,484927354
+ECE2	-0,484617735
+WDR77	-0,484600271
+AI890972	-0,484490353
+ERBB4	-0,484253264
+PSMD4	-0,483962197
+RAB6C	-0,483864006
+CSTF3	-0,483798153
+NIPA2	-0,483638091
+AK5	-0,483482302
+C17orf91	-0,483141592
+INPP4B	-0,482534933
+PJA1	-0,482372063
+BE551361	-0,482367089
+B4GALT5	-0,48224903
+MTX2	-0,481915827
+MGST3	-0,481667788
+TRMT11	-0,481613419
+PTPRN	-0,481522612
+DNAJC12	-0,48150495
+FTSJ2	-0,481162212
+CCT8	-0,48112028
+PGAP1	-0,481030935
+SLC25A44	-0,480898127
+AMIGO2	-0,480319409
+SCAMP1	-0,480275681
+RBKS	-0,480222
+SYN1	-0,48014199
+APEX1	-0,479680328
+AL157484	-0,4790893
+PAK3	-0,479026618
+SLC25A13	-0,478484409
+EIF1B	-0,478403329
+DLAT	-0,478235597
+AI375694	-0,47804406
+PMS2L1	-0,477748782
+DYNC2LI1	-0,477528415
+RANBP9	-0,477445784
+PTPN20A	-0,476653786
+ZMYM4	-0,476508652
+UQCRQ	-0,476353248
+EXOSC7	-0,476299374
+NDUFB3	-0,476207507
+LCMT1	-0,476121484
+ZNF547	-0,47597802
+TBCA	-0,475802982
+MAPK8IP3	-0,475554385
+N80935	-0,475378775
+SLC4A3	-0,475327531
+AASDHPPT	-0,475086681
+CAND2	-0,475049952
+CXorf40B	-0,474988185
+FXYD6	-0,47456179
+RNF10	-0,474499733
+ELOVL4	-0,474412575
+AAK1	-0,474378982
+SEH1L	-0,474159291
+PTPRU	-0,473978747
+LPGAT1	-0,473432618
+VPS24	-0,473360696
+MCF2	-0,473341916
+FAR2	-0,473007144
+CKMT1A	-0,472884518
+TMED3	-0,472883274
+RNASEH1	-0,47283341
+NDUFA3	-0,472657747
+GLS	-0,472644869
+FAM168A	-0,472617309
+KLHDC10	-0,472577269
+GLRX5	-0,472478522
+SYT17	-0,472292582
+PAM	-0,472018566
+CLTB	-0,471770785
+COPS2	-0,470912718
+DDA1	-0,470419616
+PCSK2	-0,470372976
+SLC25A6	-0,470332168
+TPI1	-0,470300584
+MECR	-0,47026417
+ORC4L	-0,47025895
+ITPR1	-0,470228063
+HMG20A	-0,470060529
+GNB5	-0,470039178
+TMEM208	-0,469963608
+NCAPG	-0,469752447
+GLRB	-0,469638821
+ATP6V1D	-0,469577982
+AKAP11	-0,469501191
+SH3GL2	-0,46948768
+NISCH	-0,469445416
+SIPA1L1	-0,469275377
+PFKP	-0,469125064
+LYRM4	-0,469088537
+SLC4A1AP	-0,46898494
+AP2A2	-0,468669242
+CX3CL1	-0,46850557
+WBP11	-0,468444743
+LASP1	-0,468444317
+GOT1	-0,468375399
+C6orf120	-0,468133996
+SPAG7	-0,468070563
+SERGEF	-0,467688975
+TFB2M	-0,4675501
+AP3B2	-0,467537408
+PAFAH1B1	-0,467362101
+BPGM	-0,467130793
+CRAT	-0,466839519
+DDX1	-0,466770911
+ADAM23	-0,46652833
+ASB6	-0,466473575
+PCDHA1	-0,466456945
+TUSC3	-0,465574044
+TCEA2	-0,465512943
+SMARCA4	-0,4653413
+DAPK1	-0,465142929
+DBNDD1	-0,464965333
+NDUFC2	-0,464959656
+IDH3B	-0,464778307
+CDC37L1	-0,464692992
+WDR11	-0,464429092
+CD200	-0,464378251
+TUSC2	-0,464289641
+IRGQ	-0,464009317
+CALY	-0,463919598
+NNT	-0,463872117
+MSH2	-0,463745236
+GYG1	-0,463657489
+FAM134C	-0,463380379
+RTN2	-0,463379977
+RBM12	-0,463289569
+SYNJ1	-0,463207762
+ABCA5	-0,462881594
+ENTPD4	-0,462777994
+MAP2K4	-0,462732144
+AIMP2	-0,46256199
+PITPNA	-0,462484131
+BNIP3	-0,461982272
+COPS5	-0,461956463
+BRE	-0,461910476
+MIR21	-0,461667267
+ATP5S	-0,46152488
+SIN3B	-0,461515059
+NAT10	-0,461457105
+MTCH2	-0,461117099
+ACHE	-0,461032229
+PSD3	-0,46079613
+UCHL3	-0,460466303
+SMPX	-0,459975528
+USP11	-0,459753441
+RNF187	-0,459566796
+AAGAB	-0,458932639
+ENY2	-0,458770966
+NDEL1	-0,458614173
+FAM184A	-0,458384449
+TOX4	-0,458204483
+SLC25A15	-0,458110832
+SACM1L	-0,458050139
+ADARB1	-0,458034616
+SPHK2	-0,457781426
+CES2	-0,457687554
+CYFIP2	-0,457201169
+KPNA2	-0,457034156
+ACTR1A	-0,456856222
+SLC25A22	-0,456321526
+DPYSL3	-0,456025294
+PRKAR1A	-0,455984698
+SIDT1	-0,455560984
+TIPRL	-0,455474112
+EIF5	-0,455347544
+C16orf58	-0,455176502
+RAB7A	-0,454946879
+MFSD6	-0,454914435
+NDUFS2	-0,454605666
+APOOL	-0,454580027
+GNB1	-0,454284789
+SARS	-0,454282127
+PIK3R3	-0,454240907
+SERINC3	-0,454097365
+ST3GAL5	-0,45407104
+DHRS11	-0,453695947
+NEDD8	-0,45367218
+RAB15	-0,453664346
+HSPA13	-0,453577406
+OLA1	-0,453153228
+C3orf18	-0,45312023
+AF131844	-0,453027105
+C12orf52	-0,452914604
+ACBD3	-0,452894377
+PCIF1	-0,452240197
+BMP2K	-0,451224584
+TSPYL5	-0,450674174
+SEC63	-0,450642641
+C7orf44	-0,450408444
+PWP1	-0,450360796
+SLC25A14	-0,45012674
+SYP	-0,449768016
+PRKCB	-0,449564151
+KIF2A	-0,449276369
+PEX26	-0,449100108
+SDHA	-0,448617251
+PITRM1	-0,448602767
+PPA2	-0,448269554
+MAN2A2	-0,448177121
+FAM49A	-0,448170721
+KCTD9	-0,448062861
+REEP2	-0,44801948
+NDUFS3	-0,447803075
+CHGA	-0,447356315
+UBE2E3	-0,447311178
+LOC595101	-0,447006376
+RNF170	-0,446698112
+TMCO1	-0,446651514
+PCCB	-0,446640741
+RAB1A	-0,44645249
+ATP1A1	-0,446309137
+KIAA1045	-0,446174802
+CASD1	-0,445992918
+C3orf37	-0,445975885
+RAD17	-0,445659766
+BBS4	-0,445631347
+TBC1D19	-0,445509157
+TSG101	-0,445289202
+DKK3	-0,445181251
+KCNQ2	-0,444911548
+EIF4E	-0,44477948
+LOC100134209	-0,444742688
+OSTF1	-0,444651424
+PPCS	-0,444330494
+ATP13A2	-0,443924538
+DHRS7B	-0,443866868
+TSN	-0,443785273
+AI201594	-0,443780197
+UBE2J1	-0,443536878
+C12orf51	-0,443320039
+INPP5F	-0,44324612
+KIAA0391	-0,443138749
+NDUFB8	-0,442168118
+COX8A	-0,442151263
+PLCB4	-0,442128902
+UQCRC1	-0,442055114
+RNMT	-0,442010619
+PSMB4	-0,441631296
+ATP9A	-0,441570839
+COMMD8	-0,441419712
+STX7	-0,441415012
+UQCRFS1	-0,441387219
+ARMC8	-0,441335025
+USP33	-0,441131902
+SC4MOL	-0,441051846
+AVL9	-0,440604375
+CORO1C	-0,440555184
+ATP6V0A1	-0,440500219
+AKTIP	-0,440321706
+C11orf49	-0,440065839
+ACCN1	-0,439959618
+DYNC1H1	-0,439954428
+RTN4	-0,439926435
+IFT52	-0,439664934
+ARIH1	-0,439616652
+SLC23A2	-0,439279622
+FDPS	-0,439263979
+ZW10	-0,439088192
+C6orf211	-0,438493952
+CAPZA2	-0,438442617
+TRIM9	-0,43841496
+PANK2	-0,438226487
+SLC25A36	-0,437878589
+TM7SF2	-0,437751686
+GPD1L	-0,437274057
+TM2D3	-0,437156245
+TBC1D22A	-0,436837159
+AFF2	-0,436678505
+PSMA4	-0,43652406
+SCAPER	-0,436328183
+KPNB1	-0,43624217
+C8orf33	-0,436164892
+RRAS2	-0,435924543
+PNMA1	-0,435862986
+DRD2	-0,435854058
+CCDC92	-0,435740221
+CYB5B	-0,435703661
+DNM1L	-0,435497666
+FAM98A	-0,435109538
+CYCS	-0,43500707
+UBE2B	-0,434857087
+DCTPP1	-0,434751269
+ENC1	-0,434576571
+SAP18	-0,434463135
+MED7	-0,43446171
+UBXN6	-0,433506891
+MAEA	-0,433493136
+C20orf27	-0,433220759
+ARFGEF2	-0,4331108
+FKBP9	-0,433030189
+COQ10B	-0,432955202
+SNRNP25	-0,432902395
+PHKB	-0,432809153
+CETN2	-0,432732838
+PIK3R4	-0,432641256
+EFR3A	-0,432263211
+FAM162A	-0,432255742
+LOC732160	-0,432226821
+SRPK2	-0,432044566
+USP9X	-0,431489845
+DENND2A	-0,431031563
+PPP2CA	-0,430950806
+CHST1	-0,430892555
+OSBPL9	-0,430720865
+TPM3	-0,430527364
+UGP2	-0,430314768
+AL049387	-0,430134526
+ARHGDIG	-0,429952838
+GPR161	-0,429932801
+HGSNAT	-0,429440496
+TCEAL4	-0,429402449
+KHDC1	-0,429285977
+SPATA7	-0,428924113
+NIPSNAP3B	-0,428922472
+NHP2L1	-0,42870798
+BZW2	-0,428685674
+BZW1	-0,428658261
+ABCF3	-0,428526247
+PEX19	-0,428349422
+POLR2K	-0,42820853
+FAM134B	-0,428156057
+TUBGCP4	-0,428150919
+CSNK2A1	-0,427824997
+PPP2R5D	-0,427719013
+CEND1	-0,427667723
+RNF11	-0,427514623
+EBNA1BP2	-0,427275229
+SDHC	-0,42690156
+ATP6AP2	-0,426823582
+MAPK1	-0,426681157
+YTHDC2	-0,425950246
+ACTR3B	-0,425721173
+LRRC47	-0,424928312
+ANO10	-0,424906321
+MORF4L2	-0,424702281
+NAE1	-0,424669605
+GRSF1	-0,424576498
+UBE3C	-0,42455123
+RRM1	-0,424268285
+IARS2	-0,424201991
+HINT1	-0,423973896
+B4GALT7	-0,423964657
+OBSL1	-0,423852756
+RPH3A	-0,423713255
+PTPRM	-0,423526608
+TRAP1	-0,423405292
+GSTO1	-0,423136683
+PGK1	-0,423107749
+KCTD2	-0,423033005
+AKAP9	-0,423014145
+KIAA0090	-0,422971022
+NIF3L1	-0,422805913
+SAE1	-0,422487927
+TRAPPC4	-0,422454822
+UBE3B	-0,422322842
+MRPL13	-0,422291395
+ARF1	-0,422218883
+NCKAP1	-0,421739152
+COX11	-0,421717769
+XPA	-0,421552598
+FKBP11	-0,421544606
+ZFAND1	-0,42136139
+RUSC1	-0,421250909
+PSMC2	-0,42099626
+MCM4	-0,420976269
+HEXA	-0,420954607
+PDE4A	-0,420795908
+VPS45	-0,420785909
+OGFOD1	-0,420640442
+ADPGK	-0,420505817
+AP2M1	-0,420467875
+PSMD5	-0,420139323
+PGRMC1	-0,420109613
+CLASP2	-0,419942702
+CAMTA1	-0,419843296
+COX5A	-0,419753275
+BCAP29	-0,419678508
+C21orf59	-0,419586484
+INSIG1	-0,419347593
+NDUFAF1	-0,419256514
+SNCG	-0,419205938
+NCAN	-0,418993508
+SLC24A3	-0,418714364
+MAP2K1	-0,418679322
+BRCC3	-0,418660516
+MYCBP2	-0,418420128
+PREPL	-0,41818051
+TUFM	-0,418149804
+LYRM2	-0,41810337
+ORC3L	-0,417994092
+TSR2	-0,417894679
+SLC41A3	-0,41774061
+DZIP3	-0,417712026
+MRPS11	-0,417644175
+B4GALT6	-0,41761846
+CHD5	-0,417472
+TUBA1C	-0,417351982
+OTUB1	-0,41729395
+DCAF6	-0,417154254
+UQCR10	-0,417021115
+BEX4	-0,416948363
+RTN3	-0,416868526
+GOLT1B	-0,416408995
+MRPL3	-0,416396676
+DDX19A	-0,416375948
+C4orf41	-0,416356919
+SEMA3G	-0,416349944
+TUBA3D	-0,416216957
+B4GALNT1	-0,415958605
+TOR1A	-0,415819164
+SUPT16H	-0,415597727
+ACTR3	-0,415469056
+ABCB9	-0,415410201
+SERF1B	-0,415262572
+PSMC6	-0,415072747
+GALNT2	-0,414525722
+ARF5	-0,414370994
+TCEB1	-0,414262524
+FEN1	-0,414164817
+HS2ST1	-0,413801139
+FBXL15	-0,413238338
+ANAPC10	-0,413161353
+MAPK10	-0,413048251
+FGF12	-0,412576909
+GTF2B	-0,412561968
+CALM3	-0,412474461
+C12orf5	-0,412385409
+BTRC	-0,412323302
+UBXN8	-0,411884422
+G6PC3	-0,411853401
+MARK4	-0,411850043
+SDHB	-0,411814414
+FXC1	-0,411804756
+KIAA1467	-0,411406746
+COL4A3BP	-0,411372338
+MADD	-0,411317373
+SLC25A11	-0,411257994
+APBB3	-0,411242683
+LDHB	-0,411172229
+ENTPD3	-0,410988615
+CAMK2B	-0,410817586
+C15orf24	-0,410807275
+RAB11FIP5	-0,410722406
+C18orf1	-0,410410534
+IL13RA2	-0,410393436
+TMEFF1	-0,40994415
+TAX1BP1	-0,409905258
+ABHD11	-0,409662969
+SETD4	-0,409479623
+NARS	-0,409352949
+LOC441259	-0,409193342
+SMAD2	-0,408937637
+MAGEH1	-0,408820062
+LPIN2	-0,408744346
+WRB	-0,408371938
+HSPB11	-0,408269901
+COMMD9	-0,407620354
+RMND1	-0,407542555
+RBP1	-0,407484296
+TSPAN7	-0,407465467
+YKT6	-0,407243851
+ATP5L	-0,407238078
+STAT1	-0,407123963
+SPTAN1	-0,407085674
+SLBP	-0,407034029
+FAM115A	-0,407018502
+ATP1B1	-0,407007242
+GIN1	-0,406994648
+SLC25A4	-0,406703055
+RPAP3	-0,40653888
+ELAVL4	-0,406510215
+LDHA	-0,406394191
+GABRG2	-0,406143723
+ACOT1	-0,406088493
+LZTFL1	-0,406077259
+LARP4	-0,406073312
+PTPRG	-0,405852123
+DIRAS2	-0,405793372
+SNCB	-0,405789504
+CDS1	-0,405765281
+ARL2BP	-0,405758176
+BCL2L13	-0,405729545
+STAT4	-0,405634359
+C17orf75	-0,405632179
+ELAVL2	-0,405590653
+DNM3	-0,405342092
+SNX16	-0,404866663
+TACO1	-0,40485549
+HPGD	-0,404805074
+CHMP2B	-0,404775945
+DPP8	-0,404495701
+SYBU	-0,403649563
+CHP	-0,403478973
+GTF2H5	-0,403475179
+PPP2R5B	-0,403191055
+TRAK1	-0,402996995
+ACSL4	-0,402921692
+RABGAP1L	-0,402883713
+PSMB3	-0,402864552
+ASTN1	-0,402784524
+TIMM23B	-0,402679864
+NDUFC1	-0,402669713
+GPM6A	-0,402645229
+NCDN	-0,402391637
+TMEM183A	-0,402206694
+LACTB2	-0,402125728
+SFPQ	-0,401934429
+SLC1A4	-0,401903736
+LOC731884	-0,401617561
+TTC3	-0,401599425
+APBA1	-0,401587582
+FAM20B	-0,401527926
+ISOC1	-0,401479145
+TMEM70	-0,401425176
+GLUD1	-0,401204073
+NDUFA4	-0,401152135
+SHANK2	-0,401076931
+NDUFA6	-0,400922451
+FAM128A	-0,400907344
+TSNAX	-0,400758374
+BLCAP	-0,400561763
+WASF3	-0,400514139
+MTMR6	-0,400412018
+CBARA1	-0,399961135
+SMCR7L	-0,399645568
+REXO2	-0,399637796
+ASTN2	-0,399013865
+FBXO31	-0,398919379
+MRPS10	-0,398754479
+GNAL	-0,398117434
+RDH11	-0,398104472
+ANKH	-0,398086916
+EPHA5	-0,397910595
+DPY19L2P2	-0,397861593
+NRXN1	-0,39777997
+FOXA1	-0,397622781
+AGGF1	-0,397583973
+CLCN6	-0,397581706
+PRKAG1	-0,397496639
+GRM5	-0,397456403
+BCAT1	-0,397331444
+MAP1LC3B	-0,397317027
+HMGCL	-0,397130437
+IFIT5	-0,397045055
+FAM82B	-0,397007464
+TMEM189-UBE2V1	-0,39671729
+TMEM160	-0,396535704
+PIGZ	-0,396390486
+VDAC2	-0,3962914
+BCAP31	-0,396227306
+CUL2	-0,395939867
+C5orf30	-0,395902062
+VAMP4	-0,395520757
+CLTA	-0,395495699
+NOS1AP	-0,395452681
+YWHAH	-0,395414553
+AGL	-0,39537715
+PPIA	-0,395286888
+POLR2E	-0,395239973
+FAM190B	-0,395231307
+CAND1	-0,395218949
+DIABLO	-0,395167608
+FAM155A	-0,395099838
+FAM174B	-0,394929763
+ABCA11P	-0,394841999
+LMF1	-0,394801997
+EIF3I	-0,394774336
+RRAGA	-0,39363313
+SLC25A5	-0,39336993
+BTBD3	-0,393323586
+SLC38A6	-0,393193457
+TSPYL4	-0,39289974
+NDUFA8	-0,392898828
+ERI3	-0,392853573
+CDH11	-0,392815946
+VPS11	-0,392712183
+RPP40	-0,39270293
+SMS	-0,392616216
+USP4	-0,39251437
+RAN	-0,392486577
+SYT11	-0,392234251
+SEC23IP	-0,392233152
+SUPV3L1	-0,392124663
+TOX3	-0,392048323
+OSBPL3	-0,391742979
+ATP5J	-0,391738382
+APC	-0,391687772
+EIF2AK2	-0,391678642
+MPPE1	-0,391534871
+CHD3	-0,391021702
+BE858194	-0,390954653
+GPN2	-0,390821549
+TMEM97	-0,39059622
+BRF2	-0,390477924
+NSDHL	-0,390017568
+LOC654342	-0,389476483
+SATB1	-0,389035394
+RPP14	-0,388984247
+C16orf68	-0,388858051
+PHF14	-0,388842446
+CKAP5	-0,388699527
+MMADHC	-0,388406258
+MEST	-0,388313548
+UQCRH	-0,387974488
+GBAP1	-0,387823169
+PMPCA	-0,387778282
+TMEM41B	-0,387668262
+SCLY	-0,387620138
+OXA1L	-0,387520115
+CLPX	-0,387517816
+EML1	-0,387443167
+DPP6	-0,387318033
+FBXO3	-0,387294212
+GAPDH	-0,386769027
+ATP6V1C1	-0,386766958
+PRAF2	-0,386484628
+NAA35	-0,386425969
+EIF4H	-0,386302469
+SGSH	-0,386196526
+CLCN3	-0,386084887
+SMARCA1	-0,385880429
+FAM158A	-0,385760557
+AP3S2	-0,385712457
+EIF1AX	-0,385367803
+RNF115	-0,385287305
+GPI	-0,385266179
+SEC62	-0,385020013
+G3BP2	-0,384968143
+NDUFV1	-0,38487232
+C19orf42	-0,384758261
+BEND5	-0,384699839
+KCNAB2	-0,384620267
+EVL	-0,384619104
+MTMR9	-0,384460721
+SIRT3	-0,384239932
+CNIH	-0,383916854
+TOLLIP	-0,383913386
+C11orf2	-0,383735535
+NUDCD3	-0,383703548
+MED4	-0,383545823
+RABGEF1	-0,38353381
+PTN	-0,383407974
+GBF1	-0,383365739
+C1orf163	-0,383317238
+LOC100129361	-0,383315417
+CUL4B	-0,383032231
+OXR1	-0,382758654
+TRIM33	-0,382726006
+GPC5	-0,382713696
+C11orf51	-0,382673891
+MAN1C1	-0,382595078
+FGF9	-0,382294616
+SPOCK2	-0,382267861
+GLMN	-0,382038722
+MPP1	-0,381567886
+KIF21B	-0,381555674
+RND1	-0,381481938
+PEX1	-0,381462705
+C2orf34	-0,381417191
+OTUD3	-0,381344145
+MSRB2	-0,381206334
+CCDC85B	-0,38118283
+RGS3	-0,380621769
+SERPINI1	-0,380596066
+C14orf2	-0,380470075
+IDH3G	-0,380458518
+POLR2C	-0,380378788
+CTNNA2	-0,380377628
+XRCC6	-0,380295972
+EIF3A	-0,380281294
+CRBN	-0,380214781
+RPS6KC1	-0,3801397
+NUDT2	-0,380057201
+GOLPH3L	-0,379823471
+CSNK1A1	-0,379812095
+NDUFB2	-0,379757693
+FTO	-0,37940886
+SLC6A15	-0,379271656
+PCP4	-0,379256762
+NIT1	-0,37912136
+CCNC	-0,378699092
+DGKB	-0,378485235
+RANBP6	-0,377965444
+DNAJC8	-0,377764456
+MAPRE2	-0,377675379
+ARFGAP2	-0,377574006
+BDNF	-0,377511436
+HSD17B10	-0,376728332
+AKAP7	-0,376531212
+EHD1	-0,376479944
+PSMD10	-0,376243528
+FABP5L2	-0,376090187
+VAMP7	-0,376017526
+WBP4	-0,375749974
+MAP1B	-0,375485017
+SMPDL3A	-0,375390185
+GPR89C	-0,375362209
+SEPT2	-0,37512019
+GPX3	-0,374915078
+AARSD1	-0,374664572
+HSPA9	-0,37466397
+MAP1A	-0,374598439
+C16orf62	-0,374459363
+CARKD	-0,374388504
+ASS1	-0,374197776
+WDR12	-0,374046313
+ABHD14A	-0,37397421
+SPIN2B	-0,373568971
+RAB6A	-0,373528481
+PTPRF	-0,373483075
+RRAGB	-0,373427062
+STK39	-0,373365187
+COX7B	-0,373307822
+PDCL	-0,373110957
+ATP2A2	-0,373066228
+PPM1E	-0,37285382
+TRMT61B	-0,372798595
+C21orf33	-0,372766056
+MGMT	-0,372730061
+LPHN3	-0,372647138
+WBP2	-0,372385809
+ACSBG1	-0,372296169
+PGRMC2	-0,372287654
+LRRC20	-0,372239514
+AGA	-0,372171162
+NRCAM	-0,372117405
+FUT9	-0,372053568
+C22orf28	-0,371916518
+MRPS15	-0,371914782
+UFM1	-0,371876489
+CAMK2G	-0,371790847
+AVPI1	-0,371692415
+MAST2	-0,371637676
+PPP1R7	-0,371553142
+EEF1A2	-0,371514176
+ATP5D	-0,371416456
+EEF1E1	-0,37139203
+NLRP1	-0,371368381
+PMS2CL	-0,371209965
+CDK5R1	-0,371120209
+C2orf72	-0,371108998
+OAZ2	-0,3710748
+AL109698	-0,37073584
+INPP4A	-0,370700597
+ERH	-0,370513944
+CAMK1G	-0,370474818
+MED24	-0,370430566
+DMXL1	-0,370287216
+COMMD4	-0,370258812
+NOMO3	-0,370043447
+MORF4	-0,369691968
+ZNHIT3	-0,369651044
+GDPD5	-0,369635923
+CUL5	-0,369519961
+AP1B1	-0,369511443
+YARS	-0,369387873
+ABHD10	-0,36913324
+KCNB1	-0,369083149
+SKP1	-0,369015624
+FBXO28	-0,368924883
+ATR	-0,368436696
+TMED2	-0,368132686
+ARPC1A	-0,367983188
+PHYH	-0,367958422
+MRPL22	-0,367879083
+SRRD	-0,367868238
+WDYHV1	-0,367821841
+EIF3CL	-0,367732775
+HMGB3	-0,367450086
+DENND1B	-0,36732795
+ALDH5A1	-0,367318431
+CCNA1	-0,367103911
+FAM134A	-0,367014983
+DZIP1	-0,366778091
+WASF1	-0,366602553
+ATXN3	-0,366426778
+CCDC25	-0,3658102
+ERP29	-0,365799413
+IVD	-0,365499555
+SNX24	-0,365222253
+CDK20	-0,365176415
+TTC9	-0,365148586
+RBM8A	-0,36488846
+AMACR	-0,364562114
+TBPL1	-0,364450426
+PTPMT1	-0,364434415
+CANX	-0,364232908
+ELAC2	-0,364131757
+EIF2S1	-0,364109368
+AKR1B1	-0,363915593
+ACADM	-0,363858719
+RGS16	-0,363795844
+SLC20A1	-0,363602798
+MTUS2	-0,363384151
+ZMIZ2	-0,363364816
+NDUFS4	-0,363146027
+AW242701	-0,363104323
+SNAPC3	-0,363053639
+ENOPH1	-0,362868334
+LYRM1	-0,362706602
+TRMT12	-0,362561085
+BAALC	-0,362539013
+CHMP1B	-0,362404908
+ATP1A3	-0,362300724
+TOMM20	-0,362192747
+PEX14	-0,362047536
+EIF2AK1	-0,361934247
+CNNM2	-0,361790716
+PPOX	-0,361753445
+TAC1	-0,361655557
+GLRX3	-0,361266708
+OBFC1	-0,360197329
+MFN2	-0,360036589
+DGCR14	-0,359808857
+FAM175B	-0,359691136
+PARP2	-0,359639462
+GPR107	-0,359495249
+TUBGCP5	-0,35920098
+ENSA	-0,359186957
+UMPS	-0,358973056
+SSBP1	-0,358916914
+PFDN2	-0,358707301
+IFFO1	-0,35859667
+CCT2	-0,358497035
+PSMA5	-0,358414139
+ZC3H15	-0,358397302
+EPHX2	-0,358269729
+CALB1	-0,358259257
+POP7	-0,358253841
+MRPL12	-0,357874032
+DFNA5	-0,357815106
+PIAS1	-0,357740062
+ARL4C	-0,35770713
+HRAS	-0,357592893
+CEP68	-0,35754909
+SNRPA1	-0,357535253
+SCP2	-0,357518758
+C4orf27	-0,356816465
+TMEM185B	-0,35662055
+SPAG16	-0,356585241
+ESYT1	-0,356493695
+PTP4A1	-0,356347412
+PDLIM2	-0,356333479
+MSRA	-0,355999453
+UAP1	-0,355870622
+CDK16	-0,355785531
+MBOAT7	-0,355761708
+FARSA	-0,355610517
+MRPS7	-0,355424517
+EPHB2	-0,355389176
+LOC729991-MEF2B	-0,355378273
+PDHA1	-0,355252318
+ACTL6B	-0,355166654
+SAR1A	-0,355144478
+KDM1A	-0,355067715
+PRDX3	-0,354963773
+ETF1	-0,354759299
+ARMCX2	-0,354758912
+IQSEC1	-0,35395949
+TIMM13	-0,353925241
+AP2B1	-0,353904118
+STYK1	-0,353863363
+CDK7	-0,353806664
+DLG3	-0,353783905
+SEPHS2	-0,353722454
+MTOR	-0,353463273
+PPIH	-0,353351383
+GRPEL1	-0,353254529
+C9orf91	-0,353075824
+RGS17	-0,353023569
+NTSR1	-0,352789658
+HNRNPH2	-0,352751195
+HCCS	-0,3526918
+C2orf3	-0,352661516
+TFDP2	-0,352647453
+GOSR2	-0,352396188
+PSMB1	-0,352279045
+MPI	-0,35224609
+DUSP26	-0,351953212
+HERC1	-0,351631367
+SORD	-0,351295095
+TUBB2B	-0,351140866
+LPCAT4	-0,351128323
+CFL1	-0,351124653
+ARPP19	-0,350935095
+MTMR4	-0,350923479
+COX7A2	-0,350878835
+PGM1	-0,350865278
+RHOQ	-0,350802567
+CCDC53	-0,350756677
+UQCRB	-0,350742301
+NAPA	-0,350657124
+CSDC2	-0,35061274
+BECN1	-0,350596093
+GYG2	-0,350535323
+GPKOW	-0,35045328
+FXYD7	-0,350387292
+CYLD	-0,349973469
+CSPG5	-0,349825086
+TTC15	-0,349816074
+ILF2	-0,349761198
+STOML2	-0,349586681
+CACNB2	-0,349516102
+VARS	-0,349372141
+ZSCAN18	-0,349241937
+PTRH2	-0,349224021
+P2RX5	-0,349175679
+RALB	-0,349042784
+NUBPL	-0,348899542
+NCBP2	-0,348786336
+DKFZp434H1419	-0,348772873
+UFSP2	-0,348370783
+ARHGEF17	-0,348050229
+FXR2	-0,34801331
+INSIG2	-0,347755165
+XRCC5	-0,347746659
+CLTCL1	-0,34759935
+TMEM177	-0,347585446
+VAMP2	-0,347189398
+EML2	-0,347084746
+SNUPN	-0,346850632
+GPX4	-0,346688538
+RASA1	-0,346685342
+USP46	-0,346590476
+LSM5	-0,346546029
+SEC31A	-0,34652486
+PALM2-AKAP2	-0,346447335
+CKAP2	-0,346385113
+ELOVL5	-0,346375127
+PMS2L3	-0,346133275
+PAQR3	-0,346117871
+ST8SIA3	-0,34604187
+FDX1	-0,34603415
+C12orf4	-0,345989709
+COQ7	-0,345988262
+UROD	-0,345987158
+RPE65	-0,345902642
+DCK	-0,345889475
+RARS	-0,345819092
+CAPZA1	-0,345775372
+NRN1	-0,345693574
+RNF7	-0,345545425
+ABAT	-0,345474072
+CRY2	-0,345467057
+HR	-0,345290796
+CACNA2D3	-0,345213407
+TWIST1	-0,345148814
+P4HTM	-0,345112277
+GDI1	-0,344731063
+GRIA3	-0,344721718
+D4S234E	-0,344715573
+TMEM151B	-0,344385728
+MPHOSPH6	-0,344298044
+PYGB	-0,344201683
+MARCH6	-0,344086188
+AL050136	-0,343680587
+NDUFS6	-0,343667551
+TRAPPC9	-0,343555476
+PYGL	-0,343533875
+EFNB3	-0,343417492
+SCD	-0,343398039
+TFG	-0,342863204
+PPFIA3	-0,342761025
+SENP6	-0,342750174
+KCMF1	-0,342689973
+GNAS	-0,342684217
+MAPK6	-0,342588157
+PRMT5	-0,34246621
+SEPT11	-0,342460355
+MEIS3P1	-0,342265108
+FABP3	-0,3421554
+YIPF6	-0,3420929
+FABP6	-0,342074193
+SRSF9	-0,341825092
+AP1AR	-0,341737984
+PKNOX2	-0,341609179
+PAK6	-0,341535575
+PRKAA1	-0,341378959
+UBA3	-0,34130955
+OAZ1	-0,341251276
+EID1	-0,340941987
+MRPS28	-0,340842312
+AA890010	-0,340724739
+OSBP	-0,340497775
+ATP6V0C	-0,34047911
+ARHGAP24	-0,340414643
+PNKP	-0,340118439
+PSMD7	-0,340085658
+IPO9	-0,340071575
+ARF4	-0,339993296
+TERF2	-0,339818219
+SRSF2	-0,339525933
+PSMC5	-0,33950993
+TM9SF1	-0,339389717
+ACAT2	-0,339093022
+CDK8	-0,33909169
+KIAA0196	-0,338987444
+TFPT	-0,338941882
+TRPC4AP	-0,338718194
+TUBG1	-0,338211067
+SCN2B	-0,338080627
+MTHFD1	-0,338071854
+ATPAF2	-0,338050158
+IGSF1	-0,337997383
+RGPD6	-0,337877048
+C16orf45	-0,33773508
+C10orf76	-0,337659307
+UBE2A	-0,33762595
+PQLC1	-0,337612976
+SOD1	-0,337454918
+ARPC2	-0,337418781
+MEMO1	-0,33728488
+CSDE1	-0,337036578
+PHYHIP	-0,336992273
+LYPLA1	-0,33698776
+NDUFA1	-0,336883322
+MARCKSL1	-0,336747008
+DCTN1	-0,336745427
+COX6A1	-0,336728807
+DPM1	-0,336614034
+ELP3	-0,336602956
+LOC653566	-0,336555692
+COX7BP1	-0,336528019
+CAPZB	-0,336348777
+DCUN1D4	-0,335942405
+UCHL5	-0,335933871
+PSIP1	-0,335684272
+MRS2	-0,335589123
+RABGAP1	-0,335570544
+KCNA6	-0,335454989
+RAC1	-0,335429141
+ZMYM2	-0,33542626
+MRPL17	-0,335371398
+MLF1	-0,335274724
+RFC3	-0,33507418
+ARMCX3	-0,335005795
+GMDS	-0,334931775
+KIAA0317	-0,334922749
+CAMSAP1	-0,334678333
+LSG1	-0,334628714
+PNPO	-0,334625052
+THOC5	-0,334532053
+C11orf58	-0,334154436
+MTCH1	-0,334038037
+KAL1	-0,333848755
+OMG	-0,333590731
+KLHL7	-0,333537148
+TTPAL	-0,333489991
+GLA	-0,333336937
+SEZ6L2	-0,333262252
+SNURF	-0,333035272
+ARL6IP1	-0,332988884
+BFSP1	-0,332976059
+MAPKSP1	-0,332894473
+HABP4	-0,332672498
+SLC8A2	-0,332645114
+CKAP4	-0,332543738
+NPM1	-0,332250102
+CLSTN3	-0,332157745
+RUSC2	-0,33210981
+RCHY1	-0,331805148
+CACNA1D	-0,331681156
+ZFAND5	-0,331302172
+TACC2	-0,331046487
+CHCHD3	-0,331008486
+RGS2	-0,330792786
+LDOC1	-0,330775706
+BTN2A1	-0,33075204
+WDR45	-0,330593865
+W87688	-0,330499179
+YWHAQ	-0,330473094
+RAB3GAP2	-0,33029144
+HTRA2	-0,330240669
+SNRPD1	-0,330240562
+ANXA7	-0,330030639
+KIAA1024	-0,329770804
+RAD51C	-0,329735785
+PRPF18	-0,329474331
+CCT6B	-0,329361737
+ABCD3	-0,329205796
+PARN	-0,329139621
+APOL2	-0,328983174
+MRPS18A	-0,32863432
+RASL10A	-0,328581006
+COG8	-0,328398026
+ZNF512B	-0,327877848
+ATP5H	-0,327758416
+PRDM4	-0,327710757
+TSPAN3	-0,327644045
+EPB41L3	-0,327416874
+APLNR	-0,327394979
+TFR2	-0,327337619
+GADD45A	-0,327012981
+POLR3F	-0,326871651
+FASTKD3	-0,326789822
+TCERG1	-0,326746174
+VPS41	-0,326459968
+C17orf101	-0,325979143
+EXOC3	-0,325763291
+SLC25A17	-0,325666279
+GDAP1L1	-0,325526797
+HCFC1R1	-0,325022815
+SF3B5	-0,324878766
+TEX10	-0,324812522
+PSMA7	-0,324673715
+TCTN3	-0,324389244
+NOVA1	-0,32437578
+RABEPK	-0,324366299
+ALG5	-0,324335095
+ENOSF1	-0,32427768
+SH3BGRL3	-0,32409913
+CTNND2	-0,324002004
+NKRF	-0,323983769
+SLC6A1	-0,323833407
+MAPK1IP1L	-0,323722226
+RAB22A	-0,323713658
+GRP	-0,323354345
+SDS	-0,323335387
+IBTK	-0,323304602
+CARS	-0,322679359
+WWP1	-0,322463311
+ARL8B	-0,322442301
+SLC19A2	-0,322361872
+F8A3	-0,322202521
+LPHN1	-0,322183082
+SMARCD3	-0,322148361
+GPN1	-0,322024809
+FAF2	-0,322014431
+SLC35B1	-0,321878066
+MPV17	-0,321698226
+TOM1	-0,321634922
+NEDD4L	-0,321518057
+MRFAP1L1	-0,321393672
+C6orf62	-0,321303598
+POLR3B	-0,321247444
+HTR2A	-0,321189596
+CUL3	-0,321141566
+PSMD9	-0,321108014
+LRP3	-0,32099653
+TMEM62	-0,320873847
+PLS3	-0,320803014
+SUMO1	-0,32076762
+DLG4	-0,320617015
+ANKRD17	-0,320557554
+ARFIP2	-0,320500236
+HMGN4	-0,320196335
+PRKAG2	-0,319945607
+STAR	-0,319749743
+NF1	-0,319726773
+ATOX1	-0,31967306
+UBE2M	-0,319629201
+NDRG3	-0,319446308
+SNPH	-0,319396594
+TPD52	-0,319178712
+PLK2	-0,319120325
+C1QBP	-0,318975829
+SRSF8	-0,318843616
+USP22	-0,318806098
+GPD1	-0,318728943
+MAPK8IP2	-0,318691894
+USP20	-0,318610382
+RPA2	-0,31845096
+CCPG1	-0,318358561
+NQO2	-0,318256129
+POLR3C	-0,318231923
+HBXIP	-0,318079181
+MRPS31	-0,318018334
+SNRPB2	-0,31801084
+CACNG3	-0,317104885
+CCNE1	-0,316783937
+NDUFAF4	-0,316755785
+GRK6	-0,316405946
+ZER1	-0,316363024
+CHCHD7	-0,316179658
+C20orf29	-0,315860291
+AI693193	-0,315746456
+TPMT	-0,315745725
+TPPP3	-0,315557058
+CTH	-0,315210231
+HSDL2	-0,31516145
+MAPRE3	-0,314964867
+NLE1	-0,314918022
+ARHGEF4	-0,314777145
+STK19	-0,314737564
+AW503390	-0,314280211
+KIAA1279	-0,314104435
+CA14	-0,313849822
+CYP2E1	-0,313441486
+FHL1	-0,313417456
+MYL6B	-0,313075964
+PACRG	-0,3129322
+SCN2A	-0,312912414
+POLR3G	-0,312898745
+MED6	-0,312862133
+PCSK1N	-0,312861133
+FLJ10038	-0,312756044
+PHTF1	-0,312716368
+PRPF4	-0,312654478
+RPRD1A	-0,312642779
+HLF	-0,312545473
+MTMR1	-0,312535102
+MFN1	-0,312461722
+C1orf50	-0,312398425
+QPRT	-0,312349796
+ZDHHC6	-0,31229266
+ITGAE	-0,311863717
+SLC18A1	-0,311739998
+CD83	-0,311711539
+GGCT	-0,311631664
+KIAA0100	-0,311503156
+OPN3	-0,311374884
+SSX2IP	-0,311111099
+NUCB2	-0,31105706
+UTP11L	-0,311015852
+GOLGA8B	-0,310924837
+UST	-0,310734373
+PRKCI	-0,310493775
+AP2S1	-0,310480065
+WBSCR22	-0,310476192
+PPP3CA	-0,310434457
+PDSS2	-0,310396648
+PEG3	-0,310335546
+ATP5E	-0,310319916
+GABRA5	-0,310200087
+AGPAT4	-0,310173061
+PDCD10	-0,310157516
+DDOST	-0,310094837
+RPL23	-0,309992315
+HOMER1	-0,309485866
+C1orf123	-0,309187816
+POLE3	-0,309012195
+DDX41	-0,308923345
+HSD17B8	-0,308824584
+GMPR2	-0,308792858
+SCARB2	-0,308695909
+DGUOK	-0,308606021
+MAGEF1	-0,308535371
+FOXA2	-0,308348483
+GLS2	-0,308287643
+TBCC	-0,308286536
+FBXO41	-0,308255485
+SLC12A1	-0,308214984
+PELO	-0,308137793
+KCNE1L	-0,30811412
+RBBP4	-0,308007454
+UBL5	-0,307720013
+KLHL12	-0,307571676
+FTSJ1	-0,307464516
+ZFYVE16	-0,307366442
+PPT1	-0,3073579
+ZC3H13	-0,307293327
+DYRK1A	-0,307183877
+PHACTR2	-0,306935621
+SLITRK3	-0,306872073
+PI4KA	-0,306770561
+RNPS1	-0,306364972
+RALGAPB	-0,306086767
+BRP44	-0,305953308
+BNIP1	-0,305883874
+SUPT4H1	-0,305675152
+BCKDK	-0,30566687
+PLAA	-0,305619464
+ACTR2	-0,305363631
+PION	-0,305054773
+NFU1	-0,305010295
+CCT6A	-0,304801168
+KIAA0427	-0,304585348
+EHD3	-0,304533089
+FAM63B	-0,304437794
+STK25	-0,304425083
+POLB	-0,304419007
+MRPL35	-0,304416576
+UBE2Z	-0,3043165
+GSTZ1	-0,304133065
+AP3S1	-0,30395899
+SPATS2L	-0,303776395
+LOC729580	-0,303766036
+RALGAPA1	-0,303697943
+PUF60	-0,303647762
+DAP3	-0,303640732
+AHI1	-0,303570806
+UBE2NL	-0,303361552
+TMEM164	-0,303165514
+DOCK3	-0,303099341
+CADM3	-0,303050893
+ZNF219	-0,302968533
+PRKAR1B	-0,302898104
+DOK5	-0,302798088
+ORMDL2	-0,302372011
+ACVR2A	-0,302331205
+ALDOA	-0,30171568
+ATRN	-0,301666345
+COX7C	-0,301597748
+PRKDC	-0,301229867
+GNG10	-0,300757182
+SNX17	-0,300752701
+RBMS1	-0,300466996
+AJAP1	-0,300458474
+PREP	-0,300414848
+ALDOC	-0,300361514
+LAMA4	-0,300246196
+PI4KAP1	-0,300223018
+TMEM222	-0,30010369
+PIGB	-0,299980372
+SSSCA1	-0,29997354
+DCUN1D1	-0,299517655
+DLSTP1	-0,299414392
+ITM2B	-0,299325985
+AK025651	-0,299260618
+ACOT13	-0,299073057
+ZNF593	-0,298588283
+LOC100129250	-0,298385026
+H2AFY	-0,298292243
+IGF1	-0,298232454
+KIAA0368	-0,29819687
+FKBP3	-0,298122528
+C12orf49	-0,297820161
+PRKRIR	-0,297808472
+GLUD2	-0,297805688
+NBL1	-0,297799978
+PTPN4	-0,297657679
+LOC644617	-0,297586698
+IL33	-0,297538719
+CUL4A	-0,29730361
+SIP1	-0,297199387
+POLDIP2	-0,297140479
+EBP	-0,297109427
+FASTKD2	-0,296665172
+SMPD1	-0,296658212
+FAM55C	-0,296650198
+TRPV2	-0,296465177
+DOPEY1	-0,29633822
+SCYL3	-0,296201386
+UBL3	-0,296188632
+STK38L	-0,296164266
+APITD1	-0,296017845
+SFXN1	-0,295918484
+CPT1A	-0,295754312
+USP8	-0,29570338
+MRPS30	-0,295702739
+ATG7	-0,295335659
+C10orf88	-0,29514056
+PIPOX	-0,295018193
+RAC3	-0,294600261
+CIAO1	-0,294564961
+KLC2	-0,294523931
+LEPROTL1	-0,29448316
+ENDOD1	-0,294147277
+FEM1B	-0,294007766
+IRS1	-0,293342341
+CYP51A1	-0,293155923
+DYNLRB1	-0,292974645
+TOM1L2	-0,292906836
+TDP2	-0,292808809
+MRPL49	-0,292778686
+LRP8	-0,292767989
+MOSPD1	-0,292730297
+C6orf134	-0,29255632
+TRPC1	-0,29249815
+RASL11B	-0,292459191
+AL109671	-0,292334441
+TTC37	-0,292136499
+ODZ4	-0,292070818
+KIN	-0,291741417
+KPNA1	-0,291721639
+CAST	-0,291558763
+NDUFA13	-0,291524477
+AKR1A1	-0,29149158
+QARS	-0,29146477
+MRPS22	-0,29145846
+MMACHC	-0,291414294
+UBQLN2	-0,291358191
+PIK3CB	-0,291242041
+COX6B1	-0,291081182
+PDK2	-0,290962723
+RABGGTB	-0,290962562
+SR140	-0,290943983
+ATF2	-0,290881352
+FADS1	-0,290820194
+SRP14	-0,290691218
+RAD23B	-0,290632171
+AHCY	-0,290521401
+RINT1	-0,290502144
+SRP54	-0,290224786
+COX5B	-0,289972152
+NBN	-0,289962803
+DDX50	-0,289845246
+NUFIP1	-0,289611609
+HDGFRP3	-0,289540354
+HBA2	-0,289412602
+SRP9L1	-0,289377441
+ARFGEF1	-0,289327503
+FAM13B	-0,289118442
+DIMT1L	-0,288943725
+LPO	-0,28888192
+VPS28	-0,288730564
+SSR3	-0,28867602
+SEPT7	-0,288663677
+NARS2	-0,288651232
+EMG1	-0,288493971
+HSPA8	-0,288488899
+TBC1D13	-0,288209587
+TTC35	-0,288076299
+GTPBP4	-0,287916733
+SPG7	-0,287774853
+PAFAH1B3	-0,28772138
+MAPT	-0,28765216
+RERGL	-0,287509361
+HNRNPD	-0,287438947
+PLCL2	-0,287391702
+HLA-DPA1	-0,287200849
+CD55	-0,286966384
+IDH3A	-0,286870398
+STXBP5L	-0,286801199
+MAP3K12	-0,286334641
+PPP2R1A	-0,286259611
+TMEM126B	-0,286136364
+CDKN3	-0,286064506
+ABCC5	-0,286013319
+TMEM127	-0,285913561
+DNAJC2	-0,285585137
+SEC61G	-0,285583827
+SSR1	-0,285489405
+AIMP1	-0,285281231
+YTHDF2	-0,285194578
+FAM86B1	-0,285046154
+CTBP1	-0,285027477
+CHRFAM7A	-0,285001423
+SSBP3	-0,284934817
+MRPL46	-0,284930449
+TSPAN6	-0,284861931
+MYST2	-0,284824247
+GGH	-0,284817124
+PRKACB	-0,2847024
+C2orf47	-0,284692381
+NLK	-0,284579832
+ASNS	-0,28445955
+EXOC5	-0,28439526
+OAZ3	-0,284379411
+CTNNBIP1	-0,284364924
+PVR	-0,284070802
+C16orf80	-0,284019987
+UBE3A	-0,283816198
+EAPP	-0,28376748
+IGSF3	-0,283764031
+KCND2	-0,283569047
+FOXK2	-0,283286684
+SLC35A2	-0,283204451
+TBCB	-0,283168385
+SLC38A1	-0,283158141
+ACCN2	-0,283147998
+FAM149A	-0,283126904
+TIMM22	-0,283102824
+EIF4ENIF1	-0,28310048
+THSD1P1	-0,282819454
+MAGED4	-0,282562753
+CLASP1	-0,282510547
+C1orf61	-0,282424601
+C6orf106	-0,282397365
+WDR44	-0,282155933
+GNL3	-0,282115302
+RCBTB1	-0,28192202
+OSTM1	-0,281535242
+AGPAT5	-0,281510168
+PRNP	-0,281405094
+APPBP2	-0,281330465
+GAD1	-0,281295305
+NECAB3	-0,281056363
+ABCF1	-0,280961256
+DNAJC7	-0,280750506
+EPHB1	-0,280596899
+GPRC5A	-0,280368026
+HSPA14	-0,280049432
+CLPTM1	-0,280042656
+SGPP1	-0,27999737
+ABCG4	-0,279891909
+GFRA1	-0,279146972
+ATP5SL	-0,278849245
+CTSO	-0,278677227
+DCTN4	-0,278556645
+MAP2K2	-0,278535478
+ZNF423	-0,278503712
+FUS	-0,278285124
+ACTR8	-0,278282163
+PRR13	-0,278189761
+ZNF329	-0,278179162
+RNASEH2B	-0,278151755
+LOC284244	-0,278099761
+FAM117A	-0,277715513
+MREG	-0,277651168
+C2orf18	-0,277609469
+AW612311	-0,277599115
+SYNRG	-0,277434047
+SMARCE1	-0,277346186
+DNAJA3	-0,277188103
+PPP2R5E	-0,2770317
+TMCO6	-0,276951805
+C6orf35	-0,276886272
+DDX18	-0,276619655
+TTLL1	-0,276373935
+LANCL1	-0,276361838
+SNRPE	-0,276287655
+DTX4	-0,276233703
+IDH2	-0,276017451
+SACS	-0,275814599
+ABHD2	-0,275491786
+VAMP1	-0,275092752
+AGPAT1	-0,27504004
+TYMS	-0,274913065
+ZDHHC3	-0,27479568
+LMO1	-0,274566957
+UVRAG	-0,274559415
+HBB	-0,274385467
+PSMA2	-0,274273938
+CD24	-0,27422103
+GRAMD1B	-0,27394685
+PRC1	-0,27393137
+YARS2	-0,27376193
+SIGMAR1	-0,273597834
+CPEB3	-0,273534888
+ARMC9	-0,273442678
+DNAJC10	-0,273369377
+TM9SF4	-0,27326642
+RBX1	-0,273166064
+C13orf1	-0,273151402
+PDCD4	-0,273130523
+LUZP2	-0,272843047
+APLP2	-0,272609838
+USO1	-0,272598741
+SH3BP5	-0,272512602
+PPP1R11	-0,272494252
+PEMT	-0,272485616
+CDC16	-0,272287144
+LCMT2	-0,272235596
+DCX	-0,271983078
+DDAH1	-0,271924121
+UBE2D2	-0,271815552
+TANK	-0,271664689
+AW974666	-0,271662837
+USH1C	-0,271630244
+BDH1	-0,271624449
+B9D1	-0,271589518
+BRD9	-0,271105209
+USP7	-0,271052865
+TRIM2	-0,270764995
+PARK7	-0,270634786
+NSFL1C	-0,270597248
+COQ2	-0,269953826
+HNRPDL	-0,269787459
+NOV	-0,269731303
+SLC25A28	-0,269706278
+EXT2	-0,26958066
+VLDLR	-0,269148459
+SLC4A4	-0,268895862
+SMURF1	-0,268798637
+ORC2L	-0,268275919
+ZC4H2	-0,268056536
+SDHAF1	-0,267985583
+VDAC1	-0,267895013
+ALDH1A3	-0,267738476
+PNPLA4	-0,267586498
+HAGH	-0,267406111
+CNTNAP2	-0,267355858
+KPNA3	-0,267278305
+LRBA	-0,267216793
+DPYSL4	-0,267150239
+MCCC2	-0,26714725
+KBTBD4	-0,267031071
+DCTD	-0,267005887
+C1orf21	-0,266982234
+C2orf43	-0,26679916
+SF3A3	-0,266732334
+PTPN3	-0,266674559
+FBXO21	-0,26664933
+CCT7	-0,266615147
+CLNS1A	-0,266539743
+HAPLN1	-0,266160364
+SYT13	-0,26591944
+SENP5	-0,265695364
+HMGB2	-0,265556554
+CANT1	-0,265168032
+CGREF1	-0,265157579
+GRM1	-0,26510368
+ZFHX4	-0,265049797
+PVRL3	-0,264999073
+ADAR	-0,264636454
+TRIM3	-0,264561355
+ANP32E	-0,264413865
+PDLIM7	-0,264406742
+MLH1	-0,264377914
+PRKCA	-0,264376056
+CYB5R3	-0,264120933
+PDE1A	-0,263919942
+LOC100127998	-0,263915362
+WSB2	-0,263691169
+RPF1	-0,263404659
+CXCL12	-0,26333499
+TMEM66	-0,263285506
+EIF6	-0,263232223
+NFE2L1	-0,262789646
+KLHL20	-0,262772392
+PPM1H	-0,262689193
+PIN4	-0,262483899
+TUBA4B	-0,26241982
+ECT2	-0,262276809
+MGC5566	-0,261888759
+C9orf116	-0,261830489
+ASB1	-0,261751394
+ABCC8	-0,261735107
+ELOVL2	-0,261638578
+PHB2	-0,261466477
+ZNF580	-0,261379751
+DNAJC24	-0,261364702
+PSMB10	-0,261344946
+CSE1L	-0,261292597
+ANKRD27	-0,261154598
+TUBG2	-0,261047779
+C6orf162	-0,261001828
+AL034399	-0,260886813
+GLT8D1	-0,26052144
+SRR	-0,260520305
+MCC	-0,260395686
+COX4I1	-0,260324715
+SEP15	-0,260222524
+RNF103	-0,260210477
+ZNF576	-0,260159221
+MGEA5	-0,260092677
+RSL24D1	-0,259958151
+USP13	-0,25969613
+MLLT3	-0,259631882
+SRI	-0,259268888
+NCS1	-0,259133737
+MAPKAPK5	-0,259103348
+IQCG	-0,25908825
+FN3KRP	-0,258914892
+BCKDHB	-0,258870249
+GOLGA5	-0,258736414
+RDBP	-0,258483881
+SUPT7L	-0,258355414
+METTL1	-0,258206012
+CREB3	-0,258159408
+TMEM111	-0,258136123
+NRSN2	-0,257397396
+CNTN1	-0,257314074
+COX10	-0,257277055
+SERPINB9	-0,257269621
+MTF2	-0,256976969
+EDNRB	-0,25676028
+HSF2	-0,25652969
+POLR2L	-0,256424652
+TRIM58	-0,256294322
+DACH1	-0,256241463
+UEVLD	-0,256239024
+ATP1B3	-0,256215499
+SAP130	-0,256053262
+TRPC6	-0,255890704
+HERC6	-0,255794959
+NAV3	-0,255707496
+GOSR1	-0,25567987
+CNR1	-0,255506006
+PSME4	-0,25522233
+CAMKV	-0,254605479
+ADSL	-0,254512794
+BCS1L	-0,254298738
+CCNB1	-0,253924801
+SNX2	-0,253887319
+ASAP2	-0,25387509
+WDR70	-0,253565737
+PTPRE	-0,253309549
+SEPT5	-0,253058348
+SCML1	-0,253051964
+BCR	-0,252946659
+MAGOH	-0,252829021
+SEMA4F	-0,25277628
+CLIP1	-0,252764211
+JMJD4	-0,252747043
+ZMYND11	-0,25273006
+CPSF6	-0,252574141
+PTPRA	-0,252430519
+PLA2G12A	-0,252393049
+MXRA5	-0,252290125
+RFX5	-0,252264534
+WARS	-0,252174212
+HUS1	-0,252166663
+VCAM1	-0,251733145
+CEACAM21	-0,25171453
+RHOT1	-0,251514974
+EMD	-0,251327933
+TSPYL2	-0,251307071
+THNSL1	-0,25130438
+NDUFB4	-0,251250318
+CHMP5	-0,251232028
+SKAP2	-0,251185084
+LRPAP1	-0,251070101
+COMMD3	-0,251069448
+ROGDI	-0,250917557
+PPAP2B	-0,25089017
+ADSS	-0,250852878
+LGI2	-0,250809779
+CBX6	-0,250671998
+NELF	-0,250584567
+DENND5B	-0,250357567
+ATP2C1	-0,239139672
+SUMO2	-0,233193565
+KRAS	-0,208565613
+PEX3	-0,200767265
+PRDX2	-0,195371323
+PDCD2	-0,194653063
+TM2D1	-0,189207426
+KHDRBS1	-0,16653347
+KLC1	-0,156510024
+ANK2	-0,155852142
+HBS1L	-0,155006259
+NTRK3	-0,121314135
+PTPRO	-0,110200451
+PLEKHA5	-0,10184855
+GCOM1	-0,091608137
+TIMM8A	-0,084179504
+MKRN1	-0,074942655
+PLA2G4B	-0,068760926
+RUFY3	-0,059042335
+RIMS2	-0,057507607
+C21orf2	-0,054091983
+METAP2	-0,053236401
+LRRC40	-0,040678287
+RPL10	-0,034862755
+RIOK3	-0,033313025
+SYNCRIP	-0,027340658
+UNC45A	-0,021866459
+MPZL1	-0,020796077
+RANBP1	-0,01610173
+ITGB1BP1	-0,011025016
+UBC	-0,009666523
+RER1	-0,007044099
+PDS5B	-0,005231512
+NCAM1	-0,004638056
+LIMCH1	0,003894784
+VPS13D	0,014841215
+WDFY3	0,017457694
+MRP63	0,023151675
+TSR1	0,064261585
+GRB10	0,066410415
+FAM128B	0,074972161
+PAK2	0,079518764
+PKP4	0,080237181
+TMEM144	0,083124821
+C3orf63	0,086752023
+DDAH2	0,250378216
+AF238870	0,250544885
+PTMS	0,250667518
+JAG1	0,250675664
+RPL32	0,25075902
+UXT	0,250812127
+HSP90B1	0,250888984
+SS18	0,250904748
+RND2	0,250918958
+CLEC4M	0,250931594
+AU147194	0,251115897
+IL1RAPL1	0,251119435
+EPB41L2	0,251131328
+TFDP3	0,251241244
+GAL3ST4	0,251281983
+EDN2	0,251371356
+SFTPC	0,251372616
+TRMT61A	0,251534845
+GPR4	0,251535902
+KEAP1	0,251692277
+RNF122	0,251718243
+NOTCH2	0,251745042
+WDR1	0,251871256
+NFX1	0,252023298
+DOHH	0,252100123
+NES	0,252167647
+SRSF10	0,252172984
+AQP3	0,252182392
+LOC728412	0,252404082
+RCN3	0,252455902
+CSNK1G1	0,252462493
+KCNS1	0,252601737
+CCDC71	0,252614101
+JUND	0,252645305
+LYST	0,252718314
+TPCN1	0,252770336
+MTA1	0,252823052
+RIN1	0,252841454
+ATHL1	0,252944239
+FTSJ3	0,253136044
+SERPINA1	0,253202139
+STARD7	0,2533744
+MRPL34	0,253425868
+PPID	0,25344089
+SH3PXD2A	0,253534644
+UBA7	0,253547625
+RUNX1	0,253686159
+ARNTL	0,253823553
+STAT6	0,253840779
+CASKIN2	0,25393147
+NFATC4	0,253965486
+LILRB2	0,254041373
+PPP1R13L	0,254173566
+RAP1A	0,254249533
+OTUD4	0,254380531
+ZNF516	0,254390037
+ZC3H14	0,254430628
+BTD	0,254441889
+ABHD4	0,254494909
+MT3	0,254554667
+PTCH1	0,254572046
+CDC42EP3	0,254591236
+LOC150776	0,254715807
+PTGES	0,254816225
+TPM2	0,254867646
+TAGLN	0,254960085
+AL050032	0,254984309
+HPN	0,25500915
+FLNC	0,255046574
+GJB3	0,255060346
+RAB40B	0,255071999
+CST1	0,255226531
+FGF21	0,255229382
+AW574933	0,255334628
+FGF5	0,255461872
+CLCN7	0,2555275
+BAHCC1	0,255618646
+FANCA	0,255627746
+CYBA	0,255682121
+TIE1	0,255683605
+ANKHD1-EIF4EBP3	0,255707685
+CDV3	0,255740411
+COL9A1	0,255878907
+TTC31	0,256049153
+ZIC1	0,256075896
+CCDC121	0,256090992
+FUT4	0,256155794
+UCP3	0,256197327
+AU146391	0,25625958
+MMP2	0,256269664
+STXBP2	0,256386629
+TMEM87A	0,2564575
+FXR1	0,256493521
+RDX	0,256507051
+HPS1	0,256516919
+TRAM2	0,256517872
+HYAL2	0,256778041
+TNFRSF14	0,256783849
+NEK7	0,256861333
+AGRN	0,256876471
+SMC4	0,256895131
+GAS7	0,256949822
+PDE4B	0,256950938
+CHD4	0,256970114
+SPP1	0,257084517
+HECA	0,257172806
+NXF2B	0,257181225
+LILRA5	0,257188463
+SCAP	0,257267679
+SNX1	0,257354288
+GIGYF2	0,257400552
+CELF1	0,257407908
+HSD17B14	0,257420303
+DUOX1	0,25770603
+MRM1	0,257826185
+NBR2	0,257852879
+FAM176B	0,257955278
+SYNPO	0,257997864
+GPRIN2	0,258040238
+IER3	0,25816919
+ZNF506	0,258198461
+NM_016414	0,25824817
+VPS53	0,258358594
+PGPEP1	0,258378109
+GNL1	0,25847832
+OGFR	0,258496938
+CXCR2	0,258632799
+C1orf38	0,258857462
+RPL22	0,258901214
+NM_018041	0,259005358
+MYOF	0,259133176
+NGB	0,259197495
+CLIC4	0,259260666
+TBC1D9B	0,259295717
+KCND1	0,259337213
+RNASET2	0,259420675
+EXT1	0,259568659
+AQR	0,259572114
+VWA1	0,259618684
+MUC3A	0,259647513
+CAV1	0,259682957
+IRF4	0,259719685
+OR7C1	0,259728956
+SETDB1	0,259737838
+E2F6	0,259867146
+TFEB	0,259924981
+CPSF3L	0,26005015
+MARCH8	0,260576922
+MFSD11	0,260945964
+ETAA1	0,260954881
+SMARCD2	0,260999203
+RGS12	0,261024661
+CCNG2	0,261112401
+RPS8	0,261183649
+IL17RA	0,261275371
+NUDC	0,261284708
+ZNF133	0,261329337
+ATP13A1	0,261543252
+PICK1	0,26166607
+C20orf117	0,261682534
+GIPR	0,261728602
+HIST2H4B	0,261730186
+S100A11P1	0,261732522
+MARCH3	0,26174629
+ZBED4	0,261794357
+KHK	0,261822851
+SCAMP2	0,26194666
+AF070579	0,261954742
+TECR	0,261998101
+AK024915	0,262016665
+CASP7	0,262240261
+PDK4	0,262293861
+MYO7A	0,262479993
+TUBBP5	0,262483574
+TMEM143	0,262491406
+NAP1L1	0,262524812
+PLEKHB1	0,262542861
+ING1	0,262679424
+SPSB3	0,262786186
+C9orf167	0,262955615
+NTM	0,262977412
+FIP1L1	0,263199662
+FYCO1	0,26321575
+GGT1	0,263227324
+ALG12	0,263240056
+IGL@	0,263282588
+PPBP	0,263290228
+SNX13	0,263292989
+SRSF4	0,263309909
+CYTH1	0,263721364
+AL050035	0,263831657
+TRMU	0,263920451
+TIMP1	0,263959235
+RFNG	0,263965598
+HIP1R	0,264033626
+NR1H3	0,264039538
+NT5C2	0,264091319
+FNTB	0,264115077
+SAR1B	0,264175117
+GIT1	0,26420824
+RRAGD	0,264311012
+HAP1	0,26435511
+FLT3LG	0,264378926
+NM_018612	0,264421364
+SLC7A9	0,26447762
+GLTSCR2	0,264541217
+SUN1	0,264635751
+CEP152	0,264663399
+MBTD1	0,264688291
+SYT12	0,264690461
+ACTR5	0,264835312
+EIF4A1	0,264933012
+COX7A1	0,26511391
+CMTM6	0,265385079
+FAM102A	0,265449454
+AW970584	0,265532869
+FMO5	0,265619005
+N4BP2L1	0,26587536
+SPAG11A	0,265939376
+TGFBI	0,265987004
+RYK	0,266131346
+SERBP1	0,266135884
+AK021988	0,266152576
+NCAM2	0,266199101
+AK024995	0,266233606
+RAB9A	0,266259326
+SYNJ2	0,266313048
+PHLDB1	0,266315252
+PKN1	0,266439146
+MFAP3L	0,266558078
+PPFIBP2	0,266640652
+WBP5	0,266861878
+TMX1	0,266949292
+SLC6A12	0,267009029
+C3AR1	0,267017849
+CSRP2	0,267020264
+SP3	0,267034674
+ATN1	0,267069634
+GNB3	0,267107148
+TIAL1	0,267113358
+GPATCH8	0,267177985
+PMEPA1	0,267182372
+MAP2K3	0,267199274
+NM_018033	0,267304029
+WWTR1	0,267350058
+SEMA6A	0,267400431
+RBPJ	0,267426168
+AL049279	0,267438916
+IL1RN	0,267473934
+QKI	0,267577841
+SOX15	0,267588393
+DMTF1	0,267672579
+RPL19	0,267821304
+TRIM39R	0,267839755
+SLC26A6	0,267879749
+NM_025056	0,267969441
+BBS9	0,267969882
+M85256	0,26799656
+ADORA3	0,268097905
+TMEM176B	0,268515164
+SECTM1	0,268600799
+ST14	0,268612452
+ARHGEF18	0,268652414
+SIRT5	0,268726991
+MYBPC1	0,268763379
+RPL15P22	0,268793196
+SIGLEC15	0,268860828
+DNAJA1	0,26890035
+LMBR1L	0,269042598
+GIMAP4	0,269074847
+MFAP3	0,269075993
+ABCA6	0,269120338
+AW836210	0,26919833
+LOC100133772	0,269228182
+CHST4	0,269387102
+RNASEH2A	0,269387986
+RPL18	0,269450865
+RPLP2	0,269486597
+MEPE	0,269489799
+FAM106A	0,269545639
+GATAD1	0,269621956
+PPP2R3A	0,269725552
+MASP2	0,269836416
+MYO10	0,26992164
+PIGG	0,269941407
+SMG5	0,269952017
+IFI30	0,269956381
+AK025180	0,269971157
+AMD1	0,269982316
+LMOD1	0,270125966
+SNX15	0,270191178
+SCARB1	0,270338985
+SERTAD3	0,270373355
+MBD5	0,270430073
+SLC2A5	0,270454389
+ITCH	0,270468949
+ADA	0,270490353
+PWP2	0,270541137
+ARHGEF1	0,270572389
+C2CD2	0,270675538
+EIF1	0,27071329
+C1orf35	0,270772513
+IFI16	0,270855012
+LOC285830	0,270905428
+IL10	0,271025993
+MORC4	0,2712707
+CA11	0,271346355
+C5orf54	0,271348162
+C14orf93	0,271428228
+RPL17P7	0,271481741
+TMEM161A	0,271564557
+LRCH3	0,271627825
+DFFB	0,271779652
+BAZ1B	0,271859723
+DKFZp547G183	0,271894591
+RAB11FIP2	0,271895928
+PCK1	0,27194659
+TMPRSS5	0,27195628
+TIPARP	0,272078235
+UBE2L3	0,272125747
+ZNF672	0,272142507
+GALNT10	0,272151507
+EXD2	0,272173543
+KAT2B	0,272322281
+RPS11	0,27237174
+POLR2H	0,272422791
+IGLL3	0,272574443
+AA554430	0,272578205
+DOCK10	0,272578712
+DMC1	0,272606886
+CD40	0,272762332
+CDK11A	0,272811711
+UCKL1	0,272898303
+FAM125B	0,273084179
+UBXN7	0,273084433
+SMA4	0,273204796
+DYNLT1	0,273349219
+CTTNBP2NL	0,273380758
+HSPH1	0,273396703
+CYP39A1	0,273418193
+HOMER3	0,273432217
+RRBP1	0,273480926
+ATAD2B	0,27361049
+LGALS3	0,273847411
+LASS2	0,273913098
+ZNF451	0,273935073
+NXPH4	0,27404559
+C22orf46	0,274118605
+KDM4B	0,27422483
+GPNMB	0,274363725
+CYHR1	0,274415705
+CCDC9	0,274487483
+WWC2	0,274522318
+ZNF652	0,274533788
+ILK	0,274538403
+CTDP1	0,27455992
+LOC51152	0,274810051
+AL442084	0,274963062
+CPNE7	0,275259638
+CENPB	0,275294531
+TCIRG1	0,275300556
+PRPF40A	0,275423637
+ARHGAP17	0,27552534
+LOC100133811	0,275961848
+ADAM17	0,276019886
+CRISPLD2	0,276144309
+IFIH1	0,276175289
+LOC440434	0,276293985
+DCLK2	0,276369722
+MS4A6A	0,276482788
+VASH1	0,276499979
+SRSF7	0,276513035
+B3GAT3	0,276752575
+CALHM2	0,276762436
+MAP4	0,276867434
+DULLARD	0,27687625
+CTSS	0,276943812
+BAG3	0,277040195
+KRT8P12	0,277155277
+POLR2F	0,277193722
+CD14	0,277207134
+SF3B1	0,277255775
+EZH1	0,277320185
+MBD1	0,277342685
+MITF	0,277407356
+BAIAP2	0,277445862
+FCGR2B	0,277531437
+PAQR4	0,277547889
+NFATC2IP	0,277597337
+CAT	0,277600148
+TJP2	0,277610024
+CCNA2	0,277687494
+GEM	0,277887602
+C2orf54	0,277935237
+HIRIP3	0,278018588
+MCM3APAS	0,278082892
+CFB	0,278130274
+TAGLN2	0,278365668
+AK024851	0,278382784
+HGD	0,278585783
+NR2E1	0,278716062
+SEC61A1	0,278797194
+PDE4DIP	0,278806635
+FRMD4A	0,278822955
+RHOC	0,278842121
+UBTF	0,278963815
+NCOR2	0,279024257
+PPP6R3	0,279218049
+ALAS2	0,279327775
+SPSB1	0,279537438
+SGMS1	0,279545277
+TEAD4	0,279565374
+AK024897	0,27961031
+IRS2	0,279708094
+TRIM62	0,279977776
+AF308291	0,279984986
+AK022362	0,280079092
+KIAA0495	0,280115197
+CUL7	0,280170918
+PARD3	0,280192562
+NUP98	0,280376383
+DHRS4L2	0,280391865
+AK024093	0,280444114
+VEGFB	0,280560816
+PTEN	0,280592383
+NBPF10	0,280620974
+CASP1	0,280699269
+AK2	0,280734467
+MLX	0,280792537
+GNG11	0,280826824
+HNRNPM	0,280968313
+IL12RB2	0,28098376
+CDK18	0,28098866
+RARA	0,280998983
+GYPC	0,281028129
+PAK4	0,28104576
+SEMA3F	0,281239182
+BAT2L2	0,281335934
+BRD4	0,28139016
+PAOX	0,281415979
+SMAD3	0,281446531
+PIK3R2	0,281480063
+IFT122	0,281682471
+IRAK4	0,281825175
+RASSF2	0,281825652
+RPL13A	0,282085077
+ZNF22	0,282127023
+KDM4A	0,282136199
+CPM	0,282150511
+EIF2S2	0,282316006
+USP48	0,282335945
+CLCNKB	0,282422648
+C11orf61	0,282474246
+ANKRD11	0,282516441
+PTTG1IP	0,282619596
+SEC14L1	0,282620994
+DOCK6	0,282646645
+CARHSP1	0,28271852
+RRAS	0,282814195
+TRIM38	0,283129972
+PLA1A	0,283206252
+GAB1	0,283220235
+PDLIM1	0,283254227
+SSH3	0,283308195
+KLF9	0,283315657
+N4BP2L2	0,283629404
+TNS4	0,283667599
+C15orf28	0,28383226
+ANXA11	0,283988681
+TAF12	0,283993401
+SLC39A1	0,284190806
+SAP30	0,284320416
+RNASE4	0,284337811
+RPS28P6	0,28438483
+DDR2	0,284449824
+BMP4	0,284614799
+CEPT1	0,284615091
+ITPKB	0,284650775
+PLEKHF2	0,284678379
+AW974812	0,284683098
+PTCRA	0,284827371
+SETMAR	0,2848555
+SOCS3	0,284925858
+NM_014129	0,284930906
+MYO1D	0,285094554
+RBL1	0,28514691
+HN1L	0,285254673
+LASS4	0,285307965
+RPS21	0,285547221
+PPP2R1B	0,285765143
+NEO1	0,285937917
+SEC24C	0,286013109
+BCL3	0,286014454
+KCNMA1	0,286080656
+AL137590	0,286198689
+EDIL3	0,286207431
+ARHGEF16	0,286210956
+HCK	0,286227266
+GSTA1	0,286246055
+SLA	0,286356975
+UNG	0,286379363
+SP100	0,286388329
+PRSS53	0,28642638
+MYL6	0,286728542
+CDH5	0,286728949
+C10orf116	0,286730624
+GTF2IRD1	0,286882519
+POLH	0,286995879
+SFRS16	0,287066034
+TPM4	0,28709233
+ABCD4	0,287100216
+GLT25D2	0,287127854
+COL18A1	0,287131911
+NPIPL3	0,287424398
+C1orf69	0,287453135
+MTF1	0,287488427
+IGF2BP2	0,287555495
+PALLD	0,287872078
+RPS16	0,287887395
+CYP2C9	0,287955438
+SC65	0,288029122
+CRYBG3	0,288096904
+SHC2	0,288312879
+FLNA	0,288339801
+NM_014486	0,288348194
+ISYNA1	0,288383809
+PNO1	0,288506351
+GZMK	0,2886543
+ATG13	0,288748426
+NCOR1	0,288772721
+ZSWIM1	0,288892162
+GPM6B	0,28893274
+SNTA1	0,289049438
+RHOBTB1	0,289064808
+GGA1	0,289073087
+ATXN2L	0,289088819
+FAM46A	0,289172187
+ZNF532	0,289393934
+CD40LG	0,289400418
+ZCCHC11	0,289421485
+WDR5B	0,289498086
+EPN2	0,289629137
+WNK1	0,289684816
+ZNF408	0,289721753
+LHFPL2	0,290003635
+NARG2	0,290029081
+STYXL1	0,29008917
+YY1AP1	0,290249669
+CPOX	0,290281635
+IL11RA	0,290333682
+PAXIP1	0,290387596
+ZNF282	0,290414378
+C11orf95	0,290643441
+MERTK	0,290681835
+VPS13C	0,29069039
+RPS17	0,290756898
+NEIL1	0,290762184
+ZNF292	0,290850132
+NOSIP	0,290873511
+DNAJB2	0,290950763
+INPPL1	0,29102828
+ZFX	0,29106383
+SETX	0,291138151
+SLC25A37	0,291207794
+PCDHGA8	0,291472818
+TXNIP	0,291962928
+DDX27	0,291971417
+BG389073	0,29216848
+JTB	0,292275569
+RBM10	0,292352574
+RASGRF1	0,29242252
+SYNM	0,292474024
+EXPH5	0,292481151
+NPL	0,292494012
+CHKA	0,292519533
+MGA	0,292564204
+SOX10	0,292580481
+AK024185	0,292975066
+FAM120A	0,292996604
+PLXNB1	0,293000141
+BDH2	0,293071563
+JRK	0,293136106
+SLC11A1	0,293139917
+TM4SF1	0,293242649
+EDA	0,293286441
+CDK10	0,293299298
+HLA-E	0,293305618
+LOC642846	0,293349826
+GFPT2	0,293396887
+SENP3	0,293408144
+RPS3AP44	0,293415546
+C16orf88	0,293431615
+FAM60A	0,293472328
+RPL36A	0,293501288
+SERPINA5	0,293547044
+CNOT8	0,293568161
+KDM4C	0,293620372
+POU2F2	0,293815578
+C14orf139	0,293870806
+ZNF217	0,293937173
+NM_025042	0,294034268
+NNMT	0,294200775
+VEZT	0,294224684
+KIAA0754	0,294307773
+RBM28	0,294637248
+ITPR2	0,294711729
+PPPDE1	0,294796015
+KLHL28	0,294874305
+MGP	0,294956866
+LOC729602	0,295016892
+SRSF5	0,295036903
+ROCK1	0,295267164
+SS18L2	0,295271871
+LMNA	0,29532356
+ESRRA	0,295387708
+SNHG3-RCC1	0,295411716
+TAL1	0,295434654
+SQRDL	0,295470062
+TARDBP	0,295665655
+LMAN2L	0,295705138
+RIN3	0,295771443
+PSPH	0,29602696
+DGKD	0,296027908
+WHSC1	0,296067068
+SPRY4	0,296068122
+ADARB2	0,296162399
+ELF3	0,296200778
+TLE1	0,296292637
+ACAN	0,296375799
+AK022038	0,296556116
+IL1RL1	0,296721787
+OR2A9P	0,296898432
+NCRNA00260	0,296954725
+CAD	0,296976627
+PNRC2	0,297129071
+IQCK	0,297134521
+ACOX2	0,297377087
+APOC4	0,297497329
+DGKA	0,297541846
+ZBTB1	0,297547513
+PUS1	0,297622568
+C7orf64	0,297653213
+FBLN1	0,297723957
+SBF1	0,297752819
+TMF1	0,298582891
+IL1R1	0,298701666
+LILRB3	0,298823808
+FLAD1	0,298825369
+CD163	0,299040686
+TCL6	0,299056301
+FADS3	0,299096634
+LBR	0,299180453
+AL162044	0,299184427
+ZNF337	0,299271736
+AHNAK	0,299352615
+YY1	0,299417937
+HIPK2	0,299439852
+NAT15	0,299519834
+ANKZF1	0,299817611
+NECAP2	0,299838267
+MAP3K7	0,299838407
+SAMD4A	0,299863792
+WDR8	0,300094232
+ZNF24	0,300179611
+NR3C1	0,300200063
+FGF1	0,300357727
+NPC1	0,300564708
+LMO4	0,300573598
+TTLL5	0,300853453
+AL050053	0,300945526
+RSU1	0,300958049
+C15orf39	0,301123219
+SLC14A1	0,301147038
+ELAVL1	0,301190126
+SLC17A4	0,301215925
+FANCC	0,301274346
+LRCH4	0,301338927
+EGFL7	0,301340052
+C9orf3	0,301357727
+SRGN	0,301411135
+PLCL1	0,301576339
+MAN1A1	0,301613058
+S100A8	0,301917937
+W86781	0,301984854
+HIP1	0,302012828
+OR7A5	0,302027387
+PPP1CC	0,3020408
+CGGBP1	0,302058231
+CYP3A4	0,302333153
+GALNS	0,302376776
+NR0B1	0,302394827
+SMNDC1	0,302468654
+MGST2	0,302482901
+RPL12	0,302658969
+DMPK	0,302955014
+TNRC6B	0,30299615
+PPM1D	0,303104009
+EED	0,303134999
+STAG3L1	0,3031801
+TMCC1	0,303195736
+RPL13	0,303245467
+RBPMS	0,30326423
+ARHGAP10	0,303298204
+PLCB3	0,303300054
+XPO1	0,303410309
+MYO1F	0,30341788
+SRPK1	0,303531642
+ZCWPW1	0,303562617
+MTHFD2L	0,303678034
+FAM111A	0,303798707
+TTC38	0,304186409
+COL7A1	0,304295553
+C4orf19	0,304312458
+NGLY1	0,304332742
+HTATIP2	0,304339936
+IFNAR2	0,304414877
+CXorf1	0,304737703
+UNC5B	0,304789798
+YAP1	0,30479215
+PHC2	0,30485466
+FBL	0,304914384
+CDH2	0,304939032
+FXYD2	0,304942957
+ANKRD36	0,305000603
+KRT8	0,305028726
+DSCAM	0,30505625
+SMO	0,305151387
+FCGRT	0,305420183
+PAIP2B	0,305483478
+PABPC1	0,305528523
+PIGV	0,305604211
+BACH2	0,305697602
+PLGLA	0,305722503
+MORC3	0,305845022
+DIDO1	0,305996983
+PRPF38B	0,306041882
+TRMT1	0,306054262
+NFATC1	0,306233076
+AK021495	0,306242002
+GPR1	0,306335484
+STARD13	0,306369109
+CELSR2	0,306371185
+ZNF193	0,306396574
+ABHD6	0,306458055
+PLCXD1	0,306486283
+RPAP1	0,306695411
+AL050122	0,306737964
+DHRS3	0,306750918
+C1QA	0,306800137
+AF009267	0,30681596
+SETD2	0,307047565
+STX6	0,307184977
+TMEM204	0,307304516
+SMYD2	0,307490131
+BF942161	0,307560212
+SLC44A1	0,307685609
+ELF2	0,307698089
+AATF	0,307770923
+AV761453	0,307800442
+ACTN1	0,307927265
+AI523613	0,307943372
+SOLH	0,307971092
+ZNF410	0,308222237
+GOLGA4	0,308250269
+FLJ21369	0,308352331
+FCGR2A	0,308469725
+BRD7	0,308638563
+TLR2	0,308769609
+FTHL5	0,308790654
+SPOCK1	0,308861441
+LSM14A	0,308907157
+USF2	0,309161806
+TENC1	0,309220224
+EMP2	0,309252571
+BSDC1	0,309299474
+ZNF701	0,309462113
+PLIN3	0,309516744
+SORBS1	0,309562012
+FTL	0,309588981
+AGFG2	0,309634949
+UBR5	0,309647344
+MMP14	0,30965745
+SFRS8	0,309923113
+ITPR3	0,309975876
+PLK3	0,310097184
+NUP188	0,310124261
+CROCC	0,310245563
+CHSY1	0,310328559
+CTCF	0,310675097
+EDC4	0,310685915
+NFE2L2	0,31069885
+LILRA6	0,311008878
+SATB2	0,311055754
+GTPBP6	0,311254994
+TSPAN14	0,311316513
+C10orf18	0,31133762
+SECISBP2	0,311419174
+DHX34	0,311443077
+LSS	0,311450185
+CHI3L1	0,311532669
+PDGFC	0,311715929
+BMP7	0,311741682
+MBNL1	0,311755686
+DNA2	0,311841432
+COMT	0,312081286
+LOC100133005	0,312165679
+PTOV1	0,312192713
+LCAT	0,312407744
+LRRFIP2	0,312480817
+UCN	0,312589312
+AK024606	0,312655002
+MICAL3	0,312700621
+ROM1	0,31291043
+MED12	0,312925796
+CPNE1	0,313173908
+GBP2	0,313262095
+PELI2	0,313279559
+MLL	0,313398121
+HIF3A	0,313438743
+ST18	0,313449639
+AF131777	0,313643716
+CATSPER2P1	0,313785721
+ZNF302	0,314066212
+APBB2	0,314110219
+KIAA0907	0,31421022
+ZNF592	0,314679884
+HNRNPA1	0,314773035
+TSC2	0,314882123
+SFRS15	0,314884343
+ZNF835	0,314920694
+WDR6	0,314979423
+LOC729143	0,315037798
+PPARD	0,315048839
+U2AF2	0,315118843
+MGAT1	0,315269456
+ZNF44	0,315270856
+RPL36	0,315475789
+GRAMD3	0,315513449
+PTPN2	0,315554784
+AL080072	0,315635626
+C19orf2	0,315918303
+DNAH3	0,315930745
+ZNF146	0,316341954
+SMEK1	0,316538461
+MLXIP	0,31681421
+NMT2	0,316848231
+G3BP1	0,316864559
+DDX3Y	0,316997159
+STEAP1	0,317082981
+BC002629	0,317231764
+KDM2A	0,317406731
+TMEM39A	0,317430306
+C15orf29	0,317437851
+MACF1	0,317513626
+LOC391020	0,317572673
+SETD1A	0,317586539
+KTN1	0,317889697
+RUNX3	0,31809511
+NINJ1	0,318107478
+ARMC7	0,318150459
+BMP1	0,318194029
+DKFZP586I1420	0,318199121
+JARID2	0,318226296
+AW972351	0,318303541
+PAPSS2	0,31841091
+ELTD1	0,31845583
+ETS2	0,318667898
+CREB3L2	0,318705762
+DFNB31	0,31892768
+SERHL2	0,318966243
+C10orf26	0,319058163
+NM_030892	0,319421731
+WRAP53	0,319795295
+UBQLN4	0,319828198
+RALGDS	0,319938162
+PRKCH	0,320101043
+AU146983	0,320105843
+SLC5A3	0,32021553
+DUSP1	0,320239212
+NKX2-2	0,320312108
+C1orf183	0,320387827
+PCM1	0,320482282
+THRA	0,320531901
+NM_025028	0,320726138
+SIVA1	0,320736787
+TTR	0,320757249
+IKBKB	0,320778441
+ARID1A	0,321020715
+HDAC4	0,321059842
+ZFP36L2	0,321167918
+TMEM212	0,321179342
+AA443771	0,321214505
+AGAP5	0,32125931
+PIGA	0,3216713
+SFRS12	0,321704401
+LDLRAP1	0,321832456
+CCDC21	0,321857948
+SSFA2	0,321990716
+RAMP1	0,322050077
+FLJ10357	0,322160744
+LAD1	0,322322766
+RACGAP1	0,322340831
+NPIPL2	0,322616655
+CEP350	0,322648588
+CRLF1	0,322735059
+IGSF9B	0,322744338
+PLXND1	0,322801951
+MCL1	0,322913781
+ALMS1	0,32297709
+ZNF768	0,323059066
+RSL1D1	0,323228527
+C4orf34	0,323582139
+PNPLA6	0,323738553
+MAST4	0,323801655
+NME3	0,323835175
+SNHG3	0,32391938
+S100A12	0,324014586
+PPP4R1	0,32409634
+PLD1	0,324165096
+POLG	0,324186823
+NKTR	0,324203565
+ST3GAL4	0,324231325
+TMEM63A	0,324243134
+ST20	0,32438459
+RNF114	0,324406844
+HYI	0,324468621
+DUSP6	0,324699964
+NR1H2	0,324884332
+DVL2	0,324900869
+SRSF11	0,324979841
+CLK2	0,325170283
+MKLN1	0,325287178
+SCRIB	0,325320413
+KIAA0467	0,325541973
+DMWD	0,325745064
+KLHL23	0,32579572
+RPS6	0,325948088
+ZBTB17	0,326014408
+RAI14	0,326038467
+UBE2G2	0,326143089
+ZNF562	0,326186073
+EZR	0,326282578
+TRPS1	0,326283144
+HFE	0,326390644
+MED23	0,32658232
+DDX11	0,326766632
+SHMT2	0,326784725
+LRP5	0,326954416
+PTH1R	0,327100265
+LOC731602	0,327131294
+AA401963	0,327241371
+CDK5RAP2	0,327276136
+SERP1	0,327279991
+SLC1A5	0,327303416
+BGN	0,327370767
+HSD17B1	0,327475971
+AL390143	0,327497051
+DIAPH2	0,327617697
+PITPNC1	0,327719899
+SPRY2	0,327767132
+FZD7	0,327974293
+MAP4K4	0,328171238
+TNS1	0,328369107
+ZNF783	0,328517049
+M78162	0,328518574
+ADAMTS1	0,32853944
+FKBP5	0,328911405
+AGAP8	0,329115979
+PLEKHF1	0,329179433
+DNAJB1	0,329339376
+RBMS2	0,329438459
+HNRNPH1	0,329454824
+ULK2	0,329496298
+PAPD7	0,329501864
+SURF1	0,329547559
+W61005	0,329673439
+ZNF862	0,330131081
+GNA15	0,330266409
+CHD9	0,330273108
+DLC1	0,330294104
+TMEM2	0,330321664
+AK024879	0,330353812
+N4BP1	0,330435804
+SERF2	0,330633507
+SNRPA	0,330957742
+IRF8	0,33098543
+ABCA2	0,331251046
+NPFF	0,331328402
+CP	0,331565597
+AU144887	0,331713137
+AW851559	0,33185735
+TCF4	0,332062967
+ZNF354A	0,332076549
+TMEM92	0,332352956
+NFATC3	0,332386137
+SSRP1	0,332529738
+TCF7L2	0,332651908
+PIM1	0,332716071
+PIP4K2A	0,332914219
+EIF4EBP1	0,332959146
+LOC100132863	0,333054912
+MMRN2	0,333075923
+AU147295	0,333342973
+VIM	0,333356286
+C2orf67	0,333469715
+DNMT1	0,333550022
+CEP110	0,333679402
+BAZ2B	0,33371151
+KDELR2	0,333939841
+L3MBTL	0,334448273
+CDK19	0,334505985
+CYorf15B	0,334832089
+DDX17	0,334839203
+FKBP4	0,335166906
+STOM	0,335173644
+U82303	0,335241438
+LOC202181	0,335841121
+ATM	0,335893127
+STK3	0,335957389
+MID1	0,336166241
+IGFBP5	0,336454348
+PARP4	0,336459483
+EXOC7	0,336479503
+FANCG	0,336652927
+PHF2	0,336678654
+FBRS	0,33674511
+ANP32B	0,336836072
+NCK2	0,336876937
+CASP6	0,336920233
+ZBTB3	0,337122586
+DHFR	0,337448147
+APOLD1	0,337464001
+STAG1	0,337490482
+NM_024305	0,337551103
+SIGLEC8	0,337608204
+ERLIN1	0,337809212
+POLDIP3	0,337889824
+SPTLC2	0,33799094
+C7orf26	0,338204972
+UBE2D4	0,338265561
+MAP2K7	0,3384787
+MECOM	0,338508564
+DOCK1	0,339029429
+HS1BP3	0,339148762
+PRKY	0,339216015
+GOLGA1	0,33927478
+XPC	0,339433169
+PHF3	0,33953002
+HIC2	0,339768003
+C9orf7	0,340519877
+CTDSPL	0,340591645
+ZNF83	0,34077157
+PHGDH	0,340889735
+TMEM165	0,340978736
+CLN3	0,341078466
+AU147983	0,34113627
+PATZ1	0,341151411
+DIP2C	0,341390806
+RECK	0,341533646
+EWSR1	0,342003886
+SMAD7	0,342182186
+MTRF1L	0,34225773
+TJAP1	0,342452426
+PRKD2	0,342725824
+SPOP	0,343019265
+HLA-J	0,343028528
+PLXNB2	0,343103735
+FBXL14	0,343454364
+LAMA2	0,343637649
+RNF220	0,343845541
+CLK3	0,344164444
+STARD3	0,344187457
+OGT	0,345118989
+IFITM3	0,345141829
+HMOX1	0,345196784
+EIF2C2	0,34557825
+CCND3	0,345663426
+TGFBR3	0,345676022
+POLR2J3	0,345712548
+BCAR3	0,345713549
+C14orf147	0,34610842
+CLDN15	0,34616346
+TOP1	0,346179876
+RASL12	0,346286134
+MED13L	0,346369067
+SOS2	0,346799305
+SERPING1	0,347144597
+IER5	0,347279068
+TLE2	0,347426427
+LLGL2	0,347448236
+TMCC2	0,347500013
+PHF20	0,347602909
+SIRT4	0,347862165
+OSGIN1	0,348060574
+H2BFS	0,348076316
+NM_017756	0,348230007
+NCRNA00115	0,348422218
+MT1E	0,348733923
+NACC2	0,3488369
+NFIB	0,348943619
+AKR1C3	0,349206923
+ARPC1B	0,349407208
+NIPBL	0,349628117
+RPL11	0,349803207
+MSH6	0,350014407
+PTDSS2	0,350073646
+AL050145	0,350120404
+FAM107A	0,350271118
+CHN2	0,350358174
+DAPK2	0,350378033
+DLG5	0,350436992
+OPHN1	0,350596034
+C20orf11	0,351010126
+SLC35D1	0,35135795
+SELL	0,35142274
+FAM193B	0,351790995
+NM_024880	0,352020901
+RASGRP2	0,352114346
+CAPN3	0,352194849
+THOC1	0,352289646
+TAOK3	0,352396226
+FBXO42	0,352613215
+LARP6	0,352692849
+KLKB1	0,352702835
+METTL7A	0,352961228
+STIP1	0,352968743
+WIPF2	0,353085817
+FOXD1	0,353404764
+HSPB2	0,35378232
+ENGASE	0,353978221
+LAT2	0,354239264
+HIST1H2AH	0,354250391
+GSDMD	0,354483715
+TRA2A	0,354674037
+C19orf29	0,354762053
+BRPF1	0,355002213
+NUMA1	0,355146564
+SNW1	0,355320637
+SMARCC1	0,355374541
+ZNF175	0,35555253
+BATF3	0,355680727
+HIST1H2BC	0,35575565
+ERN2	0,356098991
+ZFR	0,356185362
+AW301806	0,356253591
+SMTN	0,356289422
+RPS6KA2	0,356774064
+MIIP	0,35685635
+ARGLU1	0,356919378
+CTNNAL1	0,357152141
+PCDH9	0,357228835
+LAS1L	0,357263917
+DOK1	0,358029668
+AFTPH	0,35852635
+ZNF143	0,358674337
+C11orf71	0,35888557
+MICALL2	0,359221642
+KDM6A	0,359260932
+CFH	0,359284568
+CEBPB	0,359516672
+MTUS1	0,359547348
+AW973791	0,359548173
+SERTAD2	0,359684853
+FGFR1	0,359721729
+KPTN	0,360479451
+NR2F2	0,361169645
+RGL2	0,361384531
+NM_014120	0,361482036
+TAF5	0,361611903
+ZC3HAV1	0,362177526
+BEST1	0,362248528
+TNFRSF1A	0,362724804
+CLIP2	0,363062238
+EHMT2	0,363078239
+IFITM1	0,363162265
+GCFC1	0,363190607
+PECAM1	0,363227012
+YES1	0,363556218
+ZFP36L1	0,363744573
+SBNO2	0,364095165
+RMND5A	0,364201024
+IL10RB	0,364481295
+CBS	0,364486163
+TBC1D2B	0,364503601
+C10orf10	0,36458821
+AU144530	0,365137826
+ZNF500	0,365202134
+ATP6V0E1	0,36527949
+SEPT8	0,365711052
+VCAN	0,365762437
+RPL36AP51	0,366073863
+RPL31	0,36613283
+TAOK1	0,36613666
+GCN1L1	0,366181489
+CALCOCO1	0,366300689
+GNA11	0,366387362
+SH2B2	0,366425408
+RREB1	0,367259867
+SLC35E1	0,3672965
+GPRC5B	0,367311931
+TCF7	0,367371063
+PDIA4	0,367810651
+ZNF34	0,367845233
+MBD3	0,36793004
+CXCR4	0,368041224
+C9orf114	0,368120984
+IFITM2	0,368313531
+ZNF665	0,368328536
+ZCCHC24	0,368368275
+LOC100133944	0,369022431
+CSDA	0,369150342
+AU148255	0,369666508
+CIZ1	0,369704457
+CRTC3	0,369792369
+CTNNA1	0,369962411
+RARRES2	0,37011032
+NM_025033	0,370246707
+VSIG4	0,370274949
+FAM48A	0,370421427
+ZDHHC11	0,370675656
+NPAS2	0,370715345
+ADH1B	0,370935809
+ACSL1	0,371025369
+C1orf63	0,371083889
+TYMP	0,371266716
+LEPREL1	0,371463494
+LAMB2	0,371472469
+MAFB	0,371542293
+AW971248	0,371589606
+BC003629	0,371603781
+FAM63A	0,371786321
+ABCA1	0,371992682
+IGF2R	0,37211512
+SOX13	0,372131188
+WAPAL	0,372391179
+ZFC3H1	0,372437982
+ZNF710	0,372493324
+HSPA6	0,37258644
+CCDC101	0,372823539
+BAZ1A	0,372824952
+AXL	0,372842922
+NPIPL1	0,372916072
+HDGF	0,372923023
+KHDRBS3	0,373093219
+MT1X	0,373144553
+MTMR15	0,373164421
+AF257099	0,373262757
+AEBP1	0,37342966
+KLHL25	0,373672957
+GJB4	0,37372121
+LUC7L3	0,374023648
+U79248	0,374142769
+LOC653562	0,374188384
+RBM4	0,374375075
+ABCC10	0,374890625
+CXorf21	0,374896996
+DAXX	0,374917403
+C1R	0,375063944
+TPST2	0,375279072
+KLHL24	0,375307199
+C7orf68	0,375539219
+ZCCHC8	0,375600764
+CASP4	0,375605037
+ETV1	0,37597402
+BIN1	0,376340315
+RGS19	0,376617752
+PKNOX1	0,377091746
+CTTN	0,377173864
+TRIP10	0,377452782
+ANGEL1	0,377498562
+PLIN2	0,377879768
+NM_025007	0,377942771
+PTMA	0,378229214
+S100A11	0,378255627
+AXIN1	0,378580893
+NPRL3	0,378633074
+PNN	0,378695864
+AV727934	0,378843386
+ANGPT2	0,37912784
+AK023918	0,379250766
+CNPY3	0,37927474
+AF130051	0,37947818
+TLE4	0,379880985
+PAPOLA	0,379974199
+ITGB5	0,380683545
+FAM38B	0,380693638
+PABPN1	0,380909515
+SLC6A8	0,38116858
+RYBP	0,38121367
+NASP	0,381229843
+FGR	0,381246748
+PER1	0,381695992
+CDR2L	0,381867955
+LRRFIP1	0,382075479
+HMHA1	0,382282948
+KIAA0485	0,382313718
+GUSB	0,38235255
+RPS17P5	0,38240934
+FXYD5	0,382563723
+RBL2	0,382697586
+RANBP10	0,382980904
+NEDD9	0,383084673
+MSL2	0,383144236
+FAM50A	0,383317183
+AL080232	0,383323554
+SPG21	0,383712061
+TPD52L1	0,384098652
+H2AFX	0,384141378
+SWAP70	0,384225003
+IVNS1ABP	0,384369268
+KDELC1	0,384542393
+MYL12A	0,384757468
+FOXO3	0,384856157
+MED13	0,385128516
+AL049252	0,38560217
+AF007147	0,385820993
+PAX6	0,385884587
+DNASE2	0,38591545
+SLC12A9	0,386200858
+SIRT1	0,38637719
+ARID5B	0,386492868
+MT2A	0,38656824
+SLC38A2	0,386710042
+GNG5	0,386756333
+SRRM2	0,386841072
+SERPINB6	0,386985458
+CC2D1A	0,387023088
+LRRC37A2	0,387067777
+CSF1	0,387071999
+RPL29P11	0,38708859
+SFRS14	0,387094074
+MYO9B	0,387103012
+AW972855	0,387241981
+TRIP4	0,387728627
+ZBTB40	0,387827711
+STARD8	0,387863703
+WBSCR16	0,387992811
+NXF1	0,388021286
+CTDSP1	0,38803541
+RSAD1	0,388042285
+SUV420H1	0,38833134
+CDKN1C	0,388508896
+NM_016415	0,388588403
+E2F4	0,388673603
+KANK2	0,388702219
+ZC3H7B	0,388980025
+ANGPTL4	0,389035415
+CRY1	0,389801967
+KIAA0556	0,389845114
+TBC1D16	0,390016803
+TCOF1	0,390109025
+ZFYVE26	0,390278079
+IFRD1	0,39034324
+EIF4B	0,390385914
+SMC1A	0,390525141
+SCIN	0,3907272
+MARS	0,391061966
+PTRF	0,391089965
+POLR2J	0,391514571
+APAF1	0,391530483
+ITPK1	0,3915415
+PNRC1	0,392133859
+CLIC2	0,392140808
+KIAA0913	0,392243895
+PRKAR2A	0,392619325
+PRKX	0,392750502
+SYDE1	0,392957216
+ACSL5	0,393140899
+LRP10	0,393162277
+LPP	0,393214983
+SNTB2	0,393383504
+NADK	0,393882671
+PCBP2	0,394206896
+N51370	0,394562467
+CLIC1	0,394663761
+CTBP2	0,394785714
+PHB	0,394929787
+BCL2	0,395102709
+TAF4	0,395492947
+LOC652607	0,395562084
+YBX1	0,396079328
+PRPF3	0,396609142
+SLC38A10	0,396741732
+ERBB2IP	0,396808535
+CFLAR	0,396840203
+TNFRSF10B	0,397091951
+PHC1B	0,397196351
+ARL17A	0,397406114
+ZBTB20	0,397424403
+REPIN1	0,397830532
+BE466926	0,397930108
+MT1P2	0,398055653
+ZNF778	0,398225613
+DICER1	0,398300689
+NM_018603	0,398329284
+RAF1	0,398631868
+MXD4	0,398685167
+FBXL7	0,398770393
+CALD1	0,399121196
+GSDMB	0,399246982
+ZCCHC2	0,399293751
+PODXL	0,399691684
+ACACB	0,400136922
+VEZF1	0,400413083
+PLEKHM1	0,401187317
+CSPG4	0,401646086
+ID3	0,40170175
+RBM41	0,401719975
+KDM6B	0,401885964
+PHF15	0,402522419
+LAMP2	0,402538077
+CDC14B	0,402583482
+HNRNPL	0,403044314
+SLC4A2	0,403448509
+DDX23	0,403953946
+TUBD1	0,40407115
+SLC16A3	0,404204458
+CAPN2	0,405022548
+CBFA2T2	0,40560438
+TCEB2	0,405769952
+HNRNPF	0,406126644
+MORC2	0,406182732
+FOXO1	0,406430281
+AI962978	0,406538883
+HP1BP3	0,406567553
+CBFB	0,406789498
+RBM14	0,406886421
+SFI1	0,407058786
+ZHX3	0,407089165
+KDM3A	0,407233406
+SIRT2	0,407341821
+ANKS1A	0,407373917
+TCF3	0,407442968
+NOTCH2NL	0,407672378
+EEF1D	0,407830724
+SOX12	0,408065349
+SLCO1A2	0,40820492
+HNRNPA3	0,408299868
+GTF2H3	0,408624789
+FZD9	0,408729069
+SAFB2	0,408755308
+APBA3	0,408834306
+ASCL1	0,409161488
+CG012	0,409559201
+WDR59	0,409606436
+LAMA5	0,409632505
+ZNF276	0,409730125
+ZNF395	0,410080702
+TIMM44	0,410223052
+BGLAP	0,410749324
+ZHX2	0,411039562
+CARS2	0,411302016
+SLCO3A1	0,411338796
+LOC442497	0,411765627
+FRYL	0,411842495
+CYP2J2	0,412070197
+ABL1	0,412522321
+INF2	0,412975218
+SGK1	0,413352645
+SFTPB	0,413789208
+TIGD1L	0,41383023
+RBCK1	0,414019825
+TRAPPC10	0,414285862
+DUSP7	0,414641136
+WSCD1	0,415016303
+DCP1A	0,415308358
+LPAR1	0,415365439
+RBBP6	0,415730871
+DONSON	0,416255506
+C16orf5	0,416258918
+NCOA1	0,416350707
+CFHR1	0,416440287
+AA126763	0,416566153
+LRRC32	0,416765832
+CP110	0,41732481
+LTBP3	0,417338221
+TDRD3	0,417356196
+HMG20B	0,417456909
+CDC42EP2	0,417645635
+TAF1C	0,417736819
+NM_013344	0,41778911
+VGLL4	0,417820331
+PHKA2	0,417904785
+KDSR	0,418009802
+RELA	0,418064238
+TBL1X	0,41814877
+SIAH2	0,418727849
+MYO1E	0,418747589
+HIST1H2BD	0,419127582
+AI744451	0,419208355
+PTMAP7	0,419537834
+ARID5A	0,419593497
+CYP27A1	0,420064872
+RAB13	0,420441013
+CPSF7	0,420526378
+CPT1B	0,420770156
+LRDD	0,420794327
+PILRB	0,421599366
+STAB1	0,421733406
+FCHO1	0,422126906
+ZNF32	0,422311821
+TBC1D3H	0,422328806
+C1orf66	0,42292679
+NM_025032	0,423323973
+AI732802	0,423584905
+PCID2	0,423787762
+POGK	0,423912669
+TMEM140	0,424587207
+TMC6	0,424604298
+AL080160	0,42490597
+AK021505	0,425024442
+SCD5	0,425610027
+RAD52	0,425956612
+AF116715	0,425960499
+DCI	0,425967692
+SFRS18	0,426091505
+HCG2P7	0,426136765
+ADORA2A	0,426366158
+NM_021651	0,426442506
+MID1IP1	0,426940092
+HNRNPC	0,427103695
+NM_025024	0,427155973
+AK024315	0,427460397
+AK021514	0,427966252
+SLC29A3	0,428138792
+NSUN5	0,428255135
+PHF10	0,428599049
+DAPP1	0,428626141
+TMEM109	0,428647746
+LOC91316	0,428742129
+ITGB4	0,42956266
+SLC30A1	0,429998682
+AW150065	0,430129937
+ZCCHC6	0,430267528
+ARHGEF2	0,430371137
+AK027193	0,43049002
+TRIM52	0,430535815
+MT1G	0,430767233
+NOTCH1	0,430849119
+ZRSR2	0,43114681
+RPS6KA1	0,43184981
+KANK1	0,432456197
+FURIN	0,432618855
+APOBEC3C	0,432749845
+ANKRD40	0,432772877
+TRIOBP	0,432900403
+ZNF384	0,433116555
+CDKN1A	0,43319672
+BTG1	0,433570541
+EPHX1	0,433658916
+CNOT6	0,434207544
+HSPA1L	0,434322364
+PKD1	0,434547199
+WAS	0,434717417
+RPL23AP32	0,434993767
+P4HA1	0,434997425
+MAX	0,435160002
+UIMC1	0,435278167
+NM_025120	0,435322168
+NCOA6	0,435700178
+TPD52L2	0,435768747
+BCL6	0,435938226
+AK024108	0,436355329
+C7orf23	0,436800978
+CDC42BPA	0,437074951
+CD59	0,437137855
+POLR1B	0,437227618
+TLR5	0,437498143
+HDAC1	0,437993569
+ARHGEF7	0,438071237
+AA045174	0,438161955
+TBC1D17	0,438488128
+PRELP	0,438518539
+GTF2H2B	0,438525643
+HIST1H2BK	0,43866778
+AU147851	0,438979485
+RBM39	0,439661925
+IQGAP1	0,439786742
+RPL18AP3	0,440613252
+LTBR	0,440721546
+RPL35A	0,441136859
+ARAP2	0,441441928
+ARAF	0,441560027
+MT1H	0,441587824
+LOC441258	0,442117007
+ZCCHC14	0,442132801
+IRF7	0,442147625
+NOL12	0,442203671
+PTPLB	0,442541309
+AI683552	0,442752948
+MYST1	0,442881562
+MXI1	0,443040642
+AW974910	0,443299524
+C1orf144	0,443500279
+KRCC1	0,444417306
+PIAS4	0,444438643
+SRSF1	0,444637015
+LRP2	0,444740953
+ZDHHC18	0,445392541
+SPN	0,445443935
+ST13	0,446667878
+PHF17	0,446746739
+NACA2	0,446876872
+SASH1	0,447285208
+CD22	0,44772036
+CSNK1E	0,447902552
+COL5A3	0,447933631
+MAT2A	0,448695587
+EFHD1	0,448820126
+MAP3K3	0,448963961
+BIN3	0,449317201
+LUC7L	0,449469644
+KIF1C	0,449622117
+RNF144A	0,450034368
+TULP3	0,450626451
+CDKN2C	0,450879897
+HSD17B7	0,451226227
+ACIN1	0,451331774
+PABPC3	0,451363083
+PHF21A	0,45139036
+HNRNPH3	0,451480034
+HIST2H2BE	0,452219911
+RRP1B	0,452597128
+SOX2	0,453132172
+ZNF444	0,453296716
+FAM13A	0,453547738
+JUP	0,453753674
+PODNL1	0,453854292
+MAML1	0,453885
+SNRNP70	0,45408945
+SDCCAG3	0,45464357
+PLGLB1	0,454722494
+CDH19	0,454754165
+HSPA1B	0,455063205
+ARHGEF10	0,455229121
+NFIL3	0,455469821
+NFKBIA	0,455577982
+XRCC2	0,455670024
+ACTN4	0,455764555
+PDS5A	0,456071133
+POU2F1	0,456120351
+VPS54	0,456318614
+BANF1	0,456451252
+PGCP	0,456765652
+RPL28	0,456867479
+ICAM2	0,457066169
+SNAP23	0,457069788
+SART1	0,457941993
+AK023891	0,458253977
+BANP	0,458588544
+MAP3K11	0,458968207
+EPOR	0,459463669
+FKSG49	0,459538011
+MT1F	0,459638951
+NM_014128	0,460468204
+AP1G2	0,460676306
+GAS2L1	0,461632768
+PHIP	0,462053958
+NOL8	0,462387404
+NM_017932	0,462395281
+RNF130	0,462894529
+ZMYND8	0,463309493
+AK024525	0,463401166
+TRIM28	0,463454342
+BCAT2	0,463509769
+TYRO3	0,463574548
+PHLPP1	0,463738295
+BST2	0,465024297
+PDGFRB	0,465034704
+AL049987	0,465336929
+AKAP8L	0,466278804
+TGM2	0,467555999
+CREBBP	0,467899354
+KIAA0894	0,468325808
+DDX39	0,468959477
+NCAPD2	0,468959537
+ALPK1	0,469621875
+TGIF1	0,469902489
+PPP1R14B	0,470121069
+PNMT	0,470291567
+NAA16	0,470467422
+ZNF611	0,470526774
+ZRSR1	0,470857426
+NPIP	0,472818474
+RBM38	0,473036567
+USP34	0,473278809
+TGFB3	0,474067001
+ITSN2	0,475328182
+CEBPD	0,475754278
+MCM3AP	0,476296498
+HAPLN2	0,476718109
+POGZ	0,477224004
+NR2F1	0,477556735
+GAS1	0,478628972
+SLTM	0,478903701
+ECE1	0,479007813
+CALCOCO2	0,47910558
+RXRA	0,479821295
+MEIS2	0,480178943
+CLEC2B	0,481843785
+AL049260	0,482481089
+CHST3	0,48259726
+COL16A1	0,483094975
+SLC25A16	0,483255606
+LHPP	0,48421483
+AF010144	0,484619234
+GTSE1	0,484629217
+MUM1	0,484956644
+TNXB	0,485246904
+PRINS	0,486032909
+ANKRD49	0,486282532
+PTPRK	0,486899575
+PPAP2C	0,487395433
+C22orf9	0,488987561
+KHNYN	0,489026627
+RAPGEF3	0,489474077
+AF078844	0,489716822
+MAN2A1	0,489875474
+IFT20	0,490824284
+USP21	0,490859618
+NOP2	0,491526918
+LOC440248	0,491905455
+LOC647070	0,493492979
+MAFF	0,494072026
+BG251521	0,495196452
+C6orf145	0,496322836
+MLL4	0,496324893
+ATF4	0,49676781
+RELN	0,497310216
+PELI1	0,497491599
+P2RX7	0,497499324
+CNOT2	0,498172475
+FAM38A	0,498599859
+DCLRE1C	0,498693515
+INSR	0,502304787
+MAPKAPK2	0,502573806
+NDE1	0,50267356
+MT1M	0,502716901
+CDK5RAP3	0,504041432
+SULT1A4	0,504805398
+NSUN5P2	0,505093708
+ANKRD10	0,505841449
+LOC339047	0,506042447
+LRRC1	0,506594446
+CUX1	0,507257715
+SRRT	0,508240438
+MAF	0,508625791
+EBLN2	0,509549245
+NM_017618	0,510705903
+RBM4B	0,51138423
+FBXW12	0,511744983
+ATP8B1	0,511969804
+NM_024978	0,512045897
+KCNMB4	0,512142959
+CLMN	0,512461537
+LOC100132540	0,512589899
+SERPINH1	0,513136463
+RHBDF2	0,513703735
+PCF11	0,514081494
+HAUS2	0,514694211
+TECPR2	0,514970535
+TNIP2	0,515014912
+AUP1	0,516155581
+KIAA0101	0,516801916
+N35922	0,51703624
+STK38	0,517483454
+AZGP1P1	0,518047589
+C13orf15	0,518310047
+PRR11	0,518691616
+PDCD6	0,51972326
+AFF1	0,520716014
+AF222691	0,521107674
+BE045142	0,521502008
+PACS2	0,521749261
+PSRC1	0,522634606
+ZNF358	0,523463012
+MAPKBP1	0,523696079
+S100A4	0,524041412
+MYO1C	0,524902669
+IRF3	0,52538788
+TOB2	0,526119659
+KLHL21	0,527145117
+PGF	0,527713686
+LOC399491	0,528407104
+ARAP1	0,528556373
+AZGP1	0,528659072
+SIRT7	0,528927974
+C16orf53	0,529668261
+KLHL2	0,533153888
+AK022213	0,533802801
+ANKRD28	0,534099367
+TF	0,536170201
+MAVS	0,53636005
+MSX1	0,536723495
+C12orf35	0,537890473
+AA554945	0,538449904
+SUN2	0,539191173
+RBM6	0,54218394
+AL080112	0,542349721
+SORT1	0,542569398
+AL049285	0,542660805
+FOXO4	0,542834527
+ABCA8	0,543725594
+RING1	0,54468938
+KCNE4	0,546337688
+TAZ	0,546506594
+DIP2A	0,546907877
+CLK4	0,548788669
+ZNF277	0,549312201
+MUS81	0,551193399
+DBT	0,556696292
+EMP3	0,557013195
+DDIT4	0,557077384
+RUFY1	0,557170712
+MYST3	0,559285285
+PRPF4B	0,559881298
+LOC100132247	0,562956585
+HSPB1	0,56508456
+CHD7	0,566776564
+CHORDC1	0,566831861
+COBL	0,569205746
+STAG2	0,569603186
+CTDSP2	0,570069613
+ZNF160	0,572703009
+PDE4C	0,574535337
+WWC3	0,575159977
+BMI1	0,576213767
+CRYAB	0,577245348
+AHCTF1	0,577515066
+ADIPOR2	0,5780263
+CASC3	0,57815663
+MUTYH	0,579456271
+AK023783	0,580340854
+HIGD1B	0,583663012
+PLOD1	0,587347495
+PRR14	0,587364521
+SH3BP4	0,58788373
+C19orf28	0,587956493
+NDRG1	0,588555643
+HIST1H1C	0,591446402
+TCF12	0,592176798
+MPST	0,593408757
+SEPP1	0,593935425
+DNAJB6	0,595685757
+SIRPA	0,596218961
+FLT1	0,597923318
+MYOT	0,598968138
+HIST1H2AC	0,600586387
+HBP1	0,600714263
+KAZ	0,601415288
+PTBP1	0,602313539
+NSUN5P1	0,603090503
+GUSBP3	0,604393039
+KCNJ2	0,616084197
+KAT2A	0,620256502
+MCM7	0,622618327
+FBXW4	0,627081137
+MKNK2	0,628440154
+IL17RB	0,631530593
+CLK1	0,632420317
+LRP4	0,632833859
+FAM53B	0,641895571
+JMJD6	0,64411039
+TYK2	0,644727629
+PLOD3	0,644893842
+CXXC1	0,650530485
+AK024136	0,659066605
+PAN2	0,66036619
+NPTX2	0,665210794
+SPEN	0,669461617
+SETD5	0,670191692
+STX10	0,674048462
+CDK2AP2	0,67411425
+PPM1B	0,68382966
+SLCO4A1	0,685048974
+GLT25D1	0,706365388
+ZC3H11A	0,716021559
+ZBTB16	0,720405109
+ZNF692	0,720940567
+NUPR1	0,724120307
+FLCN	0,747339708
+NFASC	0,755177517
diff --git a/console/testFiles/pd_full/PD_151217_2/layouts/ageing.txt b/console/testFiles/pd_full/PD_151217_2/layouts/ageing.txt
index 952e851c76..d5c8ec23b4 100644
--- a/console/testFiles/pd_full/PD_151217_2/layouts/ageing.txt
+++ b/console/testFiles/pd_full/PD_151217_2/layouts/ageing.txt
@@ -1,416 +1,416 @@
-# VERSION=1.0
-# NAME=Ageing brain
+# VERSION=1.0
+# NAME=Ageing brain
 # DESCRIPTION=Differential transcriptome expression from post mortem tissue. Source: Allen Brain Atlas datasets, see PMID 25447234.
-name	value
-ELMO2	-0.547404913905166
-RGS1	0.664905640201586
-GSTT1	-0.630503181260422
-SDPR	0.576954531502211
-KCNJ2	-0.389733143810031
-DLG2	-0.622560222549952
-C2orf46	0.306481308387015
-YPEL1	-0.110679998012662
-AFF2	-0.580887248407995
-TCP11L2	-0.446138772716671
-TYROBP	0.0965004216809888
-PCK1	0.583148947380073
-C3	-0.229405245486493
-BLOC1S2	-0.501156113973434
-LPAR5	-0.252012578774993
-ACAD11	0.484415314534294
-CALB1	-0.585051808236823
-GNG2	-0.514333881323537
-GRIN3A	-0.54737874801763
-BLNK	-0.23678687239484
-SMARCD1	-0.480222958914743
-ARMC9	0.512102956486084
-CX3CR1	-0.300766155352383
-SLC31A2	-0.502055753854611
-AGPAT3	-0.413409719893933
-EFNB3	-0.382400551167611
-ELMOD2	0.402518685883201
-PRKCG	-0.34345444223993
-LAPTM5	-0.136628457581106
-IQUB	0.562346209462303
-STAM	-0.566262263187017
-OR11A1	0.178234692397988
-ZDHHC9	-0.520488129277965
-C11orf9	-0.511135500492906
-KLF4	0.640024343756592
-SYCP2L	0.555576793235834
-C20orf112	-0.63210679508749
-AP3M1	-0.436291767005889
-ALMS1P	0.310301539060874
-GREM1	-0.101042197816266
-HLCS	-0.404869146774348
-CARNS1	-0.358503492948689
-TSHZ2	-0.370201532555949
-CDKN1A	0.37878581767329
-CNDP1	-0.387074241865627
-C1orf161	0.408555295769768
-DOK6	-0.552556377657443
-C12orf43	-0.345533858224805
-SIPA1L2	-0.469893969573457
-FLJ40712	0.248899115372987
-TREM2	0.326657235461902
-MS4A6A	0.333196279374371
-RASGRF1	0.18816869654076
-RNF26	-0.576816063125611
-C7orf68	0.551320218061987
-DPP7	0.601525547176648
-OMD	0.556147496355725
-SNAI2	-0.402803074931945
-COL21A1	0.475584827359055
-APBB1IP	-0.510593783545533
-PRKCQ	-0.625167167620313
-PDGFRA	-0.593141766545025
-SLCO2B1	-0.20664851085323
-LPCAT3	-0.457401881600448
-CD37	-0.225548512842192
-IRF8	-0.513003936776053
-CSF1R	-0.17710132121375
-CD74	0.0263995452022326
-CHI3L1	0.637898420604861
-SELPLG	-0.165789940031603
-CDH8	-0.544872582360693
-CXCL12	-0.350721988871356
-TOPBP1	-0.516846284550731
-SLC16A10	0.372816060474775
-PCDHB9	-0.583344609658305
-HLA-DRA	0.249881965203208
-OLR1	0.105145169714195
-ADORA3	0.352457579745827
-ALOX5AP	0.094898490604102
-HLA-DOA	0.0912244782358314
-ZNF519	0.242878217518759
-FCER1G	0.122597294910367
-MT1H	0.274901514766897
-MFSD2A	0.12726693788776
-AIF1	-0.0853762046815476
-CTSH	0.324179727747488
-C3AR1	0.00893654957093225
-FCGR2A	-0.0476956544487118
-CXCL16	0.0931434603948185
-EVI2B	-0.236921572611684
-BACE1	-0.616602739604107
-OR1E1	0.491889127463635
-CLK1	0.423619868541565
-FLJ13197	0.340321509869536
-WBP2NL	0.590401706468574
-UGT8	-0.444926073295334
-HSD17B14	0.614959487312916
-GRIK3	-0.628539434045017
-MT1G	0.569589804148072
-BAIAP3	0.50915236570152
-TJAP1	-0.211899568999271
-PIP4K2C	-0.546592244445733
-CAMK4	-0.62370886479691
-TMEM63A	-0.349108640870675
-CCDC45	0.470491672406875
-ERLIN1	-0.590064605968872
-ATP6V1F	0.31735684237396
-EPHB2	-0.492251103302591
-ANKRD11	-0.576352445468476
-PCDHB2	-0.56247030572076
-ACSL1	-0.580402201513607
-LGR5	-0.49666928921999
-PDE3B	0.561081934872393
-C1orf21	-0.433409479731833
-LRRTM1	-0.430851468978506
-GPR12	-0.285126298493215
-VSTM2A	-0.496505850586284
-ODZ1	-0.500803022233123
-CACNG2	-0.568038440978143
-SMPD3	-0.448297258958326
-SORBS2	-0.652515435812272
-DCAF7	-0.561122254419525
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-PEG10	-0.529984214958046
-A2M	-0.0956498395825097
-THRB	-0.278461084991876
-C11orf24	-0.519543924524242
-TFG	-0.340307925442264
-MAMLD1	-0.389582104545406
-ASPHD2	-0.44086160208266
-ANKRD37	0.644400268061014
-NCKAP1L	-0.38869429192758
-CAPN5	-0.568639095894228
-SERINC3	-0.473478678274642
-CEBPB	0.386715054596765
-PRDM10	-0.575525391963737
-HCN1	-0.384931312491389
-CAMTA1	-0.435666315274373
-KLHDC1	0.27598504319864
-DUSP1	0.576414053338242
-QRICH1	-0.533552393948272
-SH3KBP1	-0.391446975914019
-EBF1	-0.379385913897609
-PPP1R16B	-0.356903880861572
-BTBD3	-0.327196312551472
-NRXN2	-0.509283550099326
-KAZ	-0.541421535478964
-KIAA0317	-0.636085461640037
-NDST3	-0.426753877235142
-GMCL1	0.45632888308336
-P2RX5	-0.283914132520413
-IGFL3	0.297606727720448
-LOC286161	-0.366837279825892
-PLEKHM1	-0.408702703852517
-RIMS1	-0.372721943202267
-UBE2Q2P1	0.327173892822723
-TTYH2	-0.407525904378876
-DES	0.06209856553185
-DBNDD2	-0.30225683329951
-ENPP2	-0.409429156664166
-NTN4	0.494337823155339
-SUN2	-0.276353435973038
-ACTG2	-0.210220455726459
-CA2	-0.0242596436213912
-THBS1	-0.221580234422776
-LDLRAD3	-0.360622764104025
-SNX1	-0.0377961368749078
-ERBB3	-0.405973590470433
-TTN	0.391623015044573
-ATRN	-0.52540142288716
-NPC1	-0.267674240960311
-GNS	-0.181466206971045
-KLK6	-0.378431280290618
-FOS	0.360516377902882
-CD69	0.377148542537053
-LYVE1	0.138789282779698
-FTL	0.237591315022414
-JUNB	0.394473562572383
-GSTM5	0.217560993654354
-NR4A1	0.24427289755837
-PGAM2	0.551801840506397
-TMEM176A	0.537931366670412
-EGR1	-0.157019974633097
-GPR183	0.107180842069747
-CXCL11	0.395003724312407
-PLA2G12A	-0.18246216314499
-HLA-DMB	0.229795197318716
-CPNE8	0.0508489313725271
-ZFP36	0.42538436064968
-AGPAT4	-0.467855141787709
-HLA-DPA1	0.408536378107808
-PIK3C2B	-0.591780318571167
-CPNE6	-0.271576531727541
-PLD3	-0.200022062788495
-PVRL1	-0.555155906198138
-GGCT	-0.279243242312552
-P2RY13	-0.360442360434042
-CNTN5	0.00258913839174191
-MCM7	0.195233154899312
-GPR120	-0.199692500084005
-GABRE	0.0682190440098052
-LRRC39	0.498683033772744
-TLR7	-0.164697853025215
-RFC3	-0.486755240432686
-CD33	0.00184280522373291
-CA8	0.363290764959567
-MAS1	-0.492009752548035
-FBLN5	-0.511286958021381
-TMTC1	-0.332133706392934
-C1orf51	0.45497717618641
-RPL35	-0.0899084146126614
-DKK2	-0.38611669080376
-USP53	0.412868805138869
-CD177	-0.217675402988493
-ELAVL1	-0.579547221944692
-AIFM3	0.577935690502709
-ASCL1	0.37568323074867
-EXPH5	-0.575008199569129
-CBWD3	0.283287779368243
-PEPD	-0.0553830875558683
-GPNMB	0.364500938005497
-NEDD4L	-0.508710397589902
-CALB2	-0.425755713683833
-FAM49A	-0.447197463197697
-NT5DC3	-0.265234061560778
-HES6	0.347000889525298
-GDA	-0.336613721691585
-RASAL1	-0.344295261121664
-ANO3	-0.518790055621458
-C14orf145	0.508493948450919
-MSRB3	0.374050410076754
-CC2D2B	0.438851338613457
-FAM65B	-0.254284575986291
-KIRREL3	-0.539616579176257
-CKLF	0.222793814048359
-DNAJA4	-0.486836211576555
-BCOR	-0.579019889055718
-CBLL1	-0.642779519205918
-CACNG3	-0.428582206819538
-GRIN2B	-0.577739683994275
-LRRC67	0.341366642004448
-RELL2	0.405916058000189
-NUDT3	-0.340375787654433
-MAST2	-0.541618527665053
-S100A10	-0.105037624066791
-OR13C2	0.379430219617317
-HSPC157	0.570528832119166
-NOP10	0.322245514370384
-C6orf174	-0.338629613564291
-LRRC61	0.0251744454575518
-FOLR2	0.131043427693804
-DYRK2	-0.522163896119695
-CALHM2	0.169628414381558
-CST7	0.313658960797421
-DUSP7	-0.523627393294567
-MTMR10	-0.415446285885383
-PPM1G	-0.464776264617981
-ADCY1	-0.454137407761092
-RPL13	0.506459486318965
-RRN3P1	0.525814578931781
-CXCL2	0.3672098081501
-RXRG	0.0402026385616925
-SRGN	0.531671866088554
-HIST1H2AE	0.293542472070096
-CYP2B6	0.275105405791745
-HHIP	-0.466578712584274
-KIAA1324L	-0.40123393199988
-FLJ90757	-0.507490069062372
-MYT1L	-0.584482026813831
-EIF2C2	-0.484852873283777
-NKAIN2	-0.549382635628517
-EIF2AK2	-0.489504988062896
-KIF21A	-0.359563932905791
-CCT6A	-0.177223944265096
-CDV3	-0.391589063759768
-HIVEP2	-0.600071683037855
-SPATA1	0.543060390879784
-FKBP11	-0.615494036116273
-NDST1	-0.475889745275566
-ARHGEF10	-0.250541551205642
-ZHX1	0.482981433720838
-SLC10A7	-0.337979122832437
-JAKMIP2	-0.415964197082499
-NAV1	-0.510622036406541
-NDUFB2	0.377202661234421
-ZNF507	-0.468104205569414
-MGAT2	0.222876912868186
-TTR	0.346175361449992
-EPB41L3	-0.411485674977879
-CNTNAP2	-0.327376463196595
-HNRNPU	-0.346139332150707
-ZNRD1	0.194397447066282
-PMF1	0.232524370350156
-TNFRSF21	-0.387936336469165
-KCNB1	-0.405472129261546
-FOXG1	-0.471157786135538
-S100A13	0.557308910766736
-BRD4	-0.517114201471415
-TIGD6	0.442112009917649
-RSPH9	0.182331610189591
-RGS20	0.417845235693366
-ASAP1	-0.536170937682141
-SLC7A14	-0.280031937135622
-MGAT3	-0.448766981367882
-IFITM4P	0.485622606827836
-SFRS15	-0.542060168583627
-PITPNM3	-0.42639997101521
-PTPRE	-0.530218005259195
-ZEB1	-0.477757026844139
-KCNQ3	-0.429926385373833
-CRB1	0.536038063001376
-MAPT	-0.50877997133818
-ABCA3	-0.360772553926051
-NPAS2	-0.419863325483148
-CLIC2	0.498878325957547
-LARP1	-0.49884819681315
-NLGN2	-0.429454573027551
-ALS2CR11	0.294226279272528
-NAP1L2	-0.313096105976879
-SLIT1	-0.434411983489453
-PHB	0.00979800238909777
-ZNF587	-0.0136127665384343
-STRN4	-0.576565248356412
-DSCAML1	-0.596992679910324
-MBD2	-0.20298332637123
-CENPQ	0.422898511661338
-PHF10	0.395502631449537
-MAP3K9	-0.405184359146696
-XRCC1	-0.370898065524857
-AKR1C3	0.453192387807177
-TTC29	0.290819126414233
-ISG20L2	-0.428905666986556
-TMEM165	0.492824884935657
-C2CD3	-0.514182826428327
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-CCDC92	-0.53622071697372
-EXT1	-0.382555479091514
-C1QL2	-0.201706565681442
-ABHD2	-0.301021168563018
-SMURF1	-0.635507196661467
-CSNK1G2	-0.414657842955022
-TSPO	0.312759943492922
-EFEMP1	0.418307207101287
-HIST1H2BC	0.155466056856681
-CACNA1G	-0.603776648047605
-FCGRT	0.35186075288181
-OR6N2	0.19188744379883
-LILRA4	0.402116115371683
-GRIA1	-0.509922904695054
-HOXD8	0.311094779788594
-UPP1	0.48025126950744
-C17orf88	0.245494799347336
-MKL2	-0.495926848441475
-TAB3	-0.397855481558619
-KRTAP19-5	0.333726211690568
-PCDHB3	-0.42089893790206
-KLRF1	0.238176912312437
-TLR4	0.293561440425403
-SEPT14	0.268206811480962
-BSN	-0.301460000103249
-GRLF1	-0.466342462809911
-C1orf61	0.409705166908955
-GSTM1	0.580671376408388
-SDCCAG3	0.339086319326061
-NHLH2	0.264436125619991
-CRTC1	-0.364358124950179
-ZNF701	0.262422484025346
-FTO	-0.484606564596535
-KIAA0430	-0.323429860829196
-HPSE2	0.444523469491999
-AAK1	-0.336960928171931
-ZNF592	-0.459711729876906
-INF2	-0.368727716463355
-UNC80	-0.203435560684691
-KCNJ9	-0.385326074668389
-CREBBP	-0.48479916887186
-TMEM187	0.353577074222219
-GIMAP6	0.196334054611495
-MSH4	0.495021650163618
-CYP2F1	-0.202379731783218
-WARS	-0.36956071999387
-EIF4H	-0.324258084689287
-LMF1	-0.465196534142832
-SLC9A11	0.380530864151023
-RPLP0	0.401187575431913
-SORCS3	-0.524716179920174
-SMPD1	-0.371378049257817
-MLL2	-0.382849048834827
-ACTA2	-0.351473562308814
-CD84	0.0440334284755635
-LRRC57	-0.0868790230732024
-ADAM28	-0.234050278113392
-FLJ37543	0.329929076805089
-NR4A2	-0.525703760298336
-METT11D1	0.315411883405057
-MEX3C	-0.570394569556345
-ST8SIA5	-0.525318796364569
-HRH1	-0.276472654345764
-RAB3IP	-0.23897971786832
-ETV6	-0.448657117826825
-LUZP2	-0.409590511647277
-TRIM44	-0.386063986999447
-MYH11	-0.280352372336459
-TPK1	0.485143439818794
-C1QC	-0.0250872517448672
-A2ML1	0.356485052871728
-ZNF365	0.476040462817264
-CCL2	0.160044975309114
-ADRA2A	-0.511689669158592
-TMPRSS5	0.299973105357606
-C5orf53	0.490994640268981
-MORC2	-0.41225212616417
+name	value
+ELMO2	-0.547404913905166
+RGS1	0.664905640201586
+GSTT1	-0.630503181260422
+SDPR	0.576954531502211
+KCNJ2	-0.389733143810031
+DLG2	-0.622560222549952
+C2orf46	0.306481308387015
+YPEL1	-0.110679998012662
+AFF2	-0.580887248407995
+TCP11L2	-0.446138772716671
+TYROBP	0.0965004216809888
+PCK1	0.583148947380073
+C3	-0.229405245486493
+BLOC1S2	-0.501156113973434
+LPAR5	-0.252012578774993
+ACAD11	0.484415314534294
+CALB1	-0.585051808236823
+GNG2	-0.514333881323537
+GRIN3A	-0.54737874801763
+BLNK	-0.23678687239484
+SMARCD1	-0.480222958914743
+ARMC9	0.512102956486084
+CX3CR1	-0.300766155352383
+SLC31A2	-0.502055753854611
+AGPAT3	-0.413409719893933
+EFNB3	-0.382400551167611
+ELMOD2	0.402518685883201
+PRKCG	-0.34345444223993
+LAPTM5	-0.136628457581106
+IQUB	0.562346209462303
+STAM	-0.566262263187017
+OR11A1	0.178234692397988
+ZDHHC9	-0.520488129277965
+C11orf9	-0.511135500492906
+KLF4	0.640024343756592
+SYCP2L	0.555576793235834
+C20orf112	-0.63210679508749
+AP3M1	-0.436291767005889
+ALMS1P	0.310301539060874
+GREM1	-0.101042197816266
+HLCS	-0.404869146774348
+CARNS1	-0.358503492948689
+TSHZ2	-0.370201532555949
+CDKN1A	0.37878581767329
+CNDP1	-0.387074241865627
+C1orf161	0.408555295769768
+DOK6	-0.552556377657443
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+SIPA1L2	-0.469893969573457
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+MS4A6A	0.333196279374371
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+DPP7	0.601525547176648
+OMD	0.556147496355725
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+APBB1IP	-0.510593783545533
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+IRF8	-0.513003936776053
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+TOPBP1	-0.516846284550731
+SLC16A10	0.372816060474775
+PCDHB9	-0.583344609658305
+HLA-DRA	0.249881965203208
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+ADORA3	0.352457579745827
+ALOX5AP	0.094898490604102
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+C3AR1	0.00893654957093225
+FCGR2A	-0.0476956544487118
+CXCL16	0.0931434603948185
+EVI2B	-0.236921572611684
+BACE1	-0.616602739604107
+OR1E1	0.491889127463635
+CLK1	0.423619868541565
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+WBP2NL	0.590401706468574
+UGT8	-0.444926073295334
+HSD17B14	0.614959487312916
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+TMEM63A	-0.349108640870675
+CCDC45	0.470491672406875
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+ATP6V1F	0.31735684237396
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+PCDHB2	-0.56247030572076
+ACSL1	-0.580402201513607
+LGR5	-0.49666928921999
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+C1orf21	-0.433409479731833
+LRRTM1	-0.430851468978506
+GPR12	-0.285126298493215
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+SMPD3	-0.448297258958326
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+CAMTA1	-0.435666315274373
+KLHDC1	0.27598504319864
+DUSP1	0.576414053338242
+QRICH1	-0.533552393948272
+SH3KBP1	-0.391446975914019
+EBF1	-0.379385913897609
+PPP1R16B	-0.356903880861572
+BTBD3	-0.327196312551472
+NRXN2	-0.509283550099326
+KAZ	-0.541421535478964
+KIAA0317	-0.636085461640037
+NDST3	-0.426753877235142
+GMCL1	0.45632888308336
+P2RX5	-0.283914132520413
+IGFL3	0.297606727720448
+LOC286161	-0.366837279825892
+PLEKHM1	-0.408702703852517
+RIMS1	-0.372721943202267
+UBE2Q2P1	0.327173892822723
+TTYH2	-0.407525904378876
+DES	0.06209856553185
+DBNDD2	-0.30225683329951
+ENPP2	-0.409429156664166
+NTN4	0.494337823155339
+SUN2	-0.276353435973038
+ACTG2	-0.210220455726459
+CA2	-0.0242596436213912
+THBS1	-0.221580234422776
+LDLRAD3	-0.360622764104025
+SNX1	-0.0377961368749078
+ERBB3	-0.405973590470433
+TTN	0.391623015044573
+ATRN	-0.52540142288716
+NPC1	-0.267674240960311
+GNS	-0.181466206971045
+KLK6	-0.378431280290618
+FOS	0.360516377902882
+CD69	0.377148542537053
+LYVE1	0.138789282779698
+FTL	0.237591315022414
+JUNB	0.394473562572383
+GSTM5	0.217560993654354
+NR4A1	0.24427289755837
+PGAM2	0.551801840506397
+TMEM176A	0.537931366670412
+EGR1	-0.157019974633097
+GPR183	0.107180842069747
+CXCL11	0.395003724312407
+PLA2G12A	-0.18246216314499
+HLA-DMB	0.229795197318716
+CPNE8	0.0508489313725271
+ZFP36	0.42538436064968
+AGPAT4	-0.467855141787709
+HLA-DPA1	0.408536378107808
+PIK3C2B	-0.591780318571167
+CPNE6	-0.271576531727541
+PLD3	-0.200022062788495
+PVRL1	-0.555155906198138
+GGCT	-0.279243242312552
+P2RY13	-0.360442360434042
+CNTN5	0.00258913839174191
+MCM7	0.195233154899312
+GPR120	-0.199692500084005
+GABRE	0.0682190440098052
+LRRC39	0.498683033772744
+TLR7	-0.164697853025215
+RFC3	-0.486755240432686
+CD33	0.00184280522373291
+CA8	0.363290764959567
+MAS1	-0.492009752548035
+FBLN5	-0.511286958021381
+TMTC1	-0.332133706392934
+C1orf51	0.45497717618641
+RPL35	-0.0899084146126614
+DKK2	-0.38611669080376
+USP53	0.412868805138869
+CD177	-0.217675402988493
+ELAVL1	-0.579547221944692
+AIFM3	0.577935690502709
+ASCL1	0.37568323074867
+EXPH5	-0.575008199569129
+CBWD3	0.283287779368243
+PEPD	-0.0553830875558683
+GPNMB	0.364500938005497
+NEDD4L	-0.508710397589902
+CALB2	-0.425755713683833
+FAM49A	-0.447197463197697
+NT5DC3	-0.265234061560778
+HES6	0.347000889525298
+GDA	-0.336613721691585
+RASAL1	-0.344295261121664
+ANO3	-0.518790055621458
+C14orf145	0.508493948450919
+MSRB3	0.374050410076754
+CC2D2B	0.438851338613457
+FAM65B	-0.254284575986291
+KIRREL3	-0.539616579176257
+CKLF	0.222793814048359
+DNAJA4	-0.486836211576555
+BCOR	-0.579019889055718
+CBLL1	-0.642779519205918
+CACNG3	-0.428582206819538
+GRIN2B	-0.577739683994275
+LRRC67	0.341366642004448
+RELL2	0.405916058000189
+NUDT3	-0.340375787654433
+MAST2	-0.541618527665053
+S100A10	-0.105037624066791
+OR13C2	0.379430219617317
+HSPC157	0.570528832119166
+NOP10	0.322245514370384
+C6orf174	-0.338629613564291
+LRRC61	0.0251744454575518
+FOLR2	0.131043427693804
+DYRK2	-0.522163896119695
+CALHM2	0.169628414381558
+CST7	0.313658960797421
+DUSP7	-0.523627393294567
+MTMR10	-0.415446285885383
+PPM1G	-0.464776264617981
+ADCY1	-0.454137407761092
+RPL13	0.506459486318965
+RRN3P1	0.525814578931781
+CXCL2	0.3672098081501
+RXRG	0.0402026385616925
+SRGN	0.531671866088554
+HIST1H2AE	0.293542472070096
+CYP2B6	0.275105405791745
+HHIP	-0.466578712584274
+KIAA1324L	-0.40123393199988
+FLJ90757	-0.507490069062372
+MYT1L	-0.584482026813831
+EIF2C2	-0.484852873283777
+NKAIN2	-0.549382635628517
+EIF2AK2	-0.489504988062896
+KIF21A	-0.359563932905791
+CCT6A	-0.177223944265096
+CDV3	-0.391589063759768
+HIVEP2	-0.600071683037855
+SPATA1	0.543060390879784
+FKBP11	-0.615494036116273
+NDST1	-0.475889745275566
+ARHGEF10	-0.250541551205642
+ZHX1	0.482981433720838
+SLC10A7	-0.337979122832437
+JAKMIP2	-0.415964197082499
+NAV1	-0.510622036406541
+NDUFB2	0.377202661234421
+ZNF507	-0.468104205569414
+MGAT2	0.222876912868186
+TTR	0.346175361449992
+EPB41L3	-0.411485674977879
+CNTNAP2	-0.327376463196595
+HNRNPU	-0.346139332150707
+ZNRD1	0.194397447066282
+PMF1	0.232524370350156
+TNFRSF21	-0.387936336469165
+KCNB1	-0.405472129261546
+FOXG1	-0.471157786135538
+S100A13	0.557308910766736
+BRD4	-0.517114201471415
+TIGD6	0.442112009917649
+RSPH9	0.182331610189591
+RGS20	0.417845235693366
+ASAP1	-0.536170937682141
+SLC7A14	-0.280031937135622
+MGAT3	-0.448766981367882
+IFITM4P	0.485622606827836
+SFRS15	-0.542060168583627
+PITPNM3	-0.42639997101521
+PTPRE	-0.530218005259195
+ZEB1	-0.477757026844139
+KCNQ3	-0.429926385373833
+CRB1	0.536038063001376
+MAPT	-0.50877997133818
+ABCA3	-0.360772553926051
+NPAS2	-0.419863325483148
+CLIC2	0.498878325957547
+LARP1	-0.49884819681315
+NLGN2	-0.429454573027551
+ALS2CR11	0.294226279272528
+NAP1L2	-0.313096105976879
+SLIT1	-0.434411983489453
+PHB	0.00979800238909777
+ZNF587	-0.0136127665384343
+STRN4	-0.576565248356412
+DSCAML1	-0.596992679910324
+MBD2	-0.20298332637123
+CENPQ	0.422898511661338
+PHF10	0.395502631449537
+MAP3K9	-0.405184359146696
+XRCC1	-0.370898065524857
+AKR1C3	0.453192387807177
+TTC29	0.290819126414233
+ISG20L2	-0.428905666986556
+TMEM165	0.492824884935657
+C2CD3	-0.514182826428327
+DPP4	0.23910770529895
+CCDC92	-0.53622071697372
+EXT1	-0.382555479091514
+C1QL2	-0.201706565681442
+ABHD2	-0.301021168563018
+SMURF1	-0.635507196661467
+CSNK1G2	-0.414657842955022
+TSPO	0.312759943492922
+EFEMP1	0.418307207101287
+HIST1H2BC	0.155466056856681
+CACNA1G	-0.603776648047605
+FCGRT	0.35186075288181
+OR6N2	0.19188744379883
+LILRA4	0.402116115371683
+GRIA1	-0.509922904695054
+HOXD8	0.311094779788594
+UPP1	0.48025126950744
+C17orf88	0.245494799347336
+MKL2	-0.495926848441475
+TAB3	-0.397855481558619
+KRTAP19-5	0.333726211690568
+PCDHB3	-0.42089893790206
+KLRF1	0.238176912312437
+TLR4	0.293561440425403
+SEPT14	0.268206811480962
+BSN	-0.301460000103249
+GRLF1	-0.466342462809911
+C1orf61	0.409705166908955
+GSTM1	0.580671376408388
+SDCCAG3	0.339086319326061
+NHLH2	0.264436125619991
+CRTC1	-0.364358124950179
+ZNF701	0.262422484025346
+FTO	-0.484606564596535
+KIAA0430	-0.323429860829196
+HPSE2	0.444523469491999
+AAK1	-0.336960928171931
+ZNF592	-0.459711729876906
+INF2	-0.368727716463355
+UNC80	-0.203435560684691
+KCNJ9	-0.385326074668389
+CREBBP	-0.48479916887186
+TMEM187	0.353577074222219
+GIMAP6	0.196334054611495
+MSH4	0.495021650163618
+CYP2F1	-0.202379731783218
+WARS	-0.36956071999387
+EIF4H	-0.324258084689287
+LMF1	-0.465196534142832
+SLC9A11	0.380530864151023
+RPLP0	0.401187575431913
+SORCS3	-0.524716179920174
+SMPD1	-0.371378049257817
+MLL2	-0.382849048834827
+ACTA2	-0.351473562308814
+CD84	0.0440334284755635
+LRRC57	-0.0868790230732024
+ADAM28	-0.234050278113392
+FLJ37543	0.329929076805089
+NR4A2	-0.525703760298336
+METT11D1	0.315411883405057
+MEX3C	-0.570394569556345
+ST8SIA5	-0.525318796364569
+HRH1	-0.276472654345764
+RAB3IP	-0.23897971786832
+ETV6	-0.448657117826825
+LUZP2	-0.409590511647277
+TRIM44	-0.386063986999447
+MYH11	-0.280352372336459
+TPK1	0.485143439818794
+C1QC	-0.0250872517448672
+A2ML1	0.356485052871728
+ZNF365	0.476040462817264
+CCL2	0.160044975309114
+ADRA2A	-0.511689669158592
+TMPRSS5	0.299973105357606
+C5orf53	0.490994640268981
+MORC2	-0.41225212616417
diff --git a/console/testFiles/pd_full/PD_160714_2/layouts/PD substantia nigra.txt b/console/testFiles/pd_full/PD_160714_2/layouts/PD substantia nigra.txt
index 8f57d5c9d2..5ed3ee8742 100644
--- a/console/testFiles/pd_full/PD_160714_2/layouts/PD substantia nigra.txt	
+++ b/console/testFiles/pd_full/PD_160714_2/layouts/PD substantia nigra.txt	
@@ -1,4342 +1,4342 @@
-# VERSION=1.0
-# NAME=PD substantia nigra
+# VERSION=1.0
+# NAME=PD substantia nigra
 # DESCRIPTION=Differential transcriptome expression from post mortem tissue. Meta-analysis from 8 published datasets, FDR = 0.05, see PMIDs 23832570 and 25447234.
-name	value
-GBE1	-0,943978048
-SLC18A2	-0,941309505
-KCNJ6	-0,894120983
-DLK1	-0,887122171
-PTDSS1	-0,851959645
-FGF13	-0,842876271
-PCDH8	-0,83524894
-ZNF226	-0,82900335
-SLC6A3	-0,824713365
-PIP5K1B	-0,812285785
-DENR	-0,81101551
-TPBG	-0,806963209
-PRKAR2B	-0,805288865
-OSBPL10	-0,80406299
-ALDH1A1	-0,795042129
-GGCX	-0,795035797
-ACP2	-0,794853979
-SLITRK5	-0,793842132
-FAM70A	-0,793715412
-HPRT1	-0,792370336
-CCNH	-0,790971864
-MYRIP	-0,78490295
-TUBB2A	-0,783142444
-ACTR10	-0,782043082
-BASP1	-0,778702387
-CADPS2	-0,777552826
-PID1	-0,775106213
-SV2C	-0,774895093
-RBM3	-0,77091551
-REEP1	-0,770000111
-RIMBP2	-0,766421185
-CNIH3	-0,765790316
-DMXL2	-0,765309344
-LOC10431	-0,762992699
-SV2B	-0,759985564
-AGK	-0,756506198
-RCAN2	-0,753762002
-LPPR4	-0,753018962
-RALYL	-0,75270126
-L1CAM	-0,751978689
-BCAS2	-0,751241508
-LOC100131795	-0,750350108
-TH	-0,748260596
-AV756161	-0,747351587
-TRIM36	-0,746057792
-MPPED2	-0,743864716
-NELL2	-0,742513977
-MAGED1	-0,739190733
-LRRC49	-0,738776851
-SYNGR3	-0,734846774
-ERC2	-0,734619705
-VBP1	-0,73223558
-UQCC	-0,729749962
-DCLK1	-0,725139215
-GSS	-0,724321987
-OPA1	-0,723790592
-PPP2R2B	-0,720892147
-COPS4	-0,720599852
-NSF	-0,720580224
-DLD	-0,72035948
-DYNC1I1	-0,719837984
-GABARAPL3	-0,717235008
-GPRASP1	-0,71302626
-NAP1L2	-0,712876929
-AMPH	-0,711957162
-PNMAL1	-0,70952389
-RGS6	-0,706463
-LDB2	-0,704777497
-TTC19	-0,704232585
-SCN3B	-0,703738866
-ATPIF1	-0,702603531
-BEX1	-0,700382911
-LMO3	-0,699029823
-TBC1D9	-0,698189481
-NDUFS1	-0,697230219
-INSM1	-0,696524737
-PARL	-0,696362568
-MRPL15	-0,688780959
-C3orf14	-0,687875821
-C19orf62	-0,687403479
-PCYOX1L	-0,686812669
-VRK1	-0,685016241
-MDH2	-0,684889561
-SMYD3	-0,684642724
-ASAH1	-0,68459801
-GSTA4	-0,684021936
-NDUFA9	-0,683116722
-ATP5C1	-0,682289667
-DDX25	-0,681511867
-GNG3	-0,681122999
-MUDENG	-0,67996077
-SCG2	-0,679728044
-MOAP1	-0,679575281
-SYT1	-0,678979261
-ATP6V1H	-0,6786546
-SHOC2	-0,677754756
-PCSK1	-0,677441918
-LBH	-0,67710638
-HK1	-0,676818391
-KIAA0319	-0,676346138
-SMAP1	-0,67618103
-EHBP1	-0,675429621
-RAP1GAP2	-0,673705297
-FABP7	-0,673485271
-LRRN3	-0,6731503
-AHNAK2	-0,672875949
-DHDDS	-0,671959403
-SNAPC5	-0,670824633
-C17orf108	-0,670563093
-AL390170	-0,67026906
-PTS	-0,669577055
-NUDT11	-0,668061506
-HMP19	-0,66794356
-IMMT	-0,667541939
-RGS4	-0,667109174
-RET	-0,667088994
-PBLD	-0,666164981
-AP3M2	-0,666056972
-WDR7	-0,665751643
-ATP6V0D1	-0,665487037
-RTF1	-0,664652469
-TUBB3	-0,664644351
-CHCHD2	-0,664529051
-DYNLT3	-0,663584428
-RAB6B	-0,662755469
-CHGB	-0,661865706
-NGFRAP1	-0,659441958
-AZIN1	-0,659394366
-EN1	-0,659313013
-SNX10	-0,659251628
-MIA3	-0,65882244
-ANK1	-0,657621479
-NR4A2	-0,65598531
-ANAPC13	-0,655864214
-RGS7	-0,654445938
-NME5	-0,652754395
-TXNDC9	-0,652019899
-PPIP5K2	-0,651763237
-RFK	-0,651442652
-BE674466	-0,651048329
-PEG10	-0,650932122
-PIAS2	-0,650823358
-CUX2	-0,649970555
-SEPT6	-0,649422911
-FKBP1B	-0,649416387
-C12orf10	-0,648407487
-HMGCS1	-0,648164918
-WDR61	-0,648133373
-GFPT1	-0,647751981
-MLLT11	-0,647471245
-AGTR1	-0,645674318
-CSNK1D	-0,645408463
-WDR47	-0,64495088
-PSMD14	-0,644669314
-CISD1	-0,643780748
-PSMD11	-0,642982055
-KCNS3	-0,642919136
-TIMM8B	-0,642730563
-RUNDC3B	-0,641744336
-ANKRD6	-0,640032629
-MDH1	-0,639623665
-STMN2	-0,639070421
-BAI3	-0,638894116
-STX12	-0,638382169
-NECAP1	-0,638376593
-NIT2	-0,638223243
-CIRBP	-0,637859912
-XK	-0,636787355
-KIAA1797	-0,636384728
-ICMT	-0,636379567
-GALT	-0,636138691
-SPINT2	-0,635454321
-PAIP1	-0,634724103
-TAGLN3	-0,63459569
-CADPS	-0,634245008
-GALNT11	-0,634168707
-SLC9A6	-0,632805526
-ANKRD34C	-0,63217094
-COPG2IT1	-0,63213856
-VPS4B	-0,63135628
-ATP6V0E2	-0,631164455
-SC5DL	-0,631137699
-CNPY2	-0,630875303
-GCC2	-0,630691438
-CRYZL1	-0,63015348
-MOBKL3	-0,630076244
-SNCA	-0,629316875
-STAM	-0,628134338
-TUBA4A	-0,627764216
-MAK16	-0,627148096
-FRY	-0,626684765
-UBE2V2	-0,626378865
-RWDD2B	-0,626170788
-FBXO9	-0,62572532
-FLJ41278	-0,6251633
-SLC30A9	-0,624759053
-LOC100132015	-0,623179237
-EXOG	-0,622056922
-RAP1GAP	-0,618803848
-DYNC1LI1	-0,618641756
-HARS	-0,618639749
-NDUFA5	-0,618245275
-SPCS1	-0,618130333
-PSMB7	-0,618122572
-NETO2	-0,618103081
-ATP5G3	-0,617855025
-UCHL1	-0,617452524
-FAM127A	-0,616124191
-TSSC1	-0,615619431
-CBLN1	-0,615519237
-CYB5R1	-0,615294192
-PSMG1	-0,61487171
-AKAP12	-0,614821543
-CYB561	-0,614281499
-KCND3	-0,613554227
-GABRB1	-0,613364723
-SLIT1	-0,613251897
-HN1	-0,612796898
-F8	-0,612749576
-VSNL1	-0,611517123
-ATP5A1	-0,611141848
-ARMCX5	-0,610703909
-AI097640	-0,610659067
-CERK	-0,610508368
-TMX4	-0,610174408
-TSPAN13	-0,609932725
-CAMLG	-0,609409157
-NDUFA7	-0,609351405
-STRAP	-0,609237631
-RTCD1	-0,607502869
-ORC5L	-0,606910471
-SCG5	-0,606870723
-HSPA12A	-0,606863939
-VAV3	-0,606070683
-TUBB2C	-0,60582666
-DCTN2	-0,605238426
-OCRL	-0,604661192
-HPCAL4	-0,604023171
-ARL1	-0,604008234
-CDK14	-0,603712397
-TLK1	-0,603591955
-BLVRA	-0,603201697
-NEFL	-0,602887281
-SLC25A32	-0,602708801
-ATXN10	-0,602624835
-UQCRC2	-0,601726567
-SLC25A3	-0,601470752
-MYL12B	-0,601373186
-CDS2	-0,601292766
-DDC	-0,601079077
-BSCL2	-0,6009448
-CACNB3	-0,598982611
-RIMS3	-0,598771066
-LASS6	-0,598387226
-FIBP	-0,598382328
-LRPPRC	-0,598144321
-PYROXD1	-0,598012671
-MAP3K9	-0,597438703
-CHL1	-0,5969101
-FJX1	-0,596748319
-PFN2	-0,596551333
-ATMIN	-0,59649395
-LIN7B	-0,596058244
-AV704232	-0,595274626
-PPP2R5C	-0,594797769
-SNAP91	-0,59414072
-AKT3	-0,593859242
-NDUFAB1	-0,593111219
-CCDC28A	-0,59307395
-GLOD4	-0,592429097
-STXBP1	-0,591440124
-HLTF	-0,591296161
-CRMP1	-0,590916915
-KIAA0513	-0,590696005
-GHITM	-0,590624599
-ATP6V1B2	-0,590367192
-USP14	-0,589739205
-RNFT2	-0,589705749
-SCG3	-0,589375952
-ATP5B	-0,588999541
-FAM136A	-0,588982627
-UBE2N	-0,588308222
-ANXA6	-0,588071667
-MRTO4	-0,58799806
-SNRK	-0,587183425
-CACNA2D2	-0,587134808
-IFT57	-0,586933566
-PPP3CB	-0,586906049
-RICH2	-0,586554767
-ME3	-0,586514247
-THOC7	-0,585617181
-FAM188A	-0,584083221
-EIF2B3	-0,582997986
-CNTNAP1	-0,582856877
-SCRN1	-0,582791752
-ACAT1	-0,582760841
-IDI1	-0,582694626
-PBX1	-0,582658829
-CDC42	-0,582658446
-NBEA	-0,582614884
-PPP1R2	-0,581839918
-ACTR6	-0,581817384
-TAF9	-0,581794162
-NIPSNAP1	-0,581711722
-SEC61A2	-0,58139821
-WDR37	-0,581272248
-VWA5A	-0,581248993
-CDC27	-0,580500838
-MYT1L	-0,580491453
-PSMC1	-0,580473356
-KATNB1	-0,578133005
-ZWINT	-0,577661475
-C12orf24	-0,577181135
-SLC25A46	-0,577144749
-DOLK	-0,576794187
-APOO	-0,576716633
-GCH1	-0,576494714
-TBC1D30	-0,575582077
-DCTN3	-0,575526778
-FBXL2	-0,575141782
-KIFAP3	-0,574923419
-CMAS	-0,574834972
-C18orf10	-0,574780811
-PNMA2	-0,574504978
-PDHX	-0,574434123
-SAMM50	-0,574204311
-NDUFA2	-0,574087728
-NPTN	-0,573534504
-HIGD1A	-0,573110642
-CYC1	-0,573010558
-HMGCR	-0,572959475
-TRAPPC2L	-0,572517332
-IMPA1	-0,572397104
-IMPACT	-0,572070372
-KIAA0802	-0,572067617
-DSTN	-0,571964512
-C5orf44	-0,571958339
-CCK	-0,571148184
-OGDHL	-0,571078621
-TCP11L1	-0,570951095
-RNF14	-0,569913578
-IARS	-0,569079443
-CDH8	-0,569072707
-RNF41	-0,568830451
-SCN3A	-0,568276898
-PSMD12	-0,567936617
-TNFRSF21	-0,567631199
-FIG4	-0,566751868
-DDX24	-0,566446037
-MARK1	-0,566206858
-ATP8A2	-0,565754513
-ACLY	-0,565055263
-DDX42	-0,564984354
-KIF3C	-0,564949485
-PIN1	-0,564290859
-PSEN2	-0,564206755
-TERF2IP	-0,564084181
-VDAC3	-0,563895581
-B3GNT1	-0,563686309
-CHN1	-0,563660153
-GLO1	-0,561564055
-RAB11A	-0,561549092
-PRPS1	-0,561391557
-MAP2	-0,561080301
-NHP2	-0,56096586
-DNAJA2	-0,560780556
-NDRG4	-0,560771764
-HNRNPA0	-0,560406816
-NDUFV2	-0,559975953
-ADH5	-0,559909821
-FAM3C	-0,559672666
-COPS7A	-0,559265307
-SULT4A1	-0,558733244
-MATN3	-0,558346148
-TMEM14A	-0,557817575
-HRASLS	-0,557799459
-TMEM14B	-0,557593404
-TTC1	-0,557573183
-R3HDM1	-0,557428266
-AUH	-0,55725646
-C5orf22	-0,55714645
-TUBB	-0,557095971
-C5orf13	-0,55663948
-COX7A2L	-0,556219721
-POMP	-0,556110434
-ATP5J2	-0,555267292
-ZNF204P	-0,555121445
-INA	-0,554984251
-NUP93	-0,55488654
-STAU2	-0,55454534
-VAT1	-0,554180752
-DDB1	-0,554146967
-THY1	-0,554057809
-SRPRB	-0,553818923
-IMP4	-0,553554219
-SRP19	-0,552319097
-FUCA1	-0,551919323
-PRKCZ	-0,551777138
-CD2BP2	-0,55167071
-C12orf43	-0,551436389
-SUSD4	-0,55137396
-W88821	-0,551080268
-LSM4	-0,550328209
-SNAP25	-0,550276399
-ACSL6	-0,549806401
-MYH10	-0,549550685
-DDHD2	-0,548942799
-PRKACA	-0,548422775
-CHRNB3	-0,547701041
-NEFM	-0,547618123
-PLD3	-0,547495065
-GSPT2	-0,547329995
-ATP6V1E1	-0,546911033
-GABBR2	-0,546899558
-IPW	-0,546596796
-SCAMP5	-0,546380917
-RFPL1S	-0,545994554
-BSN	-0,545979557
-MAGI1	-0,54490486
-DRG1	-0,544733954
-PITPNB	-0,544704547
-LETMD1	-0,544636809
-AI263044	-0,544470885
-STOML1	-0,544383238
-GBAS	-0,544103215
-RAB3GAP1	-0,543092086
-ACTG1	-0,54300405
-PPME1	-0,542943175
-AFG3L2	-0,542490245
-DNAJC6	-0,541912283
-TUBA1B	-0,541625287
-ABCE1	-0,541581351
-ARF3	-0,541401116
-SRSF3	-0,54134715
-NEFH	-0,540578844
-ADK	-0,540377244
-TIMM17A	-0,540158649
-ELOVL6	-0,540054201
-FAM189A1	-0,539987546
-ATP6V1A	-0,539816156
-OAT	-0,53960074
-KIAA0284	-0,539436564
-SLC25A12	-0,538986194
-AP3D1	-0,538816413
-ISCU	-0,53848727
-CDH10	-0,538458105
-APEH	-0,538385859
-TMEM35	-0,537944022
-NDFIP1	-0,537769873
-U79277	-0,537586945
-SYNGR1	-0,53757151
-MEAF6	-0,537175986
-DNM1	-0,536361784
-DEF8	-0,536162488
-PDXK	-0,536128962
-RIT2	-0,536060129
-AACS	-0,535868362
-RAB3A	-0,535840143
-LXN	-0,535676847
-CCBL2	-0,53559953
-ATXN7L3B	-0,535570224
-RCN2	-0,535264733
-SDC2	-0,535187449
-NRXN3	-0,534911729
-SDC1	-0,534748047
-PSMD1	-0,534162775
-UBA5	-0,534098166
-PEX11B	-0,533915774
-RAP1GDS1	-0,533764019
-NUPL1	-0,533680375
-ARMCX1	-0,533607326
-SDHAP1	-0,533209621
-PJA2	-0,532853246
-ACOT7	-0,532662038
-SEZ6L	-0,532618647
-CELF2	-0,532603645
-CXorf40A	-0,532513065
-NDUFB5	-0,532279155
-GARS	-0,532224902
-NRG1	-0,532009485
-SEC31B	-0,53180843
-ME1	-0,531466374
-PSMD8	-0,531445018
-MSL1	-0,531268404
-PCLO	-0,531166247
-RAB14	-0,531006634
-MAGED2	-0,530858407
-EIF3K	-0,530846086
-MMD	-0,530845303
-MYO5A	-0,530805656
-NCRNA00094	-0,530597959
-KIAA1107	-0,53057188
-KIAA0564	-0,530294183
-PSMB2	-0,530140819
-C1orf114	-0,530111522
-GCLM	-0,529867963
-NDN	-0,529086871
-SRD5A1	-0,528786683
-DNAJB9	-0,528374918
-SLC7A8	-0,528181836
-CLIP3	-0,527794519
-NDUFB1	-0,527724864
-CLSTN2	-0,52726691
-C14orf156	-0,527148764
-CIAPIN1	-0,527136633
-ATP5F1	-0,527047789
-PSMB5	-0,526841307
-FAM32A	-0,526499611
-KIAA1644	-0,526147045
-RTN1	-0,526062751
-EXOSC9	-0,525622526
-PFKM	-0,525053758
-TCF25	-0,524910517
-ATP5O	-0,524889972
-PTPRN2	-0,524794642
-SNX4	-0,524373257
-ATP6V1G2	-0,524016622
-SLC35E3	-0,523930118
-SLC2A6	-0,52364368
-SUCLA2	-0,523588063
-PLCB1	-0,523263994
-TMEM30A	-0,521872901
-PDE4D	-0,521870014
-RAB5A	-0,521632556
-MAPK9	-0,521572661
-CAP2	-0,521120749
-RPS6KA3	-0,520660932
-GNAO1	-0,520506337
-PSMD6	-0,520132666
-TBCE	-0,519679173
-C9orf125	-0,519623009
-MN1	-0,51937171
-MFSD1	-0,51842841
-KIF3A	-0,518357676
-SHFM1	-0,517546292
-NRIP3	-0,516545986
-ANKMY2	-0,516365077
-CDK5	-0,516196782
-REEP5	-0,516165841
-SLC1A1	-0,516141732
-UBE2K	-0,516036367
-SMEK2	-0,515537555
-PI4K2A	-0,515462049
-TTC39A	-0,514924765
-GUCY1B3	-0,514788287
-QPCT	-0,514170797
-ST6GALNAC5	-0,514077764
-ATP6V1F	-0,513941613
-HSD17B12	-0,513489073
-PPFIA2	-0,51321383
-PLCH1	-0,512855521
-CNTN6	-0,512564243
-ENTPD6	-0,512350634
-ALAS1	-0,512141897
-RUNDC3A	-0,511994377
-PCMT1	-0,511547085
-IDS	-0,511290223
-PLEKHB2	-0,510964275
-CDO1	-0,510668427
-NDUFB6	-0,510219117
-COX6C	-0,509869079
-OPTN	-0,509603205
-PSMA1	-0,509510596
-STS	-0,509361214
-TIMM10	-0,509318807
-C1D	-0,509252454
-GAP43	-0,509215292
-CCDC6	-0,509150548
-TRIM37	-0,509012308
-ATP2B2	-0,508803511
-PGAM1	-0,50863259
-GGNBP2	-0,508616013
-SRP72	-0,508482078
-TCEAL2	-0,508464868
-SV2A	-0,508330914
-CDK5R2	-0,508227652
-FHOD3	-0,508155146
-FECH	-0,508046235
-ATP2A3	-0,507932978
-SUB1	-0,507787459
-ACO2	-0,507726776
-C20orf3	-0,507526055
-SEC22B	-0,507453281
-VPS35	-0,507278509
-MRPS33	-0,507141908
-TXNL4A	-0,50704416
-ARHGEF9	-0,506224253
-RBM9	-0,506096633
-TMEM135	-0,506088817
-UHRF1BP1L	-0,505757524
-ME2	-0,505446593
-BZRAP1	-0,505378895
-MCAT	-0,50534007
-AKAP6	-0,505213579
-COPS3	-0,505110121
-MRPS35	-0,505107922
-YWHAB	-0,505015581
-PEX7	-0,504955276
-COPS8	-0,504746043
-OXCT1	-0,504643125
-MAD2L1	-0,504589351
-MCTS1	-0,504510155
-LGALS8	-0,50448664
-ACP1	-0,504339709
-MX1	-0,50393674
-NCALD	-0,50389725
-TASP1	-0,503797818
-AGTPBP1	-0,503605082
-RNF128	-0,503554068
-PSMD13	-0,503503704
-TXN	-0,50336484
-NHLH2	-0,50325399
-USP12	-0,503149229
-PFDN4	-0,502988386
-NAP1L3	-0,502893901
-MRPL20	-0,502624211
-ACSL3	-0,502355771
-MTPAP	-0,502307088
-PMPCB	-0,502239978
-SH3GL3	-0,502227406
-API5	-0,502196949
-CAPNS1	-0,5020898
-YWHAZ	-0,501747483
-TOMM70A	-0,501591565
-STX18	-0,501503813
-HNRNPK	-0,501464694
-LRP1B	-0,501433491
-CDC123	-0,500993468
-DCTN6	-0,500740808
-VAPB	-0,500599356
-CCDC56	-0,499906136
-GOT2	-0,499477446
-RHEB	-0,499343134
-PSMD2	-0,499333749
-YPEL5	-0,49910251
-ATP5G1	-0,499077107
-TUBA1A	-0,498949544
-GSTM3	-0,498766376
-EPB41L1	-0,498605796
-EPS15	-0,498447403
-ENO2	-0,498261848
-ASMTL	-0,498100631
-FH	-0,498098378
-CLTC	-0,497596743
-PSMA3	-0,497405846
-UROS	-0,497291028
-OLFM1	-0,496832922
-ATP6V1G1	-0,496818916
-B3GALNT1	-0,496135395
-PHLPP2	-0,496077027
-TSPYL1	-0,495383913
-SERINC1	-0,49538338
-RPL15	-0,495355843
-ITFG1	-0,495195881
-PDHB	-0,494999933
-RABL3	-0,494855325
-TMEM22	-0,49462563
-MCFD2	-0,494506103
-GABARAPL1	-0,494373853
-MAGEL2	-0,493987847
-VPS33B	-0,493750355
-CDIPT	-0,493440531
-ATP6V0B	-0,493438352
-CLGN	-0,493358721
-SEC23A	-0,493255831
-C7orf43	-0,49286586
-ARL3	-0,492481932
-SLC12A5	-0,492392187
-LAPTM4B	-0,492348426
-LOC285359	-0,492290998
-LARP1	-0,49192011
-YME1L1	-0,491725992
-RAB2A	-0,491586306
-SPATA20	-0,490991626
-ASH2L	-0,490785052
-PTBP2	-0,490747846
-WTAP	-0,490599757
-NANS	-0,490410248
-SCFD1	-0,490269997
-EPB49	-0,489916122
-TUFT1	-0,489843226
-POP4	-0,489594415
-CACNA1G	-0,489236615
-PRPF19	-0,48917604
-NCOA4	-0,488872014
-C1orf216	-0,488856307
-TXNL1	-0,488777426
-AMPD2	-0,48875487
-ASL	-0,488300478
-PFDN1	-0,48807629
-EXTL2	-0,488020888
-RPA3	-0,48773487
-ACVR1B	-0,487609726
-ANKRD46	-0,487476076
-GRIA1	-0,48726366
-PSMB6	-0,487099126
-CAPRIN2	-0,486969775
-SRGAP3	-0,48684289
-ARPC5L	-0,486786621
-PSME3	-0,486309204
-NME2	-0,486066455
-ISCA1	-0,485683262
-ZNF365	-0,485504618
-PINK1	-0,485341061
-RWDD2A	-0,48504437
-EXOC1	-0,484927354
-ECE2	-0,484617735
-WDR77	-0,484600271
-AI890972	-0,484490353
-ERBB4	-0,484253264
-PSMD4	-0,483962197
-RAB6C	-0,483864006
-CSTF3	-0,483798153
-NIPA2	-0,483638091
-AK5	-0,483482302
-C17orf91	-0,483141592
-INPP4B	-0,482534933
-PJA1	-0,482372063
-BE551361	-0,482367089
-B4GALT5	-0,48224903
-MTX2	-0,481915827
-MGST3	-0,481667788
-TRMT11	-0,481613419
-PTPRN	-0,481522612
-DNAJC12	-0,48150495
-FTSJ2	-0,481162212
-CCT8	-0,48112028
-PGAP1	-0,481030935
-SLC25A44	-0,480898127
-AMIGO2	-0,480319409
-SCAMP1	-0,480275681
-RBKS	-0,480222
-SYN1	-0,48014199
-APEX1	-0,479680328
-AL157484	-0,4790893
-PAK3	-0,479026618
-SLC25A13	-0,478484409
-EIF1B	-0,478403329
-DLAT	-0,478235597
-AI375694	-0,47804406
-PMS2L1	-0,477748782
-DYNC2LI1	-0,477528415
-RANBP9	-0,477445784
-PTPN20A	-0,476653786
-ZMYM4	-0,476508652
-UQCRQ	-0,476353248
-EXOSC7	-0,476299374
-NDUFB3	-0,476207507
-LCMT1	-0,476121484
-ZNF547	-0,47597802
-TBCA	-0,475802982
-MAPK8IP3	-0,475554385
-N80935	-0,475378775
-SLC4A3	-0,475327531
-AASDHPPT	-0,475086681
-CAND2	-0,475049952
-CXorf40B	-0,474988185
-FXYD6	-0,47456179
-RNF10	-0,474499733
-ELOVL4	-0,474412575
-AAK1	-0,474378982
-SEH1L	-0,474159291
-PTPRU	-0,473978747
-LPGAT1	-0,473432618
-VPS24	-0,473360696
-MCF2	-0,473341916
-FAR2	-0,473007144
-CKMT1A	-0,472884518
-TMED3	-0,472883274
-RNASEH1	-0,47283341
-NDUFA3	-0,472657747
-GLS	-0,472644869
-FAM168A	-0,472617309
-KLHDC10	-0,472577269
-GLRX5	-0,472478522
-SYT17	-0,472292582
-PAM	-0,472018566
-CLTB	-0,471770785
-COPS2	-0,470912718
-DDA1	-0,470419616
-PCSK2	-0,470372976
-SLC25A6	-0,470332168
-TPI1	-0,470300584
-MECR	-0,47026417
-ORC4L	-0,47025895
-ITPR1	-0,470228063
-HMG20A	-0,470060529
-GNB5	-0,470039178
-TMEM208	-0,469963608
-NCAPG	-0,469752447
-GLRB	-0,469638821
-ATP6V1D	-0,469577982
-AKAP11	-0,469501191
-SH3GL2	-0,46948768
-NISCH	-0,469445416
-SIPA1L1	-0,469275377
-PFKP	-0,469125064
-LYRM4	-0,469088537
-SLC4A1AP	-0,46898494
-AP2A2	-0,468669242
-CX3CL1	-0,46850557
-WBP11	-0,468444743
-LASP1	-0,468444317
-GOT1	-0,468375399
-C6orf120	-0,468133996
-SPAG7	-0,468070563
-SERGEF	-0,467688975
-TFB2M	-0,4675501
-AP3B2	-0,467537408
-PAFAH1B1	-0,467362101
-BPGM	-0,467130793
-CRAT	-0,466839519
-DDX1	-0,466770911
-ADAM23	-0,46652833
-ASB6	-0,466473575
-PCDHA1	-0,466456945
-TUSC3	-0,465574044
-TCEA2	-0,465512943
-SMARCA4	-0,4653413
-DAPK1	-0,465142929
-DBNDD1	-0,464965333
-NDUFC2	-0,464959656
-IDH3B	-0,464778307
-CDC37L1	-0,464692992
-WDR11	-0,464429092
-CD200	-0,464378251
-TUSC2	-0,464289641
-IRGQ	-0,464009317
-CALY	-0,463919598
-NNT	-0,463872117
-MSH2	-0,463745236
-GYG1	-0,463657489
-FAM134C	-0,463380379
-RTN2	-0,463379977
-RBM12	-0,463289569
-SYNJ1	-0,463207762
-ABCA5	-0,462881594
-ENTPD4	-0,462777994
-MAP2K4	-0,462732144
-AIMP2	-0,46256199
-PITPNA	-0,462484131
-BNIP3	-0,461982272
-COPS5	-0,461956463
-BRE	-0,461910476
-MIR21	-0,461667267
-ATP5S	-0,46152488
-SIN3B	-0,461515059
-NAT10	-0,461457105
-MTCH2	-0,461117099
-ACHE	-0,461032229
-PSD3	-0,46079613
-UCHL3	-0,460466303
-SMPX	-0,459975528
-USP11	-0,459753441
-RNF187	-0,459566796
-AAGAB	-0,458932639
-ENY2	-0,458770966
-NDEL1	-0,458614173
-FAM184A	-0,458384449
-TOX4	-0,458204483
-SLC25A15	-0,458110832
-SACM1L	-0,458050139
-ADARB1	-0,458034616
-SPHK2	-0,457781426
-CES2	-0,457687554
-CYFIP2	-0,457201169
-KPNA2	-0,457034156
-ACTR1A	-0,456856222
-SLC25A22	-0,456321526
-DPYSL3	-0,456025294
-PRKAR1A	-0,455984698
-SIDT1	-0,455560984
-TIPRL	-0,455474112
-EIF5	-0,455347544
-C16orf58	-0,455176502
-RAB7A	-0,454946879
-MFSD6	-0,454914435
-NDUFS2	-0,454605666
-APOOL	-0,454580027
-GNB1	-0,454284789
-SARS	-0,454282127
-PIK3R3	-0,454240907
-SERINC3	-0,454097365
-ST3GAL5	-0,45407104
-DHRS11	-0,453695947
-NEDD8	-0,45367218
-RAB15	-0,453664346
-HSPA13	-0,453577406
-OLA1	-0,453153228
-C3orf18	-0,45312023
-AF131844	-0,453027105
-C12orf52	-0,452914604
-ACBD3	-0,452894377
-PCIF1	-0,452240197
-BMP2K	-0,451224584
-TSPYL5	-0,450674174
-SEC63	-0,450642641
-C7orf44	-0,450408444
-PWP1	-0,450360796
-SLC25A14	-0,45012674
-SYP	-0,449768016
-PRKCB	-0,449564151
-KIF2A	-0,449276369
-PEX26	-0,449100108
-SDHA	-0,448617251
-PITRM1	-0,448602767
-PPA2	-0,448269554
-MAN2A2	-0,448177121
-FAM49A	-0,448170721
-KCTD9	-0,448062861
-REEP2	-0,44801948
-NDUFS3	-0,447803075
-CHGA	-0,447356315
-UBE2E3	-0,447311178
-LOC595101	-0,447006376
-RNF170	-0,446698112
-TMCO1	-0,446651514
-PCCB	-0,446640741
-RAB1A	-0,44645249
-ATP1A1	-0,446309137
-KIAA1045	-0,446174802
-CASD1	-0,445992918
-C3orf37	-0,445975885
-RAD17	-0,445659766
-BBS4	-0,445631347
-TBC1D19	-0,445509157
-TSG101	-0,445289202
-DKK3	-0,445181251
-KCNQ2	-0,444911548
-EIF4E	-0,44477948
-LOC100134209	-0,444742688
-OSTF1	-0,444651424
-PPCS	-0,444330494
-ATP13A2	-0,443924538
-DHRS7B	-0,443866868
-TSN	-0,443785273
-AI201594	-0,443780197
-UBE2J1	-0,443536878
-C12orf51	-0,443320039
-INPP5F	-0,44324612
-KIAA0391	-0,443138749
-NDUFB8	-0,442168118
-COX8A	-0,442151263
-PLCB4	-0,442128902
-UQCRC1	-0,442055114
-RNMT	-0,442010619
-PSMB4	-0,441631296
-ATP9A	-0,441570839
-COMMD8	-0,441419712
-STX7	-0,441415012
-UQCRFS1	-0,441387219
-ARMC8	-0,441335025
-USP33	-0,441131902
-SC4MOL	-0,441051846
-AVL9	-0,440604375
-CORO1C	-0,440555184
-ATP6V0A1	-0,440500219
-AKTIP	-0,440321706
-C11orf49	-0,440065839
-ACCN1	-0,439959618
-DYNC1H1	-0,439954428
-RTN4	-0,439926435
-IFT52	-0,439664934
-ARIH1	-0,439616652
-SLC23A2	-0,439279622
-FDPS	-0,439263979
-ZW10	-0,439088192
-C6orf211	-0,438493952
-CAPZA2	-0,438442617
-TRIM9	-0,43841496
-PANK2	-0,438226487
-SLC25A36	-0,437878589
-TM7SF2	-0,437751686
-GPD1L	-0,437274057
-TM2D3	-0,437156245
-TBC1D22A	-0,436837159
-AFF2	-0,436678505
-PSMA4	-0,43652406
-SCAPER	-0,436328183
-KPNB1	-0,43624217
-C8orf33	-0,436164892
-RRAS2	-0,435924543
-PNMA1	-0,435862986
-DRD2	-0,435854058
-CCDC92	-0,435740221
-CYB5B	-0,435703661
-DNM1L	-0,435497666
-FAM98A	-0,435109538
-CYCS	-0,43500707
-UBE2B	-0,434857087
-DCTPP1	-0,434751269
-ENC1	-0,434576571
-SAP18	-0,434463135
-MED7	-0,43446171
-UBXN6	-0,433506891
-MAEA	-0,433493136
-C20orf27	-0,433220759
-ARFGEF2	-0,4331108
-FKBP9	-0,433030189
-COQ10B	-0,432955202
-SNRNP25	-0,432902395
-PHKB	-0,432809153
-CETN2	-0,432732838
-PIK3R4	-0,432641256
-EFR3A	-0,432263211
-FAM162A	-0,432255742
-LOC732160	-0,432226821
-SRPK2	-0,432044566
-USP9X	-0,431489845
-DENND2A	-0,431031563
-PPP2CA	-0,430950806
-CHST1	-0,430892555
-OSBPL9	-0,430720865
-TPM3	-0,430527364
-UGP2	-0,430314768
-AL049387	-0,430134526
-ARHGDIG	-0,429952838
-GPR161	-0,429932801
-HGSNAT	-0,429440496
-TCEAL4	-0,429402449
-KHDC1	-0,429285977
-SPATA7	-0,428924113
-NIPSNAP3B	-0,428922472
-NHP2L1	-0,42870798
-BZW2	-0,428685674
-BZW1	-0,428658261
-ABCF3	-0,428526247
-PEX19	-0,428349422
-POLR2K	-0,42820853
-FAM134B	-0,428156057
-TUBGCP4	-0,428150919
-CSNK2A1	-0,427824997
-PPP2R5D	-0,427719013
-CEND1	-0,427667723
-RNF11	-0,427514623
-EBNA1BP2	-0,427275229
-SDHC	-0,42690156
-ATP6AP2	-0,426823582
-MAPK1	-0,426681157
-YTHDC2	-0,425950246
-ACTR3B	-0,425721173
-LRRC47	-0,424928312
-ANO10	-0,424906321
-MORF4L2	-0,424702281
-NAE1	-0,424669605
-GRSF1	-0,424576498
-UBE3C	-0,42455123
-RRM1	-0,424268285
-IARS2	-0,424201991
-HINT1	-0,423973896
-B4GALT7	-0,423964657
-OBSL1	-0,423852756
-RPH3A	-0,423713255
-PTPRM	-0,423526608
-TRAP1	-0,423405292
-GSTO1	-0,423136683
-PGK1	-0,423107749
-KCTD2	-0,423033005
-AKAP9	-0,423014145
-KIAA0090	-0,422971022
-NIF3L1	-0,422805913
-SAE1	-0,422487927
-TRAPPC4	-0,422454822
-UBE3B	-0,422322842
-MRPL13	-0,422291395
-ARF1	-0,422218883
-NCKAP1	-0,421739152
-COX11	-0,421717769
-XPA	-0,421552598
-FKBP11	-0,421544606
-ZFAND1	-0,42136139
-RUSC1	-0,421250909
-PSMC2	-0,42099626
-MCM4	-0,420976269
-HEXA	-0,420954607
-PDE4A	-0,420795908
-VPS45	-0,420785909
-OGFOD1	-0,420640442
-ADPGK	-0,420505817
-AP2M1	-0,420467875
-PSMD5	-0,420139323
-PGRMC1	-0,420109613
-CLASP2	-0,419942702
-CAMTA1	-0,419843296
-COX5A	-0,419753275
-BCAP29	-0,419678508
-C21orf59	-0,419586484
-INSIG1	-0,419347593
-NDUFAF1	-0,419256514
-SNCG	-0,419205938
-NCAN	-0,418993508
-SLC24A3	-0,418714364
-MAP2K1	-0,418679322
-BRCC3	-0,418660516
-MYCBP2	-0,418420128
-PREPL	-0,41818051
-TUFM	-0,418149804
-LYRM2	-0,41810337
-ORC3L	-0,417994092
-TSR2	-0,417894679
-SLC41A3	-0,41774061
-DZIP3	-0,417712026
-MRPS11	-0,417644175
-B4GALT6	-0,41761846
-CHD5	-0,417472
-TUBA1C	-0,417351982
-OTUB1	-0,41729395
-DCAF6	-0,417154254
-UQCR10	-0,417021115
-BEX4	-0,416948363
-RTN3	-0,416868526
-GOLT1B	-0,416408995
-MRPL3	-0,416396676
-DDX19A	-0,416375948
-C4orf41	-0,416356919
-SEMA3G	-0,416349944
-TUBA3D	-0,416216957
-B4GALNT1	-0,415958605
-TOR1A	-0,415819164
-SUPT16H	-0,415597727
-ACTR3	-0,415469056
-ABCB9	-0,415410201
-SERF1B	-0,415262572
-PSMC6	-0,415072747
-GALNT2	-0,414525722
-ARF5	-0,414370994
-TCEB1	-0,414262524
-FEN1	-0,414164817
-HS2ST1	-0,413801139
-FBXL15	-0,413238338
-ANAPC10	-0,413161353
-MAPK10	-0,413048251
-FGF12	-0,412576909
-GTF2B	-0,412561968
-CALM3	-0,412474461
-C12orf5	-0,412385409
-BTRC	-0,412323302
-UBXN8	-0,411884422
-G6PC3	-0,411853401
-MARK4	-0,411850043
-SDHB	-0,411814414
-FXC1	-0,411804756
-KIAA1467	-0,411406746
-COL4A3BP	-0,411372338
-MADD	-0,411317373
-SLC25A11	-0,411257994
-APBB3	-0,411242683
-LDHB	-0,411172229
-ENTPD3	-0,410988615
-CAMK2B	-0,410817586
-C15orf24	-0,410807275
-RAB11FIP5	-0,410722406
-C18orf1	-0,410410534
-IL13RA2	-0,410393436
-TMEFF1	-0,40994415
-TAX1BP1	-0,409905258
-ABHD11	-0,409662969
-SETD4	-0,409479623
-NARS	-0,409352949
-LOC441259	-0,409193342
-SMAD2	-0,408937637
-MAGEH1	-0,408820062
-LPIN2	-0,408744346
-WRB	-0,408371938
-HSPB11	-0,408269901
-COMMD9	-0,407620354
-RMND1	-0,407542555
-RBP1	-0,407484296
-TSPAN7	-0,407465467
-YKT6	-0,407243851
-ATP5L	-0,407238078
-STAT1	-0,407123963
-SPTAN1	-0,407085674
-SLBP	-0,407034029
-FAM115A	-0,407018502
-ATP1B1	-0,407007242
-GIN1	-0,406994648
-SLC25A4	-0,406703055
-RPAP3	-0,40653888
-ELAVL4	-0,406510215
-LDHA	-0,406394191
-GABRG2	-0,406143723
-ACOT1	-0,406088493
-LZTFL1	-0,406077259
-LARP4	-0,406073312
-PTPRG	-0,405852123
-DIRAS2	-0,405793372
-SNCB	-0,405789504
-CDS1	-0,405765281
-ARL2BP	-0,405758176
-BCL2L13	-0,405729545
-STAT4	-0,405634359
-C17orf75	-0,405632179
-ELAVL2	-0,405590653
-DNM3	-0,405342092
-SNX16	-0,404866663
-TACO1	-0,40485549
-HPGD	-0,404805074
-CHMP2B	-0,404775945
-DPP8	-0,404495701
-SYBU	-0,403649563
-CHP	-0,403478973
-GTF2H5	-0,403475179
-PPP2R5B	-0,403191055
-TRAK1	-0,402996995
-ACSL4	-0,402921692
-RABGAP1L	-0,402883713
-PSMB3	-0,402864552
-ASTN1	-0,402784524
-TIMM23B	-0,402679864
-NDUFC1	-0,402669713
-GPM6A	-0,402645229
-NCDN	-0,402391637
-TMEM183A	-0,402206694
-LACTB2	-0,402125728
-SFPQ	-0,401934429
-SLC1A4	-0,401903736
-LOC731884	-0,401617561
-TTC3	-0,401599425
-APBA1	-0,401587582
-FAM20B	-0,401527926
-ISOC1	-0,401479145
-TMEM70	-0,401425176
-GLUD1	-0,401204073
-NDUFA4	-0,401152135
-SHANK2	-0,401076931
-NDUFA6	-0,400922451
-FAM128A	-0,400907344
-TSNAX	-0,400758374
-BLCAP	-0,400561763
-WASF3	-0,400514139
-MTMR6	-0,400412018
-CBARA1	-0,399961135
-SMCR7L	-0,399645568
-REXO2	-0,399637796
-ASTN2	-0,399013865
-FBXO31	-0,398919379
-MRPS10	-0,398754479
-GNAL	-0,398117434
-RDH11	-0,398104472
-ANKH	-0,398086916
-EPHA5	-0,397910595
-DPY19L2P2	-0,397861593
-NRXN1	-0,39777997
-FOXA1	-0,397622781
-AGGF1	-0,397583973
-CLCN6	-0,397581706
-PRKAG1	-0,397496639
-GRM5	-0,397456403
-BCAT1	-0,397331444
-MAP1LC3B	-0,397317027
-HMGCL	-0,397130437
-IFIT5	-0,397045055
-FAM82B	-0,397007464
-TMEM189-UBE2V1	-0,39671729
-TMEM160	-0,396535704
-PIGZ	-0,396390486
-VDAC2	-0,3962914
-BCAP31	-0,396227306
-CUL2	-0,395939867
-C5orf30	-0,395902062
-VAMP4	-0,395520757
-CLTA	-0,395495699
-NOS1AP	-0,395452681
-YWHAH	-0,395414553
-AGL	-0,39537715
-PPIA	-0,395286888
-POLR2E	-0,395239973
-FAM190B	-0,395231307
-CAND1	-0,395218949
-DIABLO	-0,395167608
-FAM155A	-0,395099838
-FAM174B	-0,394929763
-ABCA11P	-0,394841999
-LMF1	-0,394801997
-EIF3I	-0,394774336
-RRAGA	-0,39363313
-SLC25A5	-0,39336993
-BTBD3	-0,393323586
-SLC38A6	-0,393193457
-TSPYL4	-0,39289974
-NDUFA8	-0,392898828
-ERI3	-0,392853573
-CDH11	-0,392815946
-VPS11	-0,392712183
-RPP40	-0,39270293
-SMS	-0,392616216
-USP4	-0,39251437
-RAN	-0,392486577
-SYT11	-0,392234251
-SEC23IP	-0,392233152
-SUPV3L1	-0,392124663
-TOX3	-0,392048323
-OSBPL3	-0,391742979
-ATP5J	-0,391738382
-APC	-0,391687772
-EIF2AK2	-0,391678642
-MPPE1	-0,391534871
-CHD3	-0,391021702
-BE858194	-0,390954653
-GPN2	-0,390821549
-TMEM97	-0,39059622
-BRF2	-0,390477924
-NSDHL	-0,390017568
-LOC654342	-0,389476483
-SATB1	-0,389035394
-RPP14	-0,388984247
-C16orf68	-0,388858051
-PHF14	-0,388842446
-CKAP5	-0,388699527
-MMADHC	-0,388406258
-MEST	-0,388313548
-UQCRH	-0,387974488
-GBAP1	-0,387823169
-PMPCA	-0,387778282
-TMEM41B	-0,387668262
-SCLY	-0,387620138
-OXA1L	-0,387520115
-CLPX	-0,387517816
-EML1	-0,387443167
-DPP6	-0,387318033
-FBXO3	-0,387294212
-GAPDH	-0,386769027
-ATP6V1C1	-0,386766958
-PRAF2	-0,386484628
-NAA35	-0,386425969
-EIF4H	-0,386302469
-SGSH	-0,386196526
-CLCN3	-0,386084887
-SMARCA1	-0,385880429
-FAM158A	-0,385760557
-AP3S2	-0,385712457
-EIF1AX	-0,385367803
-RNF115	-0,385287305
-GPI	-0,385266179
-SEC62	-0,385020013
-G3BP2	-0,384968143
-NDUFV1	-0,38487232
-C19orf42	-0,384758261
-BEND5	-0,384699839
-KCNAB2	-0,384620267
-EVL	-0,384619104
-MTMR9	-0,384460721
-SIRT3	-0,384239932
-CNIH	-0,383916854
-TOLLIP	-0,383913386
-C11orf2	-0,383735535
-NUDCD3	-0,383703548
-MED4	-0,383545823
-RABGEF1	-0,38353381
-PTN	-0,383407974
-GBF1	-0,383365739
-C1orf163	-0,383317238
-LOC100129361	-0,383315417
-CUL4B	-0,383032231
-OXR1	-0,382758654
-TRIM33	-0,382726006
-GPC5	-0,382713696
-C11orf51	-0,382673891
-MAN1C1	-0,382595078
-FGF9	-0,382294616
-SPOCK2	-0,382267861
-GLMN	-0,382038722
-MPP1	-0,381567886
-KIF21B	-0,381555674
-RND1	-0,381481938
-PEX1	-0,381462705
-C2orf34	-0,381417191
-OTUD3	-0,381344145
-MSRB2	-0,381206334
-CCDC85B	-0,38118283
-RGS3	-0,380621769
-SERPINI1	-0,380596066
-C14orf2	-0,380470075
-IDH3G	-0,380458518
-POLR2C	-0,380378788
-CTNNA2	-0,380377628
-XRCC6	-0,380295972
-EIF3A	-0,380281294
-CRBN	-0,380214781
-RPS6KC1	-0,3801397
-NUDT2	-0,380057201
-GOLPH3L	-0,379823471
-CSNK1A1	-0,379812095
-NDUFB2	-0,379757693
-FTO	-0,37940886
-SLC6A15	-0,379271656
-PCP4	-0,379256762
-NIT1	-0,37912136
-CCNC	-0,378699092
-DGKB	-0,378485235
-RANBP6	-0,377965444
-DNAJC8	-0,377764456
-MAPRE2	-0,377675379
-ARFGAP2	-0,377574006
-BDNF	-0,377511436
-HSD17B10	-0,376728332
-AKAP7	-0,376531212
-EHD1	-0,376479944
-PSMD10	-0,376243528
-FABP5L2	-0,376090187
-VAMP7	-0,376017526
-WBP4	-0,375749974
-MAP1B	-0,375485017
-SMPDL3A	-0,375390185
-GPR89C	-0,375362209
-SEPT2	-0,37512019
-GPX3	-0,374915078
-AARSD1	-0,374664572
-HSPA9	-0,37466397
-MAP1A	-0,374598439
-C16orf62	-0,374459363
-CARKD	-0,374388504
-ASS1	-0,374197776
-WDR12	-0,374046313
-ABHD14A	-0,37397421
-SPIN2B	-0,373568971
-RAB6A	-0,373528481
-PTPRF	-0,373483075
-RRAGB	-0,373427062
-STK39	-0,373365187
-COX7B	-0,373307822
-PDCL	-0,373110957
-ATP2A2	-0,373066228
-PPM1E	-0,37285382
-TRMT61B	-0,372798595
-C21orf33	-0,372766056
-MGMT	-0,372730061
-LPHN3	-0,372647138
-WBP2	-0,372385809
-ACSBG1	-0,372296169
-PGRMC2	-0,372287654
-LRRC20	-0,372239514
-AGA	-0,372171162
-NRCAM	-0,372117405
-FUT9	-0,372053568
-C22orf28	-0,371916518
-MRPS15	-0,371914782
-UFM1	-0,371876489
-CAMK2G	-0,371790847
-AVPI1	-0,371692415
-MAST2	-0,371637676
-PPP1R7	-0,371553142
-EEF1A2	-0,371514176
-ATP5D	-0,371416456
-EEF1E1	-0,37139203
-NLRP1	-0,371368381
-PMS2CL	-0,371209965
-CDK5R1	-0,371120209
-C2orf72	-0,371108998
-OAZ2	-0,3710748
-AL109698	-0,37073584
-INPP4A	-0,370700597
-ERH	-0,370513944
-CAMK1G	-0,370474818
-MED24	-0,370430566
-DMXL1	-0,370287216
-COMMD4	-0,370258812
-NOMO3	-0,370043447
-MORF4	-0,369691968
-ZNHIT3	-0,369651044
-GDPD5	-0,369635923
-CUL5	-0,369519961
-AP1B1	-0,369511443
-YARS	-0,369387873
-ABHD10	-0,36913324
-KCNB1	-0,369083149
-SKP1	-0,369015624
-FBXO28	-0,368924883
-ATR	-0,368436696
-TMED2	-0,368132686
-ARPC1A	-0,367983188
-PHYH	-0,367958422
-MRPL22	-0,367879083
-SRRD	-0,367868238
-WDYHV1	-0,367821841
-EIF3CL	-0,367732775
-HMGB3	-0,367450086
-DENND1B	-0,36732795
-ALDH5A1	-0,367318431
-CCNA1	-0,367103911
-FAM134A	-0,367014983
-DZIP1	-0,366778091
-WASF1	-0,366602553
-ATXN3	-0,366426778
-CCDC25	-0,3658102
-ERP29	-0,365799413
-IVD	-0,365499555
-SNX24	-0,365222253
-CDK20	-0,365176415
-TTC9	-0,365148586
-RBM8A	-0,36488846
-AMACR	-0,364562114
-TBPL1	-0,364450426
-PTPMT1	-0,364434415
-CANX	-0,364232908
-ELAC2	-0,364131757
-EIF2S1	-0,364109368
-AKR1B1	-0,363915593
-ACADM	-0,363858719
-RGS16	-0,363795844
-SLC20A1	-0,363602798
-MTUS2	-0,363384151
-ZMIZ2	-0,363364816
-NDUFS4	-0,363146027
-AW242701	-0,363104323
-SNAPC3	-0,363053639
-ENOPH1	-0,362868334
-LYRM1	-0,362706602
-TRMT12	-0,362561085
-BAALC	-0,362539013
-CHMP1B	-0,362404908
-ATP1A3	-0,362300724
-TOMM20	-0,362192747
-PEX14	-0,362047536
-EIF2AK1	-0,361934247
-CNNM2	-0,361790716
-PPOX	-0,361753445
-TAC1	-0,361655557
-GLRX3	-0,361266708
-OBFC1	-0,360197329
-MFN2	-0,360036589
-DGCR14	-0,359808857
-FAM175B	-0,359691136
-PARP2	-0,359639462
-GPR107	-0,359495249
-TUBGCP5	-0,35920098
-ENSA	-0,359186957
-UMPS	-0,358973056
-SSBP1	-0,358916914
-PFDN2	-0,358707301
-IFFO1	-0,35859667
-CCT2	-0,358497035
-PSMA5	-0,358414139
-ZC3H15	-0,358397302
-EPHX2	-0,358269729
-CALB1	-0,358259257
-POP7	-0,358253841
-MRPL12	-0,357874032
-DFNA5	-0,357815106
-PIAS1	-0,357740062
-ARL4C	-0,35770713
-HRAS	-0,357592893
-CEP68	-0,35754909
-SNRPA1	-0,357535253
-SCP2	-0,357518758
-C4orf27	-0,356816465
-TMEM185B	-0,35662055
-SPAG16	-0,356585241
-ESYT1	-0,356493695
-PTP4A1	-0,356347412
-PDLIM2	-0,356333479
-MSRA	-0,355999453
-UAP1	-0,355870622
-CDK16	-0,355785531
-MBOAT7	-0,355761708
-FARSA	-0,355610517
-MRPS7	-0,355424517
-EPHB2	-0,355389176
-LOC729991-MEF2B	-0,355378273
-PDHA1	-0,355252318
-ACTL6B	-0,355166654
-SAR1A	-0,355144478
-KDM1A	-0,355067715
-PRDX3	-0,354963773
-ETF1	-0,354759299
-ARMCX2	-0,354758912
-IQSEC1	-0,35395949
-TIMM13	-0,353925241
-AP2B1	-0,353904118
-STYK1	-0,353863363
-CDK7	-0,353806664
-DLG3	-0,353783905
-SEPHS2	-0,353722454
-MTOR	-0,353463273
-PPIH	-0,353351383
-GRPEL1	-0,353254529
-C9orf91	-0,353075824
-RGS17	-0,353023569
-NTSR1	-0,352789658
-HNRNPH2	-0,352751195
-HCCS	-0,3526918
-C2orf3	-0,352661516
-TFDP2	-0,352647453
-GOSR2	-0,352396188
-PSMB1	-0,352279045
-MPI	-0,35224609
-DUSP26	-0,351953212
-HERC1	-0,351631367
-SORD	-0,351295095
-TUBB2B	-0,351140866
-LPCAT4	-0,351128323
-CFL1	-0,351124653
-ARPP19	-0,350935095
-MTMR4	-0,350923479
-COX7A2	-0,350878835
-PGM1	-0,350865278
-RHOQ	-0,350802567
-CCDC53	-0,350756677
-UQCRB	-0,350742301
-NAPA	-0,350657124
-CSDC2	-0,35061274
-BECN1	-0,350596093
-GYG2	-0,350535323
-GPKOW	-0,35045328
-FXYD7	-0,350387292
-CYLD	-0,349973469
-CSPG5	-0,349825086
-TTC15	-0,349816074
-ILF2	-0,349761198
-STOML2	-0,349586681
-CACNB2	-0,349516102
-VARS	-0,349372141
-ZSCAN18	-0,349241937
-PTRH2	-0,349224021
-P2RX5	-0,349175679
-RALB	-0,349042784
-NUBPL	-0,348899542
-NCBP2	-0,348786336
-DKFZp434H1419	-0,348772873
-UFSP2	-0,348370783
-ARHGEF17	-0,348050229
-FXR2	-0,34801331
-INSIG2	-0,347755165
-XRCC5	-0,347746659
-CLTCL1	-0,34759935
-TMEM177	-0,347585446
-VAMP2	-0,347189398
-EML2	-0,347084746
-SNUPN	-0,346850632
-GPX4	-0,346688538
-RASA1	-0,346685342
-USP46	-0,346590476
-LSM5	-0,346546029
-SEC31A	-0,34652486
-PALM2-AKAP2	-0,346447335
-CKAP2	-0,346385113
-ELOVL5	-0,346375127
-PMS2L3	-0,346133275
-PAQR3	-0,346117871
-ST8SIA3	-0,34604187
-FDX1	-0,34603415
-C12orf4	-0,345989709
-COQ7	-0,345988262
-UROD	-0,345987158
-RPE65	-0,345902642
-DCK	-0,345889475
-RARS	-0,345819092
-CAPZA1	-0,345775372
-NRN1	-0,345693574
-RNF7	-0,345545425
-ABAT	-0,345474072
-CRY2	-0,345467057
-HR	-0,345290796
-CACNA2D3	-0,345213407
-TWIST1	-0,345148814
-P4HTM	-0,345112277
-GDI1	-0,344731063
-GRIA3	-0,344721718
-D4S234E	-0,344715573
-TMEM151B	-0,344385728
-MPHOSPH6	-0,344298044
-PYGB	-0,344201683
-MARCH6	-0,344086188
-AL050136	-0,343680587
-NDUFS6	-0,343667551
-TRAPPC9	-0,343555476
-PYGL	-0,343533875
-EFNB3	-0,343417492
-SCD	-0,343398039
-TFG	-0,342863204
-PPFIA3	-0,342761025
-SENP6	-0,342750174
-KCMF1	-0,342689973
-GNAS	-0,342684217
-MAPK6	-0,342588157
-PRMT5	-0,34246621
-SEPT11	-0,342460355
-MEIS3P1	-0,342265108
-FABP3	-0,3421554
-YIPF6	-0,3420929
-FABP6	-0,342074193
-SRSF9	-0,341825092
-AP1AR	-0,341737984
-PKNOX2	-0,341609179
-PAK6	-0,341535575
-PRKAA1	-0,341378959
-UBA3	-0,34130955
-OAZ1	-0,341251276
-EID1	-0,340941987
-MRPS28	-0,340842312
-AA890010	-0,340724739
-OSBP	-0,340497775
-ATP6V0C	-0,34047911
-ARHGAP24	-0,340414643
-PNKP	-0,340118439
-PSMD7	-0,340085658
-IPO9	-0,340071575
-ARF4	-0,339993296
-TERF2	-0,339818219
-SRSF2	-0,339525933
-PSMC5	-0,33950993
-TM9SF1	-0,339389717
-ACAT2	-0,339093022
-CDK8	-0,33909169
-KIAA0196	-0,338987444
-TFPT	-0,338941882
-TRPC4AP	-0,338718194
-TUBG1	-0,338211067
-SCN2B	-0,338080627
-MTHFD1	-0,338071854
-ATPAF2	-0,338050158
-IGSF1	-0,337997383
-RGPD6	-0,337877048
-C16orf45	-0,33773508
-C10orf76	-0,337659307
-UBE2A	-0,33762595
-PQLC1	-0,337612976
-SOD1	-0,337454918
-ARPC2	-0,337418781
-MEMO1	-0,33728488
-CSDE1	-0,337036578
-PHYHIP	-0,336992273
-LYPLA1	-0,33698776
-NDUFA1	-0,336883322
-MARCKSL1	-0,336747008
-DCTN1	-0,336745427
-COX6A1	-0,336728807
-DPM1	-0,336614034
-ELP3	-0,336602956
-LOC653566	-0,336555692
-COX7BP1	-0,336528019
-CAPZB	-0,336348777
-DCUN1D4	-0,335942405
-UCHL5	-0,335933871
-PSIP1	-0,335684272
-MRS2	-0,335589123
-RABGAP1	-0,335570544
-KCNA6	-0,335454989
-RAC1	-0,335429141
-ZMYM2	-0,33542626
-MRPL17	-0,335371398
-MLF1	-0,335274724
-RFC3	-0,33507418
-ARMCX3	-0,335005795
-GMDS	-0,334931775
-KIAA0317	-0,334922749
-CAMSAP1	-0,334678333
-LSG1	-0,334628714
-PNPO	-0,334625052
-THOC5	-0,334532053
-C11orf58	-0,334154436
-MTCH1	-0,334038037
-KAL1	-0,333848755
-OMG	-0,333590731
-KLHL7	-0,333537148
-TTPAL	-0,333489991
-GLA	-0,333336937
-SEZ6L2	-0,333262252
-SNURF	-0,333035272
-ARL6IP1	-0,332988884
-BFSP1	-0,332976059
-MAPKSP1	-0,332894473
-HABP4	-0,332672498
-SLC8A2	-0,332645114
-CKAP4	-0,332543738
-NPM1	-0,332250102
-CLSTN3	-0,332157745
-RUSC2	-0,33210981
-RCHY1	-0,331805148
-CACNA1D	-0,331681156
-ZFAND5	-0,331302172
-TACC2	-0,331046487
-CHCHD3	-0,331008486
-RGS2	-0,330792786
-LDOC1	-0,330775706
-BTN2A1	-0,33075204
-WDR45	-0,330593865
-W87688	-0,330499179
-YWHAQ	-0,330473094
-RAB3GAP2	-0,33029144
-HTRA2	-0,330240669
-SNRPD1	-0,330240562
-ANXA7	-0,330030639
-KIAA1024	-0,329770804
-RAD51C	-0,329735785
-PRPF18	-0,329474331
-CCT6B	-0,329361737
-ABCD3	-0,329205796
-PARN	-0,329139621
-APOL2	-0,328983174
-MRPS18A	-0,32863432
-RASL10A	-0,328581006
-COG8	-0,328398026
-ZNF512B	-0,327877848
-ATP5H	-0,327758416
-PRDM4	-0,327710757
-TSPAN3	-0,327644045
-EPB41L3	-0,327416874
-APLNR	-0,327394979
-TFR2	-0,327337619
-GADD45A	-0,327012981
-POLR3F	-0,326871651
-FASTKD3	-0,326789822
-TCERG1	-0,326746174
-VPS41	-0,326459968
-C17orf101	-0,325979143
-EXOC3	-0,325763291
-SLC25A17	-0,325666279
-GDAP1L1	-0,325526797
-HCFC1R1	-0,325022815
-SF3B5	-0,324878766
-TEX10	-0,324812522
-PSMA7	-0,324673715
-TCTN3	-0,324389244
-NOVA1	-0,32437578
-RABEPK	-0,324366299
-ALG5	-0,324335095
-ENOSF1	-0,32427768
-SH3BGRL3	-0,32409913
-CTNND2	-0,324002004
-NKRF	-0,323983769
-SLC6A1	-0,323833407
-MAPK1IP1L	-0,323722226
-RAB22A	-0,323713658
-GRP	-0,323354345
-SDS	-0,323335387
-IBTK	-0,323304602
-CARS	-0,322679359
-WWP1	-0,322463311
-ARL8B	-0,322442301
-SLC19A2	-0,322361872
-F8A3	-0,322202521
-LPHN1	-0,322183082
-SMARCD3	-0,322148361
-GPN1	-0,322024809
-FAF2	-0,322014431
-SLC35B1	-0,321878066
-MPV17	-0,321698226
-TOM1	-0,321634922
-NEDD4L	-0,321518057
-MRFAP1L1	-0,321393672
-C6orf62	-0,321303598
-POLR3B	-0,321247444
-HTR2A	-0,321189596
-CUL3	-0,321141566
-PSMD9	-0,321108014
-LRP3	-0,32099653
-TMEM62	-0,320873847
-PLS3	-0,320803014
-SUMO1	-0,32076762
-DLG4	-0,320617015
-ANKRD17	-0,320557554
-ARFIP2	-0,320500236
-HMGN4	-0,320196335
-PRKAG2	-0,319945607
-STAR	-0,319749743
-NF1	-0,319726773
-ATOX1	-0,31967306
-UBE2M	-0,319629201
-NDRG3	-0,319446308
-SNPH	-0,319396594
-TPD52	-0,319178712
-PLK2	-0,319120325
-C1QBP	-0,318975829
-SRSF8	-0,318843616
-USP22	-0,318806098
-GPD1	-0,318728943
-MAPK8IP2	-0,318691894
-USP20	-0,318610382
-RPA2	-0,31845096
-CCPG1	-0,318358561
-NQO2	-0,318256129
-POLR3C	-0,318231923
-HBXIP	-0,318079181
-MRPS31	-0,318018334
-SNRPB2	-0,31801084
-CACNG3	-0,317104885
-CCNE1	-0,316783937
-NDUFAF4	-0,316755785
-GRK6	-0,316405946
-ZER1	-0,316363024
-CHCHD7	-0,316179658
-C20orf29	-0,315860291
-AI693193	-0,315746456
-TPMT	-0,315745725
-TPPP3	-0,315557058
-CTH	-0,315210231
-HSDL2	-0,31516145
-MAPRE3	-0,314964867
-NLE1	-0,314918022
-ARHGEF4	-0,314777145
-STK19	-0,314737564
-AW503390	-0,314280211
-KIAA1279	-0,314104435
-CA14	-0,313849822
-CYP2E1	-0,313441486
-FHL1	-0,313417456
-MYL6B	-0,313075964
-PACRG	-0,3129322
-SCN2A	-0,312912414
-POLR3G	-0,312898745
-MED6	-0,312862133
-PCSK1N	-0,312861133
-FLJ10038	-0,312756044
-PHTF1	-0,312716368
-PRPF4	-0,312654478
-RPRD1A	-0,312642779
-HLF	-0,312545473
-MTMR1	-0,312535102
-MFN1	-0,312461722
-C1orf50	-0,312398425
-QPRT	-0,312349796
-ZDHHC6	-0,31229266
-ITGAE	-0,311863717
-SLC18A1	-0,311739998
-CD83	-0,311711539
-GGCT	-0,311631664
-KIAA0100	-0,311503156
-OPN3	-0,311374884
-SSX2IP	-0,311111099
-NUCB2	-0,31105706
-UTP11L	-0,311015852
-GOLGA8B	-0,310924837
-UST	-0,310734373
-PRKCI	-0,310493775
-AP2S1	-0,310480065
-WBSCR22	-0,310476192
-PPP3CA	-0,310434457
-PDSS2	-0,310396648
-PEG3	-0,310335546
-ATP5E	-0,310319916
-GABRA5	-0,310200087
-AGPAT4	-0,310173061
-PDCD10	-0,310157516
-DDOST	-0,310094837
-RPL23	-0,309992315
-HOMER1	-0,309485866
-C1orf123	-0,309187816
-POLE3	-0,309012195
-DDX41	-0,308923345
-HSD17B8	-0,308824584
-GMPR2	-0,308792858
-SCARB2	-0,308695909
-DGUOK	-0,308606021
-MAGEF1	-0,308535371
-FOXA2	-0,308348483
-GLS2	-0,308287643
-TBCC	-0,308286536
-FBXO41	-0,308255485
-SLC12A1	-0,308214984
-PELO	-0,308137793
-KCNE1L	-0,30811412
-RBBP4	-0,308007454
-UBL5	-0,307720013
-KLHL12	-0,307571676
-FTSJ1	-0,307464516
-ZFYVE16	-0,307366442
-PPT1	-0,3073579
-ZC3H13	-0,307293327
-DYRK1A	-0,307183877
-PHACTR2	-0,306935621
-SLITRK3	-0,306872073
-PI4KA	-0,306770561
-RNPS1	-0,306364972
-RALGAPB	-0,306086767
-BRP44	-0,305953308
-BNIP1	-0,305883874
-SUPT4H1	-0,305675152
-BCKDK	-0,30566687
-PLAA	-0,305619464
-ACTR2	-0,305363631
-PION	-0,305054773
-NFU1	-0,305010295
-CCT6A	-0,304801168
-KIAA0427	-0,304585348
-EHD3	-0,304533089
-FAM63B	-0,304437794
-STK25	-0,304425083
-POLB	-0,304419007
-MRPL35	-0,304416576
-UBE2Z	-0,3043165
-GSTZ1	-0,304133065
-AP3S1	-0,30395899
-SPATS2L	-0,303776395
-LOC729580	-0,303766036
-RALGAPA1	-0,303697943
-PUF60	-0,303647762
-DAP3	-0,303640732
-AHI1	-0,303570806
-UBE2NL	-0,303361552
-TMEM164	-0,303165514
-DOCK3	-0,303099341
-CADM3	-0,303050893
-ZNF219	-0,302968533
-PRKAR1B	-0,302898104
-DOK5	-0,302798088
-ORMDL2	-0,302372011
-ACVR2A	-0,302331205
-ALDOA	-0,30171568
-ATRN	-0,301666345
-COX7C	-0,301597748
-PRKDC	-0,301229867
-GNG10	-0,300757182
-SNX17	-0,300752701
-RBMS1	-0,300466996
-AJAP1	-0,300458474
-PREP	-0,300414848
-ALDOC	-0,300361514
-LAMA4	-0,300246196
-PI4KAP1	-0,300223018
-TMEM222	-0,30010369
-PIGB	-0,299980372
-SSSCA1	-0,29997354
-DCUN1D1	-0,299517655
-DLSTP1	-0,299414392
-ITM2B	-0,299325985
-AK025651	-0,299260618
-ACOT13	-0,299073057
-ZNF593	-0,298588283
-LOC100129250	-0,298385026
-H2AFY	-0,298292243
-IGF1	-0,298232454
-KIAA0368	-0,29819687
-FKBP3	-0,298122528
-C12orf49	-0,297820161
-PRKRIR	-0,297808472
-GLUD2	-0,297805688
-NBL1	-0,297799978
-PTPN4	-0,297657679
-LOC644617	-0,297586698
-IL33	-0,297538719
-CUL4A	-0,29730361
-SIP1	-0,297199387
-POLDIP2	-0,297140479
-EBP	-0,297109427
-FASTKD2	-0,296665172
-SMPD1	-0,296658212
-FAM55C	-0,296650198
-TRPV2	-0,296465177
-DOPEY1	-0,29633822
-SCYL3	-0,296201386
-UBL3	-0,296188632
-STK38L	-0,296164266
-APITD1	-0,296017845
-SFXN1	-0,295918484
-CPT1A	-0,295754312
-USP8	-0,29570338
-MRPS30	-0,295702739
-ATG7	-0,295335659
-C10orf88	-0,29514056
-PIPOX	-0,295018193
-RAC3	-0,294600261
-CIAO1	-0,294564961
-KLC2	-0,294523931
-LEPROTL1	-0,29448316
-ENDOD1	-0,294147277
-FEM1B	-0,294007766
-IRS1	-0,293342341
-CYP51A1	-0,293155923
-DYNLRB1	-0,292974645
-TOM1L2	-0,292906836
-TDP2	-0,292808809
-MRPL49	-0,292778686
-LRP8	-0,292767989
-MOSPD1	-0,292730297
-C6orf134	-0,29255632
-TRPC1	-0,29249815
-RASL11B	-0,292459191
-AL109671	-0,292334441
-TTC37	-0,292136499
-ODZ4	-0,292070818
-KIN	-0,291741417
-KPNA1	-0,291721639
-CAST	-0,291558763
-NDUFA13	-0,291524477
-AKR1A1	-0,29149158
-QARS	-0,29146477
-MRPS22	-0,29145846
-MMACHC	-0,291414294
-UBQLN2	-0,291358191
-PIK3CB	-0,291242041
-COX6B1	-0,291081182
-PDK2	-0,290962723
-RABGGTB	-0,290962562
-SR140	-0,290943983
-ATF2	-0,290881352
-FADS1	-0,290820194
-SRP14	-0,290691218
-RAD23B	-0,290632171
-AHCY	-0,290521401
-RINT1	-0,290502144
-SRP54	-0,290224786
-COX5B	-0,289972152
-NBN	-0,289962803
-DDX50	-0,289845246
-NUFIP1	-0,289611609
-HDGFRP3	-0,289540354
-HBA2	-0,289412602
-SRP9L1	-0,289377441
-ARFGEF1	-0,289327503
-FAM13B	-0,289118442
-DIMT1L	-0,288943725
-LPO	-0,28888192
-VPS28	-0,288730564
-SSR3	-0,28867602
-SEPT7	-0,288663677
-NARS2	-0,288651232
-EMG1	-0,288493971
-HSPA8	-0,288488899
-TBC1D13	-0,288209587
-TTC35	-0,288076299
-GTPBP4	-0,287916733
-SPG7	-0,287774853
-PAFAH1B3	-0,28772138
-MAPT	-0,28765216
-RERGL	-0,287509361
-HNRNPD	-0,287438947
-PLCL2	-0,287391702
-HLA-DPA1	-0,287200849
-CD55	-0,286966384
-IDH3A	-0,286870398
-STXBP5L	-0,286801199
-MAP3K12	-0,286334641
-PPP2R1A	-0,286259611
-TMEM126B	-0,286136364
-CDKN3	-0,286064506
-ABCC5	-0,286013319
-TMEM127	-0,285913561
-DNAJC2	-0,285585137
-SEC61G	-0,285583827
-SSR1	-0,285489405
-AIMP1	-0,285281231
-YTHDF2	-0,285194578
-FAM86B1	-0,285046154
-CTBP1	-0,285027477
-CHRFAM7A	-0,285001423
-SSBP3	-0,284934817
-MRPL46	-0,284930449
-TSPAN6	-0,284861931
-MYST2	-0,284824247
-GGH	-0,284817124
-PRKACB	-0,2847024
-C2orf47	-0,284692381
-NLK	-0,284579832
-ASNS	-0,28445955
-EXOC5	-0,28439526
-OAZ3	-0,284379411
-CTNNBIP1	-0,284364924
-PVR	-0,284070802
-C16orf80	-0,284019987
-UBE3A	-0,283816198
-EAPP	-0,28376748
-IGSF3	-0,283764031
-KCND2	-0,283569047
-FOXK2	-0,283286684
-SLC35A2	-0,283204451
-TBCB	-0,283168385
-SLC38A1	-0,283158141
-ACCN2	-0,283147998
-FAM149A	-0,283126904
-TIMM22	-0,283102824
-EIF4ENIF1	-0,28310048
-THSD1P1	-0,282819454
-MAGED4	-0,282562753
-CLASP1	-0,282510547
-C1orf61	-0,282424601
-C6orf106	-0,282397365
-WDR44	-0,282155933
-GNL3	-0,282115302
-RCBTB1	-0,28192202
-OSTM1	-0,281535242
-AGPAT5	-0,281510168
-PRNP	-0,281405094
-APPBP2	-0,281330465
-GAD1	-0,281295305
-NECAB3	-0,281056363
-ABCF1	-0,280961256
-DNAJC7	-0,280750506
-EPHB1	-0,280596899
-GPRC5A	-0,280368026
-HSPA14	-0,280049432
-CLPTM1	-0,280042656
-SGPP1	-0,27999737
-ABCG4	-0,279891909
-GFRA1	-0,279146972
-ATP5SL	-0,278849245
-CTSO	-0,278677227
-DCTN4	-0,278556645
-MAP2K2	-0,278535478
-ZNF423	-0,278503712
-FUS	-0,278285124
-ACTR8	-0,278282163
-PRR13	-0,278189761
-ZNF329	-0,278179162
-RNASEH2B	-0,278151755
-LOC284244	-0,278099761
-FAM117A	-0,277715513
-MREG	-0,277651168
-C2orf18	-0,277609469
-AW612311	-0,277599115
-SYNRG	-0,277434047
-SMARCE1	-0,277346186
-DNAJA3	-0,277188103
-PPP2R5E	-0,2770317
-TMCO6	-0,276951805
-C6orf35	-0,276886272
-DDX18	-0,276619655
-TTLL1	-0,276373935
-LANCL1	-0,276361838
-SNRPE	-0,276287655
-DTX4	-0,276233703
-IDH2	-0,276017451
-SACS	-0,275814599
-ABHD2	-0,275491786
-VAMP1	-0,275092752
-AGPAT1	-0,27504004
-TYMS	-0,274913065
-ZDHHC3	-0,27479568
-LMO1	-0,274566957
-UVRAG	-0,274559415
-HBB	-0,274385467
-PSMA2	-0,274273938
-CD24	-0,27422103
-GRAMD1B	-0,27394685
-PRC1	-0,27393137
-YARS2	-0,27376193
-SIGMAR1	-0,273597834
-CPEB3	-0,273534888
-ARMC9	-0,273442678
-DNAJC10	-0,273369377
-TM9SF4	-0,27326642
-RBX1	-0,273166064
-C13orf1	-0,273151402
-PDCD4	-0,273130523
-LUZP2	-0,272843047
-APLP2	-0,272609838
-USO1	-0,272598741
-SH3BP5	-0,272512602
-PPP1R11	-0,272494252
-PEMT	-0,272485616
-CDC16	-0,272287144
-LCMT2	-0,272235596
-DCX	-0,271983078
-DDAH1	-0,271924121
-UBE2D2	-0,271815552
-TANK	-0,271664689
-AW974666	-0,271662837
-USH1C	-0,271630244
-BDH1	-0,271624449
-B9D1	-0,271589518
-BRD9	-0,271105209
-USP7	-0,271052865
-TRIM2	-0,270764995
-PARK7	-0,270634786
-NSFL1C	-0,270597248
-COQ2	-0,269953826
-HNRPDL	-0,269787459
-NOV	-0,269731303
-SLC25A28	-0,269706278
-EXT2	-0,26958066
-VLDLR	-0,269148459
-SLC4A4	-0,268895862
-SMURF1	-0,268798637
-ORC2L	-0,268275919
-ZC4H2	-0,268056536
-SDHAF1	-0,267985583
-VDAC1	-0,267895013
-ALDH1A3	-0,267738476
-PNPLA4	-0,267586498
-HAGH	-0,267406111
-CNTNAP2	-0,267355858
-KPNA3	-0,267278305
-LRBA	-0,267216793
-DPYSL4	-0,267150239
-MCCC2	-0,26714725
-KBTBD4	-0,267031071
-DCTD	-0,267005887
-C1orf21	-0,266982234
-C2orf43	-0,26679916
-SF3A3	-0,266732334
-PTPN3	-0,266674559
-FBXO21	-0,26664933
-CCT7	-0,266615147
-CLNS1A	-0,266539743
-HAPLN1	-0,266160364
-SYT13	-0,26591944
-SENP5	-0,265695364
-HMGB2	-0,265556554
-CANT1	-0,265168032
-CGREF1	-0,265157579
-GRM1	-0,26510368
-ZFHX4	-0,265049797
-PVRL3	-0,264999073
-ADAR	-0,264636454
-TRIM3	-0,264561355
-ANP32E	-0,264413865
-PDLIM7	-0,264406742
-MLH1	-0,264377914
-PRKCA	-0,264376056
-CYB5R3	-0,264120933
-PDE1A	-0,263919942
-LOC100127998	-0,263915362
-WSB2	-0,263691169
-RPF1	-0,263404659
-CXCL12	-0,26333499
-TMEM66	-0,263285506
-EIF6	-0,263232223
-NFE2L1	-0,262789646
-KLHL20	-0,262772392
-PPM1H	-0,262689193
-PIN4	-0,262483899
-TUBA4B	-0,26241982
-ECT2	-0,262276809
-MGC5566	-0,261888759
-C9orf116	-0,261830489
-ASB1	-0,261751394
-ABCC8	-0,261735107
-ELOVL2	-0,261638578
-PHB2	-0,261466477
-ZNF580	-0,261379751
-DNAJC24	-0,261364702
-PSMB10	-0,261344946
-CSE1L	-0,261292597
-ANKRD27	-0,261154598
-TUBG2	-0,261047779
-C6orf162	-0,261001828
-AL034399	-0,260886813
-GLT8D1	-0,26052144
-SRR	-0,260520305
-MCC	-0,260395686
-COX4I1	-0,260324715
-SEP15	-0,260222524
-RNF103	-0,260210477
-ZNF576	-0,260159221
-MGEA5	-0,260092677
-RSL24D1	-0,259958151
-USP13	-0,25969613
-MLLT3	-0,259631882
-SRI	-0,259268888
-NCS1	-0,259133737
-MAPKAPK5	-0,259103348
-IQCG	-0,25908825
-FN3KRP	-0,258914892
-BCKDHB	-0,258870249
-GOLGA5	-0,258736414
-RDBP	-0,258483881
-SUPT7L	-0,258355414
-METTL1	-0,258206012
-CREB3	-0,258159408
-TMEM111	-0,258136123
-NRSN2	-0,257397396
-CNTN1	-0,257314074
-COX10	-0,257277055
-SERPINB9	-0,257269621
-MTF2	-0,256976969
-EDNRB	-0,25676028
-HSF2	-0,25652969
-POLR2L	-0,256424652
-TRIM58	-0,256294322
-DACH1	-0,256241463
-UEVLD	-0,256239024
-ATP1B3	-0,256215499
-SAP130	-0,256053262
-TRPC6	-0,255890704
-HERC6	-0,255794959
-NAV3	-0,255707496
-GOSR1	-0,25567987
-CNR1	-0,255506006
-PSME4	-0,25522233
-CAMKV	-0,254605479
-ADSL	-0,254512794
-BCS1L	-0,254298738
-CCNB1	-0,253924801
-SNX2	-0,253887319
-ASAP2	-0,25387509
-WDR70	-0,253565737
-PTPRE	-0,253309549
-SEPT5	-0,253058348
-SCML1	-0,253051964
-BCR	-0,252946659
-MAGOH	-0,252829021
-SEMA4F	-0,25277628
-CLIP1	-0,252764211
-JMJD4	-0,252747043
-ZMYND11	-0,25273006
-CPSF6	-0,252574141
-PTPRA	-0,252430519
-PLA2G12A	-0,252393049
-MXRA5	-0,252290125
-RFX5	-0,252264534
-WARS	-0,252174212
-HUS1	-0,252166663
-VCAM1	-0,251733145
-CEACAM21	-0,25171453
-RHOT1	-0,251514974
-EMD	-0,251327933
-TSPYL2	-0,251307071
-THNSL1	-0,25130438
-NDUFB4	-0,251250318
-CHMP5	-0,251232028
-SKAP2	-0,251185084
-LRPAP1	-0,251070101
-COMMD3	-0,251069448
-ROGDI	-0,250917557
-PPAP2B	-0,25089017
-ADSS	-0,250852878
-LGI2	-0,250809779
-CBX6	-0,250671998
-NELF	-0,250584567
-DENND5B	-0,250357567
-ATP2C1	-0,239139672
-SUMO2	-0,233193565
-KRAS	-0,208565613
-PEX3	-0,200767265
-PRDX2	-0,195371323
-PDCD2	-0,194653063
-TM2D1	-0,189207426
-KHDRBS1	-0,16653347
-KLC1	-0,156510024
-ANK2	-0,155852142
-HBS1L	-0,155006259
-NTRK3	-0,121314135
-PTPRO	-0,110200451
-PLEKHA5	-0,10184855
-GCOM1	-0,091608137
-TIMM8A	-0,084179504
-MKRN1	-0,074942655
-PLA2G4B	-0,068760926
-RUFY3	-0,059042335
-RIMS2	-0,057507607
-C21orf2	-0,054091983
-METAP2	-0,053236401
-LRRC40	-0,040678287
-RPL10	-0,034862755
-RIOK3	-0,033313025
-SYNCRIP	-0,027340658
-UNC45A	-0,021866459
-MPZL1	-0,020796077
-RANBP1	-0,01610173
-ITGB1BP1	-0,011025016
-UBC	-0,009666523
-RER1	-0,007044099
-PDS5B	-0,005231512
-NCAM1	-0,004638056
-LIMCH1	0,003894784
-VPS13D	0,014841215
-WDFY3	0,017457694
-MRP63	0,023151675
-TSR1	0,064261585
-GRB10	0,066410415
-FAM128B	0,074972161
-PAK2	0,079518764
-PKP4	0,080237181
-TMEM144	0,083124821
-C3orf63	0,086752023
-DDAH2	0,250378216
-AF238870	0,250544885
-PTMS	0,250667518
-JAG1	0,250675664
-RPL32	0,25075902
-UXT	0,250812127
-HSP90B1	0,250888984
-SS18	0,250904748
-RND2	0,250918958
-CLEC4M	0,250931594
-AU147194	0,251115897
-IL1RAPL1	0,251119435
-EPB41L2	0,251131328
-TFDP3	0,251241244
-GAL3ST4	0,251281983
-EDN2	0,251371356
-SFTPC	0,251372616
-TRMT61A	0,251534845
-GPR4	0,251535902
-KEAP1	0,251692277
-RNF122	0,251718243
-NOTCH2	0,251745042
-WDR1	0,251871256
-NFX1	0,252023298
-DOHH	0,252100123
-NES	0,252167647
-SRSF10	0,252172984
-AQP3	0,252182392
-LOC728412	0,252404082
-RCN3	0,252455902
-CSNK1G1	0,252462493
-KCNS1	0,252601737
-CCDC71	0,252614101
-JUND	0,252645305
-LYST	0,252718314
-TPCN1	0,252770336
-MTA1	0,252823052
-RIN1	0,252841454
-ATHL1	0,252944239
-FTSJ3	0,253136044
-SERPINA1	0,253202139
-STARD7	0,2533744
-MRPL34	0,253425868
-PPID	0,25344089
-SH3PXD2A	0,253534644
-UBA7	0,253547625
-RUNX1	0,253686159
-ARNTL	0,253823553
-STAT6	0,253840779
-CASKIN2	0,25393147
-NFATC4	0,253965486
-LILRB2	0,254041373
-PPP1R13L	0,254173566
-RAP1A	0,254249533
-OTUD4	0,254380531
-ZNF516	0,254390037
-ZC3H14	0,254430628
-BTD	0,254441889
-ABHD4	0,254494909
-MT3	0,254554667
-PTCH1	0,254572046
-CDC42EP3	0,254591236
-LOC150776	0,254715807
-PTGES	0,254816225
-TPM2	0,254867646
-TAGLN	0,254960085
-AL050032	0,254984309
-HPN	0,25500915
-FLNC	0,255046574
-GJB3	0,255060346
-RAB40B	0,255071999
-CST1	0,255226531
-FGF21	0,255229382
-AW574933	0,255334628
-FGF5	0,255461872
-CLCN7	0,2555275
-BAHCC1	0,255618646
-FANCA	0,255627746
-CYBA	0,255682121
-TIE1	0,255683605
-ANKHD1-EIF4EBP3	0,255707685
-CDV3	0,255740411
-COL9A1	0,255878907
-TTC31	0,256049153
-ZIC1	0,256075896
-CCDC121	0,256090992
-FUT4	0,256155794
-UCP3	0,256197327
-AU146391	0,25625958
-MMP2	0,256269664
-STXBP2	0,256386629
-TMEM87A	0,2564575
-FXR1	0,256493521
-RDX	0,256507051
-HPS1	0,256516919
-TRAM2	0,256517872
-HYAL2	0,256778041
-TNFRSF14	0,256783849
-NEK7	0,256861333
-AGRN	0,256876471
-SMC4	0,256895131
-GAS7	0,256949822
-PDE4B	0,256950938
-CHD4	0,256970114
-SPP1	0,257084517
-HECA	0,257172806
-NXF2B	0,257181225
-LILRA5	0,257188463
-SCAP	0,257267679
-SNX1	0,257354288
-GIGYF2	0,257400552
-CELF1	0,257407908
-HSD17B14	0,257420303
-DUOX1	0,25770603
-MRM1	0,257826185
-NBR2	0,257852879
-FAM176B	0,257955278
-SYNPO	0,257997864
-GPRIN2	0,258040238
-IER3	0,25816919
-ZNF506	0,258198461
-NM_016414	0,25824817
-VPS53	0,258358594
-PGPEP1	0,258378109
-GNL1	0,25847832
-OGFR	0,258496938
-CXCR2	0,258632799
-C1orf38	0,258857462
-RPL22	0,258901214
-NM_018041	0,259005358
-MYOF	0,259133176
-NGB	0,259197495
-CLIC4	0,259260666
-TBC1D9B	0,259295717
-KCND1	0,259337213
-RNASET2	0,259420675
-EXT1	0,259568659
-AQR	0,259572114
-VWA1	0,259618684
-MUC3A	0,259647513
-CAV1	0,259682957
-IRF4	0,259719685
-OR7C1	0,259728956
-SETDB1	0,259737838
-E2F6	0,259867146
-TFEB	0,259924981
-CPSF3L	0,26005015
-MARCH8	0,260576922
-MFSD11	0,260945964
-ETAA1	0,260954881
-SMARCD2	0,260999203
-RGS12	0,261024661
-CCNG2	0,261112401
-RPS8	0,261183649
-IL17RA	0,261275371
-NUDC	0,261284708
-ZNF133	0,261329337
-ATP13A1	0,261543252
-PICK1	0,26166607
-C20orf117	0,261682534
-GIPR	0,261728602
-HIST2H4B	0,261730186
-S100A11P1	0,261732522
-MARCH3	0,26174629
-ZBED4	0,261794357
-KHK	0,261822851
-SCAMP2	0,26194666
-AF070579	0,261954742
-TECR	0,261998101
-AK024915	0,262016665
-CASP7	0,262240261
-PDK4	0,262293861
-MYO7A	0,262479993
-TUBBP5	0,262483574
-TMEM143	0,262491406
-NAP1L1	0,262524812
-PLEKHB1	0,262542861
-ING1	0,262679424
-SPSB3	0,262786186
-C9orf167	0,262955615
-NTM	0,262977412
-FIP1L1	0,263199662
-FYCO1	0,26321575
-GGT1	0,263227324
-ALG12	0,263240056
-IGL@	0,263282588
-PPBP	0,263290228
-SNX13	0,263292989
-SRSF4	0,263309909
-CYTH1	0,263721364
-AL050035	0,263831657
-TRMU	0,263920451
-TIMP1	0,263959235
-RFNG	0,263965598
-HIP1R	0,264033626
-NR1H3	0,264039538
-NT5C2	0,264091319
-FNTB	0,264115077
-SAR1B	0,264175117
-GIT1	0,26420824
-RRAGD	0,264311012
-HAP1	0,26435511
-FLT3LG	0,264378926
-NM_018612	0,264421364
-SLC7A9	0,26447762
-GLTSCR2	0,264541217
-SUN1	0,264635751
-CEP152	0,264663399
-MBTD1	0,264688291
-SYT12	0,264690461
-ACTR5	0,264835312
-EIF4A1	0,264933012
-COX7A1	0,26511391
-CMTM6	0,265385079
-FAM102A	0,265449454
-AW970584	0,265532869
-FMO5	0,265619005
-N4BP2L1	0,26587536
-SPAG11A	0,265939376
-TGFBI	0,265987004
-RYK	0,266131346
-SERBP1	0,266135884
-AK021988	0,266152576
-NCAM2	0,266199101
-AK024995	0,266233606
-RAB9A	0,266259326
-SYNJ2	0,266313048
-PHLDB1	0,266315252
-PKN1	0,266439146
-MFAP3L	0,266558078
-PPFIBP2	0,266640652
-WBP5	0,266861878
-TMX1	0,266949292
-SLC6A12	0,267009029
-C3AR1	0,267017849
-CSRP2	0,267020264
-SP3	0,267034674
-ATN1	0,267069634
-GNB3	0,267107148
-TIAL1	0,267113358
-GPATCH8	0,267177985
-PMEPA1	0,267182372
-MAP2K3	0,267199274
-NM_018033	0,267304029
-WWTR1	0,267350058
-SEMA6A	0,267400431
-RBPJ	0,267426168
-AL049279	0,267438916
-IL1RN	0,267473934
-QKI	0,267577841
-SOX15	0,267588393
-DMTF1	0,267672579
-RPL19	0,267821304
-TRIM39R	0,267839755
-SLC26A6	0,267879749
-NM_025056	0,267969441
-BBS9	0,267969882
-M85256	0,26799656
-ADORA3	0,268097905
-TMEM176B	0,268515164
-SECTM1	0,268600799
-ST14	0,268612452
-ARHGEF18	0,268652414
-SIRT5	0,268726991
-MYBPC1	0,268763379
-RPL15P22	0,268793196
-SIGLEC15	0,268860828
-DNAJA1	0,26890035
-LMBR1L	0,269042598
-GIMAP4	0,269074847
-MFAP3	0,269075993
-ABCA6	0,269120338
-AW836210	0,26919833
-LOC100133772	0,269228182
-CHST4	0,269387102
-RNASEH2A	0,269387986
-RPL18	0,269450865
-RPLP2	0,269486597
-MEPE	0,269489799
-FAM106A	0,269545639
-GATAD1	0,269621956
-PPP2R3A	0,269725552
-MASP2	0,269836416
-MYO10	0,26992164
-PIGG	0,269941407
-SMG5	0,269952017
-IFI30	0,269956381
-AK025180	0,269971157
-AMD1	0,269982316
-LMOD1	0,270125966
-SNX15	0,270191178
-SCARB1	0,270338985
-SERTAD3	0,270373355
-MBD5	0,270430073
-SLC2A5	0,270454389
-ITCH	0,270468949
-ADA	0,270490353
-PWP2	0,270541137
-ARHGEF1	0,270572389
-C2CD2	0,270675538
-EIF1	0,27071329
-C1orf35	0,270772513
-IFI16	0,270855012
-LOC285830	0,270905428
-IL10	0,271025993
-MORC4	0,2712707
-CA11	0,271346355
-C5orf54	0,271348162
-C14orf93	0,271428228
-RPL17P7	0,271481741
-TMEM161A	0,271564557
-LRCH3	0,271627825
-DFFB	0,271779652
-BAZ1B	0,271859723
-DKFZp547G183	0,271894591
-RAB11FIP2	0,271895928
-PCK1	0,27194659
-TMPRSS5	0,27195628
-TIPARP	0,272078235
-UBE2L3	0,272125747
-ZNF672	0,272142507
-GALNT10	0,272151507
-EXD2	0,272173543
-KAT2B	0,272322281
-RPS11	0,27237174
-POLR2H	0,272422791
-IGLL3	0,272574443
-AA554430	0,272578205
-DOCK10	0,272578712
-DMC1	0,272606886
-CD40	0,272762332
-CDK11A	0,272811711
-UCKL1	0,272898303
-FAM125B	0,273084179
-UBXN7	0,273084433
-SMA4	0,273204796
-DYNLT1	0,273349219
-CTTNBP2NL	0,273380758
-HSPH1	0,273396703
-CYP39A1	0,273418193
-HOMER3	0,273432217
-RRBP1	0,273480926
-ATAD2B	0,27361049
-LGALS3	0,273847411
-LASS2	0,273913098
-ZNF451	0,273935073
-NXPH4	0,27404559
-C22orf46	0,274118605
-KDM4B	0,27422483
-GPNMB	0,274363725
-CYHR1	0,274415705
-CCDC9	0,274487483
-WWC2	0,274522318
-ZNF652	0,274533788
-ILK	0,274538403
-CTDP1	0,27455992
-LOC51152	0,274810051
-AL442084	0,274963062
-CPNE7	0,275259638
-CENPB	0,275294531
-TCIRG1	0,275300556
-PRPF40A	0,275423637
-ARHGAP17	0,27552534
-LOC100133811	0,275961848
-ADAM17	0,276019886
-CRISPLD2	0,276144309
-IFIH1	0,276175289
-LOC440434	0,276293985
-DCLK2	0,276369722
-MS4A6A	0,276482788
-VASH1	0,276499979
-SRSF7	0,276513035
-B3GAT3	0,276752575
-CALHM2	0,276762436
-MAP4	0,276867434
-DULLARD	0,27687625
-CTSS	0,276943812
-BAG3	0,277040195
-KRT8P12	0,277155277
-POLR2F	0,277193722
-CD14	0,277207134
-SF3B1	0,277255775
-EZH1	0,277320185
-MBD1	0,277342685
-MITF	0,277407356
-BAIAP2	0,277445862
-FCGR2B	0,277531437
-PAQR4	0,277547889
-NFATC2IP	0,277597337
-CAT	0,277600148
-TJP2	0,277610024
-CCNA2	0,277687494
-GEM	0,277887602
-C2orf54	0,277935237
-HIRIP3	0,278018588
-MCM3APAS	0,278082892
-CFB	0,278130274
-TAGLN2	0,278365668
-AK024851	0,278382784
-HGD	0,278585783
-NR2E1	0,278716062
-SEC61A1	0,278797194
-PDE4DIP	0,278806635
-FRMD4A	0,278822955
-RHOC	0,278842121
-UBTF	0,278963815
-NCOR2	0,279024257
-PPP6R3	0,279218049
-ALAS2	0,279327775
-SPSB1	0,279537438
-SGMS1	0,279545277
-TEAD4	0,279565374
-AK024897	0,27961031
-IRS2	0,279708094
-TRIM62	0,279977776
-AF308291	0,279984986
-AK022362	0,280079092
-KIAA0495	0,280115197
-CUL7	0,280170918
-PARD3	0,280192562
-NUP98	0,280376383
-DHRS4L2	0,280391865
-AK024093	0,280444114
-VEGFB	0,280560816
-PTEN	0,280592383
-NBPF10	0,280620974
-CASP1	0,280699269
-AK2	0,280734467
-MLX	0,280792537
-GNG11	0,280826824
-HNRNPM	0,280968313
-IL12RB2	0,28098376
-CDK18	0,28098866
-RARA	0,280998983
-GYPC	0,281028129
-PAK4	0,28104576
-SEMA3F	0,281239182
-BAT2L2	0,281335934
-BRD4	0,28139016
-PAOX	0,281415979
-SMAD3	0,281446531
-PIK3R2	0,281480063
-IFT122	0,281682471
-IRAK4	0,281825175
-RASSF2	0,281825652
-RPL13A	0,282085077
-ZNF22	0,282127023
-KDM4A	0,282136199
-CPM	0,282150511
-EIF2S2	0,282316006
-USP48	0,282335945
-CLCNKB	0,282422648
-C11orf61	0,282474246
-ANKRD11	0,282516441
-PTTG1IP	0,282619596
-SEC14L1	0,282620994
-DOCK6	0,282646645
-CARHSP1	0,28271852
-RRAS	0,282814195
-TRIM38	0,283129972
-PLA1A	0,283206252
-GAB1	0,283220235
-PDLIM1	0,283254227
-SSH3	0,283308195
-KLF9	0,283315657
-N4BP2L2	0,283629404
-TNS4	0,283667599
-C15orf28	0,28383226
-ANXA11	0,283988681
-TAF12	0,283993401
-SLC39A1	0,284190806
-SAP30	0,284320416
-RNASE4	0,284337811
-RPS28P6	0,28438483
-DDR2	0,284449824
-BMP4	0,284614799
-CEPT1	0,284615091
-ITPKB	0,284650775
-PLEKHF2	0,284678379
-AW974812	0,284683098
-PTCRA	0,284827371
-SETMAR	0,2848555
-SOCS3	0,284925858
-NM_014129	0,284930906
-MYO1D	0,285094554
-RBL1	0,28514691
-HN1L	0,285254673
-LASS4	0,285307965
-RPS21	0,285547221
-PPP2R1B	0,285765143
-NEO1	0,285937917
-SEC24C	0,286013109
-BCL3	0,286014454
-KCNMA1	0,286080656
-AL137590	0,286198689
-EDIL3	0,286207431
-ARHGEF16	0,286210956
-HCK	0,286227266
-GSTA1	0,286246055
-SLA	0,286356975
-UNG	0,286379363
-SP100	0,286388329
-PRSS53	0,28642638
-MYL6	0,286728542
-CDH5	0,286728949
-C10orf116	0,286730624
-GTF2IRD1	0,286882519
-POLH	0,286995879
-SFRS16	0,287066034
-TPM4	0,28709233
-ABCD4	0,287100216
-GLT25D2	0,287127854
-COL18A1	0,287131911
-NPIPL3	0,287424398
-C1orf69	0,287453135
-MTF1	0,287488427
-IGF2BP2	0,287555495
-PALLD	0,287872078
-RPS16	0,287887395
-CYP2C9	0,287955438
-SC65	0,288029122
-CRYBG3	0,288096904
-SHC2	0,288312879
-FLNA	0,288339801
-NM_014486	0,288348194
-ISYNA1	0,288383809
-PNO1	0,288506351
-GZMK	0,2886543
-ATG13	0,288748426
-NCOR1	0,288772721
-ZSWIM1	0,288892162
-GPM6B	0,28893274
-SNTA1	0,289049438
-RHOBTB1	0,289064808
-GGA1	0,289073087
-ATXN2L	0,289088819
-FAM46A	0,289172187
-ZNF532	0,289393934
-CD40LG	0,289400418
-ZCCHC11	0,289421485
-WDR5B	0,289498086
-EPN2	0,289629137
-WNK1	0,289684816
-ZNF408	0,289721753
-LHFPL2	0,290003635
-NARG2	0,290029081
-STYXL1	0,29008917
-YY1AP1	0,290249669
-CPOX	0,290281635
-IL11RA	0,290333682
-PAXIP1	0,290387596
-ZNF282	0,290414378
-C11orf95	0,290643441
-MERTK	0,290681835
-VPS13C	0,29069039
-RPS17	0,290756898
-NEIL1	0,290762184
-ZNF292	0,290850132
-NOSIP	0,290873511
-DNAJB2	0,290950763
-INPPL1	0,29102828
-ZFX	0,29106383
-SETX	0,291138151
-SLC25A37	0,291207794
-PCDHGA8	0,291472818
-TXNIP	0,291962928
-DDX27	0,291971417
-BG389073	0,29216848
-JTB	0,292275569
-RBM10	0,292352574
-RASGRF1	0,29242252
-SYNM	0,292474024
-EXPH5	0,292481151
-NPL	0,292494012
-CHKA	0,292519533
-MGA	0,292564204
-SOX10	0,292580481
-AK024185	0,292975066
-FAM120A	0,292996604
-PLXNB1	0,293000141
-BDH2	0,293071563
-JRK	0,293136106
-SLC11A1	0,293139917
-TM4SF1	0,293242649
-EDA	0,293286441
-CDK10	0,293299298
-HLA-E	0,293305618
-LOC642846	0,293349826
-GFPT2	0,293396887
-SENP3	0,293408144
-RPS3AP44	0,293415546
-C16orf88	0,293431615
-FAM60A	0,293472328
-RPL36A	0,293501288
-SERPINA5	0,293547044
-CNOT8	0,293568161
-KDM4C	0,293620372
-POU2F2	0,293815578
-C14orf139	0,293870806
-ZNF217	0,293937173
-NM_025042	0,294034268
-NNMT	0,294200775
-VEZT	0,294224684
-KIAA0754	0,294307773
-RBM28	0,294637248
-ITPR2	0,294711729
-PPPDE1	0,294796015
-KLHL28	0,294874305
-MGP	0,294956866
-LOC729602	0,295016892
-SRSF5	0,295036903
-ROCK1	0,295267164
-SS18L2	0,295271871
-LMNA	0,29532356
-ESRRA	0,295387708
-SNHG3-RCC1	0,295411716
-TAL1	0,295434654
-SQRDL	0,295470062
-TARDBP	0,295665655
-LMAN2L	0,295705138
-RIN3	0,295771443
-PSPH	0,29602696
-DGKD	0,296027908
-WHSC1	0,296067068
-SPRY4	0,296068122
-ADARB2	0,296162399
-ELF3	0,296200778
-TLE1	0,296292637
-ACAN	0,296375799
-AK022038	0,296556116
-IL1RL1	0,296721787
-OR2A9P	0,296898432
-NCRNA00260	0,296954725
-CAD	0,296976627
-PNRC2	0,297129071
-IQCK	0,297134521
-ACOX2	0,297377087
-APOC4	0,297497329
-DGKA	0,297541846
-ZBTB1	0,297547513
-PUS1	0,297622568
-C7orf64	0,297653213
-FBLN1	0,297723957
-SBF1	0,297752819
-TMF1	0,298582891
-IL1R1	0,298701666
-LILRB3	0,298823808
-FLAD1	0,298825369
-CD163	0,299040686
-TCL6	0,299056301
-FADS3	0,299096634
-LBR	0,299180453
-AL162044	0,299184427
-ZNF337	0,299271736
-AHNAK	0,299352615
-YY1	0,299417937
-HIPK2	0,299439852
-NAT15	0,299519834
-ANKZF1	0,299817611
-NECAP2	0,299838267
-MAP3K7	0,299838407
-SAMD4A	0,299863792
-WDR8	0,300094232
-ZNF24	0,300179611
-NR3C1	0,300200063
-FGF1	0,300357727
-NPC1	0,300564708
-LMO4	0,300573598
-TTLL5	0,300853453
-AL050053	0,300945526
-RSU1	0,300958049
-C15orf39	0,301123219
-SLC14A1	0,301147038
-ELAVL1	0,301190126
-SLC17A4	0,301215925
-FANCC	0,301274346
-LRCH4	0,301338927
-EGFL7	0,301340052
-C9orf3	0,301357727
-SRGN	0,301411135
-PLCL1	0,301576339
-MAN1A1	0,301613058
-S100A8	0,301917937
-W86781	0,301984854
-HIP1	0,302012828
-OR7A5	0,302027387
-PPP1CC	0,3020408
-CGGBP1	0,302058231
-CYP3A4	0,302333153
-GALNS	0,302376776
-NR0B1	0,302394827
-SMNDC1	0,302468654
-MGST2	0,302482901
-RPL12	0,302658969
-DMPK	0,302955014
-TNRC6B	0,30299615
-PPM1D	0,303104009
-EED	0,303134999
-STAG3L1	0,3031801
-TMCC1	0,303195736
-RPL13	0,303245467
-RBPMS	0,30326423
-ARHGAP10	0,303298204
-PLCB3	0,303300054
-XPO1	0,303410309
-MYO1F	0,30341788
-SRPK1	0,303531642
-ZCWPW1	0,303562617
-MTHFD2L	0,303678034
-FAM111A	0,303798707
-TTC38	0,304186409
-COL7A1	0,304295553
-C4orf19	0,304312458
-NGLY1	0,304332742
-HTATIP2	0,304339936
-IFNAR2	0,304414877
-CXorf1	0,304737703
-UNC5B	0,304789798
-YAP1	0,30479215
-PHC2	0,30485466
-FBL	0,304914384
-CDH2	0,304939032
-FXYD2	0,304942957
-ANKRD36	0,305000603
-KRT8	0,305028726
-DSCAM	0,30505625
-SMO	0,305151387
-FCGRT	0,305420183
-PAIP2B	0,305483478
-PABPC1	0,305528523
-PIGV	0,305604211
-BACH2	0,305697602
-PLGLA	0,305722503
-MORC3	0,305845022
-DIDO1	0,305996983
-PRPF38B	0,306041882
-TRMT1	0,306054262
-NFATC1	0,306233076
-AK021495	0,306242002
-GPR1	0,306335484
-STARD13	0,306369109
-CELSR2	0,306371185
-ZNF193	0,306396574
-ABHD6	0,306458055
-PLCXD1	0,306486283
-RPAP1	0,306695411
-AL050122	0,306737964
-DHRS3	0,306750918
-C1QA	0,306800137
-AF009267	0,30681596
-SETD2	0,307047565
-STX6	0,307184977
-TMEM204	0,307304516
-SMYD2	0,307490131
-BF942161	0,307560212
-SLC44A1	0,307685609
-ELF2	0,307698089
-AATF	0,307770923
-AV761453	0,307800442
-ACTN1	0,307927265
-AI523613	0,307943372
-SOLH	0,307971092
-ZNF410	0,308222237
-GOLGA4	0,308250269
-FLJ21369	0,308352331
-FCGR2A	0,308469725
-BRD7	0,308638563
-TLR2	0,308769609
-FTHL5	0,308790654
-SPOCK1	0,308861441
-LSM14A	0,308907157
-USF2	0,309161806
-TENC1	0,309220224
-EMP2	0,309252571
-BSDC1	0,309299474
-ZNF701	0,309462113
-PLIN3	0,309516744
-SORBS1	0,309562012
-FTL	0,309588981
-AGFG2	0,309634949
-UBR5	0,309647344
-MMP14	0,30965745
-SFRS8	0,309923113
-ITPR3	0,309975876
-PLK3	0,310097184
-NUP188	0,310124261
-CROCC	0,310245563
-CHSY1	0,310328559
-CTCF	0,310675097
-EDC4	0,310685915
-NFE2L2	0,31069885
-LILRA6	0,311008878
-SATB2	0,311055754
-GTPBP6	0,311254994
-TSPAN14	0,311316513
-C10orf18	0,31133762
-SECISBP2	0,311419174
-DHX34	0,311443077
-LSS	0,311450185
-CHI3L1	0,311532669
-PDGFC	0,311715929
-BMP7	0,311741682
-MBNL1	0,311755686
-DNA2	0,311841432
-COMT	0,312081286
-LOC100133005	0,312165679
-PTOV1	0,312192713
-LCAT	0,312407744
-LRRFIP2	0,312480817
-UCN	0,312589312
-AK024606	0,312655002
-MICAL3	0,312700621
-ROM1	0,31291043
-MED12	0,312925796
-CPNE1	0,313173908
-GBP2	0,313262095
-PELI2	0,313279559
-MLL	0,313398121
-HIF3A	0,313438743
-ST18	0,313449639
-AF131777	0,313643716
-CATSPER2P1	0,313785721
-ZNF302	0,314066212
-APBB2	0,314110219
-KIAA0907	0,31421022
-ZNF592	0,314679884
-HNRNPA1	0,314773035
-TSC2	0,314882123
-SFRS15	0,314884343
-ZNF835	0,314920694
-WDR6	0,314979423
-LOC729143	0,315037798
-PPARD	0,315048839
-U2AF2	0,315118843
-MGAT1	0,315269456
-ZNF44	0,315270856
-RPL36	0,315475789
-GRAMD3	0,315513449
-PTPN2	0,315554784
-AL080072	0,315635626
-C19orf2	0,315918303
-DNAH3	0,315930745
-ZNF146	0,316341954
-SMEK1	0,316538461
-MLXIP	0,31681421
-NMT2	0,316848231
-G3BP1	0,316864559
-DDX3Y	0,316997159
-STEAP1	0,317082981
-BC002629	0,317231764
-KDM2A	0,317406731
-TMEM39A	0,317430306
-C15orf29	0,317437851
-MACF1	0,317513626
-LOC391020	0,317572673
-SETD1A	0,317586539
-KTN1	0,317889697
-RUNX3	0,31809511
-NINJ1	0,318107478
-ARMC7	0,318150459
-BMP1	0,318194029
-DKFZP586I1420	0,318199121
-JARID2	0,318226296
-AW972351	0,318303541
-PAPSS2	0,31841091
-ELTD1	0,31845583
-ETS2	0,318667898
-CREB3L2	0,318705762
-DFNB31	0,31892768
-SERHL2	0,318966243
-C10orf26	0,319058163
-NM_030892	0,319421731
-WRAP53	0,319795295
-UBQLN4	0,319828198
-RALGDS	0,319938162
-PRKCH	0,320101043
-AU146983	0,320105843
-SLC5A3	0,32021553
-DUSP1	0,320239212
-NKX2-2	0,320312108
-C1orf183	0,320387827
-PCM1	0,320482282
-THRA	0,320531901
-NM_025028	0,320726138
-SIVA1	0,320736787
-TTR	0,320757249
-IKBKB	0,320778441
-ARID1A	0,321020715
-HDAC4	0,321059842
-ZFP36L2	0,321167918
-TMEM212	0,321179342
-AA443771	0,321214505
-AGAP5	0,32125931
-PIGA	0,3216713
-SFRS12	0,321704401
-LDLRAP1	0,321832456
-CCDC21	0,321857948
-SSFA2	0,321990716
-RAMP1	0,322050077
-FLJ10357	0,322160744
-LAD1	0,322322766
-RACGAP1	0,322340831
-NPIPL2	0,322616655
-CEP350	0,322648588
-CRLF1	0,322735059
-IGSF9B	0,322744338
-PLXND1	0,322801951
-MCL1	0,322913781
-ALMS1	0,32297709
-ZNF768	0,323059066
-RSL1D1	0,323228527
-C4orf34	0,323582139
-PNPLA6	0,323738553
-MAST4	0,323801655
-NME3	0,323835175
-SNHG3	0,32391938
-S100A12	0,324014586
-PPP4R1	0,32409634
-PLD1	0,324165096
-POLG	0,324186823
-NKTR	0,324203565
-ST3GAL4	0,324231325
-TMEM63A	0,324243134
-ST20	0,32438459
-RNF114	0,324406844
-HYI	0,324468621
-DUSP6	0,324699964
-NR1H2	0,324884332
-DVL2	0,324900869
-SRSF11	0,324979841
-CLK2	0,325170283
-MKLN1	0,325287178
-SCRIB	0,325320413
-KIAA0467	0,325541973
-DMWD	0,325745064
-KLHL23	0,32579572
-RPS6	0,325948088
-ZBTB17	0,326014408
-RAI14	0,326038467
-UBE2G2	0,326143089
-ZNF562	0,326186073
-EZR	0,326282578
-TRPS1	0,326283144
-HFE	0,326390644
-MED23	0,32658232
-DDX11	0,326766632
-SHMT2	0,326784725
-LRP5	0,326954416
-PTH1R	0,327100265
-LOC731602	0,327131294
-AA401963	0,327241371
-CDK5RAP2	0,327276136
-SERP1	0,327279991
-SLC1A5	0,327303416
-BGN	0,327370767
-HSD17B1	0,327475971
-AL390143	0,327497051
-DIAPH2	0,327617697
-PITPNC1	0,327719899
-SPRY2	0,327767132
-FZD7	0,327974293
-MAP4K4	0,328171238
-TNS1	0,328369107
-ZNF783	0,328517049
-M78162	0,328518574
-ADAMTS1	0,32853944
-FKBP5	0,328911405
-AGAP8	0,329115979
-PLEKHF1	0,329179433
-DNAJB1	0,329339376
-RBMS2	0,329438459
-HNRNPH1	0,329454824
-ULK2	0,329496298
-PAPD7	0,329501864
-SURF1	0,329547559
-W61005	0,329673439
-ZNF862	0,330131081
-GNA15	0,330266409
-CHD9	0,330273108
-DLC1	0,330294104
-TMEM2	0,330321664
-AK024879	0,330353812
-N4BP1	0,330435804
-SERF2	0,330633507
-SNRPA	0,330957742
-IRF8	0,33098543
-ABCA2	0,331251046
-NPFF	0,331328402
-CP	0,331565597
-AU144887	0,331713137
-AW851559	0,33185735
-TCF4	0,332062967
-ZNF354A	0,332076549
-TMEM92	0,332352956
-NFATC3	0,332386137
-SSRP1	0,332529738
-TCF7L2	0,332651908
-PIM1	0,332716071
-PIP4K2A	0,332914219
-EIF4EBP1	0,332959146
-LOC100132863	0,333054912
-MMRN2	0,333075923
-AU147295	0,333342973
-VIM	0,333356286
-C2orf67	0,333469715
-DNMT1	0,333550022
-CEP110	0,333679402
-BAZ2B	0,33371151
-KDELR2	0,333939841
-L3MBTL	0,334448273
-CDK19	0,334505985
-CYorf15B	0,334832089
-DDX17	0,334839203
-FKBP4	0,335166906
-STOM	0,335173644
-U82303	0,335241438
-LOC202181	0,335841121
-ATM	0,335893127
-STK3	0,335957389
-MID1	0,336166241
-IGFBP5	0,336454348
-PARP4	0,336459483
-EXOC7	0,336479503
-FANCG	0,336652927
-PHF2	0,336678654
-FBRS	0,33674511
-ANP32B	0,336836072
-NCK2	0,336876937
-CASP6	0,336920233
-ZBTB3	0,337122586
-DHFR	0,337448147
-APOLD1	0,337464001
-STAG1	0,337490482
-NM_024305	0,337551103
-SIGLEC8	0,337608204
-ERLIN1	0,337809212
-POLDIP3	0,337889824
-SPTLC2	0,33799094
-C7orf26	0,338204972
-UBE2D4	0,338265561
-MAP2K7	0,3384787
-MECOM	0,338508564
-DOCK1	0,339029429
-HS1BP3	0,339148762
-PRKY	0,339216015
-GOLGA1	0,33927478
-XPC	0,339433169
-PHF3	0,33953002
-HIC2	0,339768003
-C9orf7	0,340519877
-CTDSPL	0,340591645
-ZNF83	0,34077157
-PHGDH	0,340889735
-TMEM165	0,340978736
-CLN3	0,341078466
-AU147983	0,34113627
-PATZ1	0,341151411
-DIP2C	0,341390806
-RECK	0,341533646
-EWSR1	0,342003886
-SMAD7	0,342182186
-MTRF1L	0,34225773
-TJAP1	0,342452426
-PRKD2	0,342725824
-SPOP	0,343019265
-HLA-J	0,343028528
-PLXNB2	0,343103735
-FBXL14	0,343454364
-LAMA2	0,343637649
-RNF220	0,343845541
-CLK3	0,344164444
-STARD3	0,344187457
-OGT	0,345118989
-IFITM3	0,345141829
-HMOX1	0,345196784
-EIF2C2	0,34557825
-CCND3	0,345663426
-TGFBR3	0,345676022
-POLR2J3	0,345712548
-BCAR3	0,345713549
-C14orf147	0,34610842
-CLDN15	0,34616346
-TOP1	0,346179876
-RASL12	0,346286134
-MED13L	0,346369067
-SOS2	0,346799305
-SERPING1	0,347144597
-IER5	0,347279068
-TLE2	0,347426427
-LLGL2	0,347448236
-TMCC2	0,347500013
-PHF20	0,347602909
-SIRT4	0,347862165
-OSGIN1	0,348060574
-H2BFS	0,348076316
-NM_017756	0,348230007
-NCRNA00115	0,348422218
-MT1E	0,348733923
-NACC2	0,3488369
-NFIB	0,348943619
-AKR1C3	0,349206923
-ARPC1B	0,349407208
-NIPBL	0,349628117
-RPL11	0,349803207
-MSH6	0,350014407
-PTDSS2	0,350073646
-AL050145	0,350120404
-FAM107A	0,350271118
-CHN2	0,350358174
-DAPK2	0,350378033
-DLG5	0,350436992
-OPHN1	0,350596034
-C20orf11	0,351010126
-SLC35D1	0,35135795
-SELL	0,35142274
-FAM193B	0,351790995
-NM_024880	0,352020901
-RASGRP2	0,352114346
-CAPN3	0,352194849
-THOC1	0,352289646
-TAOK3	0,352396226
-FBXO42	0,352613215
-LARP6	0,352692849
-KLKB1	0,352702835
-METTL7A	0,352961228
-STIP1	0,352968743
-WIPF2	0,353085817
-FOXD1	0,353404764
-HSPB2	0,35378232
-ENGASE	0,353978221
-LAT2	0,354239264
-HIST1H2AH	0,354250391
-GSDMD	0,354483715
-TRA2A	0,354674037
-C19orf29	0,354762053
-BRPF1	0,355002213
-NUMA1	0,355146564
-SNW1	0,355320637
-SMARCC1	0,355374541
-ZNF175	0,35555253
-BATF3	0,355680727
-HIST1H2BC	0,35575565
-ERN2	0,356098991
-ZFR	0,356185362
-AW301806	0,356253591
-SMTN	0,356289422
-RPS6KA2	0,356774064
-MIIP	0,35685635
-ARGLU1	0,356919378
-CTNNAL1	0,357152141
-PCDH9	0,357228835
-LAS1L	0,357263917
-DOK1	0,358029668
-AFTPH	0,35852635
-ZNF143	0,358674337
-C11orf71	0,35888557
-MICALL2	0,359221642
-KDM6A	0,359260932
-CFH	0,359284568
-CEBPB	0,359516672
-MTUS1	0,359547348
-AW973791	0,359548173
-SERTAD2	0,359684853
-FGFR1	0,359721729
-KPTN	0,360479451
-NR2F2	0,361169645
-RGL2	0,361384531
-NM_014120	0,361482036
-TAF5	0,361611903
-ZC3HAV1	0,362177526
-BEST1	0,362248528
-TNFRSF1A	0,362724804
-CLIP2	0,363062238
-EHMT2	0,363078239
-IFITM1	0,363162265
-GCFC1	0,363190607
-PECAM1	0,363227012
-YES1	0,363556218
-ZFP36L1	0,363744573
-SBNO2	0,364095165
-RMND5A	0,364201024
-IL10RB	0,364481295
-CBS	0,364486163
-TBC1D2B	0,364503601
-C10orf10	0,36458821
-AU144530	0,365137826
-ZNF500	0,365202134
-ATP6V0E1	0,36527949
-SEPT8	0,365711052
-VCAN	0,365762437
-RPL36AP51	0,366073863
-RPL31	0,36613283
-TAOK1	0,36613666
-GCN1L1	0,366181489
-CALCOCO1	0,366300689
-GNA11	0,366387362
-SH2B2	0,366425408
-RREB1	0,367259867
-SLC35E1	0,3672965
-GPRC5B	0,367311931
-TCF7	0,367371063
-PDIA4	0,367810651
-ZNF34	0,367845233
-MBD3	0,36793004
-CXCR4	0,368041224
-C9orf114	0,368120984
-IFITM2	0,368313531
-ZNF665	0,368328536
-ZCCHC24	0,368368275
-LOC100133944	0,369022431
-CSDA	0,369150342
-AU148255	0,369666508
-CIZ1	0,369704457
-CRTC3	0,369792369
-CTNNA1	0,369962411
-RARRES2	0,37011032
-NM_025033	0,370246707
-VSIG4	0,370274949
-FAM48A	0,370421427
-ZDHHC11	0,370675656
-NPAS2	0,370715345
-ADH1B	0,370935809
-ACSL1	0,371025369
-C1orf63	0,371083889
-TYMP	0,371266716
-LEPREL1	0,371463494
-LAMB2	0,371472469
-MAFB	0,371542293
-AW971248	0,371589606
-BC003629	0,371603781
-FAM63A	0,371786321
-ABCA1	0,371992682
-IGF2R	0,37211512
-SOX13	0,372131188
-WAPAL	0,372391179
-ZFC3H1	0,372437982
-ZNF710	0,372493324
-HSPA6	0,37258644
-CCDC101	0,372823539
-BAZ1A	0,372824952
-AXL	0,372842922
-NPIPL1	0,372916072
-HDGF	0,372923023
-KHDRBS3	0,373093219
-MT1X	0,373144553
-MTMR15	0,373164421
-AF257099	0,373262757
-AEBP1	0,37342966
-KLHL25	0,373672957
-GJB4	0,37372121
-LUC7L3	0,374023648
-U79248	0,374142769
-LOC653562	0,374188384
-RBM4	0,374375075
-ABCC10	0,374890625
-CXorf21	0,374896996
-DAXX	0,374917403
-C1R	0,375063944
-TPST2	0,375279072
-KLHL24	0,375307199
-C7orf68	0,375539219
-ZCCHC8	0,375600764
-CASP4	0,375605037
-ETV1	0,37597402
-BIN1	0,376340315
-RGS19	0,376617752
-PKNOX1	0,377091746
-CTTN	0,377173864
-TRIP10	0,377452782
-ANGEL1	0,377498562
-PLIN2	0,377879768
-NM_025007	0,377942771
-PTMA	0,378229214
-S100A11	0,378255627
-AXIN1	0,378580893
-NPRL3	0,378633074
-PNN	0,378695864
-AV727934	0,378843386
-ANGPT2	0,37912784
-AK023918	0,379250766
-CNPY3	0,37927474
-AF130051	0,37947818
-TLE4	0,379880985
-PAPOLA	0,379974199
-ITGB5	0,380683545
-FAM38B	0,380693638
-PABPN1	0,380909515
-SLC6A8	0,38116858
-RYBP	0,38121367
-NASP	0,381229843
-FGR	0,381246748
-PER1	0,381695992
-CDR2L	0,381867955
-LRRFIP1	0,382075479
-HMHA1	0,382282948
-KIAA0485	0,382313718
-GUSB	0,38235255
-RPS17P5	0,38240934
-FXYD5	0,382563723
-RBL2	0,382697586
-RANBP10	0,382980904
-NEDD9	0,383084673
-MSL2	0,383144236
-FAM50A	0,383317183
-AL080232	0,383323554
-SPG21	0,383712061
-TPD52L1	0,384098652
-H2AFX	0,384141378
-SWAP70	0,384225003
-IVNS1ABP	0,384369268
-KDELC1	0,384542393
-MYL12A	0,384757468
-FOXO3	0,384856157
-MED13	0,385128516
-AL049252	0,38560217
-AF007147	0,385820993
-PAX6	0,385884587
-DNASE2	0,38591545
-SLC12A9	0,386200858
-SIRT1	0,38637719
-ARID5B	0,386492868
-MT2A	0,38656824
-SLC38A2	0,386710042
-GNG5	0,386756333
-SRRM2	0,386841072
-SERPINB6	0,386985458
-CC2D1A	0,387023088
-LRRC37A2	0,387067777
-CSF1	0,387071999
-RPL29P11	0,38708859
-SFRS14	0,387094074
-MYO9B	0,387103012
-AW972855	0,387241981
-TRIP4	0,387728627
-ZBTB40	0,387827711
-STARD8	0,387863703
-WBSCR16	0,387992811
-NXF1	0,388021286
-CTDSP1	0,38803541
-RSAD1	0,388042285
-SUV420H1	0,38833134
-CDKN1C	0,388508896
-NM_016415	0,388588403
-E2F4	0,388673603
-KANK2	0,388702219
-ZC3H7B	0,388980025
-ANGPTL4	0,389035415
-CRY1	0,389801967
-KIAA0556	0,389845114
-TBC1D16	0,390016803
-TCOF1	0,390109025
-ZFYVE26	0,390278079
-IFRD1	0,39034324
-EIF4B	0,390385914
-SMC1A	0,390525141
-SCIN	0,3907272
-MARS	0,391061966
-PTRF	0,391089965
-POLR2J	0,391514571
-APAF1	0,391530483
-ITPK1	0,3915415
-PNRC1	0,392133859
-CLIC2	0,392140808
-KIAA0913	0,392243895
-PRKAR2A	0,392619325
-PRKX	0,392750502
-SYDE1	0,392957216
-ACSL5	0,393140899
-LRP10	0,393162277
-LPP	0,393214983
-SNTB2	0,393383504
-NADK	0,393882671
-PCBP2	0,394206896
-N51370	0,394562467
-CLIC1	0,394663761
-CTBP2	0,394785714
-PHB	0,394929787
-BCL2	0,395102709
-TAF4	0,395492947
-LOC652607	0,395562084
-YBX1	0,396079328
-PRPF3	0,396609142
-SLC38A10	0,396741732
-ERBB2IP	0,396808535
-CFLAR	0,396840203
-TNFRSF10B	0,397091951
-PHC1B	0,397196351
-ARL17A	0,397406114
-ZBTB20	0,397424403
-REPIN1	0,397830532
-BE466926	0,397930108
-MT1P2	0,398055653
-ZNF778	0,398225613
-DICER1	0,398300689
-NM_018603	0,398329284
-RAF1	0,398631868
-MXD4	0,398685167
-FBXL7	0,398770393
-CALD1	0,399121196
-GSDMB	0,399246982
-ZCCHC2	0,399293751
-PODXL	0,399691684
-ACACB	0,400136922
-VEZF1	0,400413083
-PLEKHM1	0,401187317
-CSPG4	0,401646086
-ID3	0,40170175
-RBM41	0,401719975
-KDM6B	0,401885964
-PHF15	0,402522419
-LAMP2	0,402538077
-CDC14B	0,402583482
-HNRNPL	0,403044314
-SLC4A2	0,403448509
-DDX23	0,403953946
-TUBD1	0,40407115
-SLC16A3	0,404204458
-CAPN2	0,405022548
-CBFA2T2	0,40560438
-TCEB2	0,405769952
-HNRNPF	0,406126644
-MORC2	0,406182732
-FOXO1	0,406430281
-AI962978	0,406538883
-HP1BP3	0,406567553
-CBFB	0,406789498
-RBM14	0,406886421
-SFI1	0,407058786
-ZHX3	0,407089165
-KDM3A	0,407233406
-SIRT2	0,407341821
-ANKS1A	0,407373917
-TCF3	0,407442968
-NOTCH2NL	0,407672378
-EEF1D	0,407830724
-SOX12	0,408065349
-SLCO1A2	0,40820492
-HNRNPA3	0,408299868
-GTF2H3	0,408624789
-FZD9	0,408729069
-SAFB2	0,408755308
-APBA3	0,408834306
-ASCL1	0,409161488
-CG012	0,409559201
-WDR59	0,409606436
-LAMA5	0,409632505
-ZNF276	0,409730125
-ZNF395	0,410080702
-TIMM44	0,410223052
-BGLAP	0,410749324
-ZHX2	0,411039562
-CARS2	0,411302016
-SLCO3A1	0,411338796
-LOC442497	0,411765627
-FRYL	0,411842495
-CYP2J2	0,412070197
-ABL1	0,412522321
-INF2	0,412975218
-SGK1	0,413352645
-SFTPB	0,413789208
-TIGD1L	0,41383023
-RBCK1	0,414019825
-TRAPPC10	0,414285862
-DUSP7	0,414641136
-WSCD1	0,415016303
-DCP1A	0,415308358
-LPAR1	0,415365439
-RBBP6	0,415730871
-DONSON	0,416255506
-C16orf5	0,416258918
-NCOA1	0,416350707
-CFHR1	0,416440287
-AA126763	0,416566153
-LRRC32	0,416765832
-CP110	0,41732481
-LTBP3	0,417338221
-TDRD3	0,417356196
-HMG20B	0,417456909
-CDC42EP2	0,417645635
-TAF1C	0,417736819
-NM_013344	0,41778911
-VGLL4	0,417820331
-PHKA2	0,417904785
-KDSR	0,418009802
-RELA	0,418064238
-TBL1X	0,41814877
-SIAH2	0,418727849
-MYO1E	0,418747589
-HIST1H2BD	0,419127582
-AI744451	0,419208355
-PTMAP7	0,419537834
-ARID5A	0,419593497
-CYP27A1	0,420064872
-RAB13	0,420441013
-CPSF7	0,420526378
-CPT1B	0,420770156
-LRDD	0,420794327
-PILRB	0,421599366
-STAB1	0,421733406
-FCHO1	0,422126906
-ZNF32	0,422311821
-TBC1D3H	0,422328806
-C1orf66	0,42292679
-NM_025032	0,423323973
-AI732802	0,423584905
-PCID2	0,423787762
-POGK	0,423912669
-TMEM140	0,424587207
-TMC6	0,424604298
-AL080160	0,42490597
-AK021505	0,425024442
-SCD5	0,425610027
-RAD52	0,425956612
-AF116715	0,425960499
-DCI	0,425967692
-SFRS18	0,426091505
-HCG2P7	0,426136765
-ADORA2A	0,426366158
-NM_021651	0,426442506
-MID1IP1	0,426940092
-HNRNPC	0,427103695
-NM_025024	0,427155973
-AK024315	0,427460397
-AK021514	0,427966252
-SLC29A3	0,428138792
-NSUN5	0,428255135
-PHF10	0,428599049
-DAPP1	0,428626141
-TMEM109	0,428647746
-LOC91316	0,428742129
-ITGB4	0,42956266
-SLC30A1	0,429998682
-AW150065	0,430129937
-ZCCHC6	0,430267528
-ARHGEF2	0,430371137
-AK027193	0,43049002
-TRIM52	0,430535815
-MT1G	0,430767233
-NOTCH1	0,430849119
-ZRSR2	0,43114681
-RPS6KA1	0,43184981
-KANK1	0,432456197
-FURIN	0,432618855
-APOBEC3C	0,432749845
-ANKRD40	0,432772877
-TRIOBP	0,432900403
-ZNF384	0,433116555
-CDKN1A	0,43319672
-BTG1	0,433570541
-EPHX1	0,433658916
-CNOT6	0,434207544
-HSPA1L	0,434322364
-PKD1	0,434547199
-WAS	0,434717417
-RPL23AP32	0,434993767
-P4HA1	0,434997425
-MAX	0,435160002
-UIMC1	0,435278167
-NM_025120	0,435322168
-NCOA6	0,435700178
-TPD52L2	0,435768747
-BCL6	0,435938226
-AK024108	0,436355329
-C7orf23	0,436800978
-CDC42BPA	0,437074951
-CD59	0,437137855
-POLR1B	0,437227618
-TLR5	0,437498143
-HDAC1	0,437993569
-ARHGEF7	0,438071237
-AA045174	0,438161955
-TBC1D17	0,438488128
-PRELP	0,438518539
-GTF2H2B	0,438525643
-HIST1H2BK	0,43866778
-AU147851	0,438979485
-RBM39	0,439661925
-IQGAP1	0,439786742
-RPL18AP3	0,440613252
-LTBR	0,440721546
-RPL35A	0,441136859
-ARAP2	0,441441928
-ARAF	0,441560027
-MT1H	0,441587824
-LOC441258	0,442117007
-ZCCHC14	0,442132801
-IRF7	0,442147625
-NOL12	0,442203671
-PTPLB	0,442541309
-AI683552	0,442752948
-MYST1	0,442881562
-MXI1	0,443040642
-AW974910	0,443299524
-C1orf144	0,443500279
-KRCC1	0,444417306
-PIAS4	0,444438643
-SRSF1	0,444637015
-LRP2	0,444740953
-ZDHHC18	0,445392541
-SPN	0,445443935
-ST13	0,446667878
-PHF17	0,446746739
-NACA2	0,446876872
-SASH1	0,447285208
-CD22	0,44772036
-CSNK1E	0,447902552
-COL5A3	0,447933631
-MAT2A	0,448695587
-EFHD1	0,448820126
-MAP3K3	0,448963961
-BIN3	0,449317201
-LUC7L	0,449469644
-KIF1C	0,449622117
-RNF144A	0,450034368
-TULP3	0,450626451
-CDKN2C	0,450879897
-HSD17B7	0,451226227
-ACIN1	0,451331774
-PABPC3	0,451363083
-PHF21A	0,45139036
-HNRNPH3	0,451480034
-HIST2H2BE	0,452219911
-RRP1B	0,452597128
-SOX2	0,453132172
-ZNF444	0,453296716
-FAM13A	0,453547738
-JUP	0,453753674
-PODNL1	0,453854292
-MAML1	0,453885
-SNRNP70	0,45408945
-SDCCAG3	0,45464357
-PLGLB1	0,454722494
-CDH19	0,454754165
-HSPA1B	0,455063205
-ARHGEF10	0,455229121
-NFIL3	0,455469821
-NFKBIA	0,455577982
-XRCC2	0,455670024
-ACTN4	0,455764555
-PDS5A	0,456071133
-POU2F1	0,456120351
-VPS54	0,456318614
-BANF1	0,456451252
-PGCP	0,456765652
-RPL28	0,456867479
-ICAM2	0,457066169
-SNAP23	0,457069788
-SART1	0,457941993
-AK023891	0,458253977
-BANP	0,458588544
-MAP3K11	0,458968207
-EPOR	0,459463669
-FKSG49	0,459538011
-MT1F	0,459638951
-NM_014128	0,460468204
-AP1G2	0,460676306
-GAS2L1	0,461632768
-PHIP	0,462053958
-NOL8	0,462387404
-NM_017932	0,462395281
-RNF130	0,462894529
-ZMYND8	0,463309493
-AK024525	0,463401166
-TRIM28	0,463454342
-BCAT2	0,463509769
-TYRO3	0,463574548
-PHLPP1	0,463738295
-BST2	0,465024297
-PDGFRB	0,465034704
-AL049987	0,465336929
-AKAP8L	0,466278804
-TGM2	0,467555999
-CREBBP	0,467899354
-KIAA0894	0,468325808
-DDX39	0,468959477
-NCAPD2	0,468959537
-ALPK1	0,469621875
-TGIF1	0,469902489
-PPP1R14B	0,470121069
-PNMT	0,470291567
-NAA16	0,470467422
-ZNF611	0,470526774
-ZRSR1	0,470857426
-NPIP	0,472818474
-RBM38	0,473036567
-USP34	0,473278809
-TGFB3	0,474067001
-ITSN2	0,475328182
-CEBPD	0,475754278
-MCM3AP	0,476296498
-HAPLN2	0,476718109
-POGZ	0,477224004
-NR2F1	0,477556735
-GAS1	0,478628972
-SLTM	0,478903701
-ECE1	0,479007813
-CALCOCO2	0,47910558
-RXRA	0,479821295
-MEIS2	0,480178943
-CLEC2B	0,481843785
-AL049260	0,482481089
-CHST3	0,48259726
-COL16A1	0,483094975
-SLC25A16	0,483255606
-LHPP	0,48421483
-AF010144	0,484619234
-GTSE1	0,484629217
-MUM1	0,484956644
-TNXB	0,485246904
-PRINS	0,486032909
-ANKRD49	0,486282532
-PTPRK	0,486899575
-PPAP2C	0,487395433
-C22orf9	0,488987561
-KHNYN	0,489026627
-RAPGEF3	0,489474077
-AF078844	0,489716822
-MAN2A1	0,489875474
-IFT20	0,490824284
-USP21	0,490859618
-NOP2	0,491526918
-LOC440248	0,491905455
-LOC647070	0,493492979
-MAFF	0,494072026
-BG251521	0,495196452
-C6orf145	0,496322836
-MLL4	0,496324893
-ATF4	0,49676781
-RELN	0,497310216
-PELI1	0,497491599
-P2RX7	0,497499324
-CNOT2	0,498172475
-FAM38A	0,498599859
-DCLRE1C	0,498693515
-INSR	0,502304787
-MAPKAPK2	0,502573806
-NDE1	0,50267356
-MT1M	0,502716901
-CDK5RAP3	0,504041432
-SULT1A4	0,504805398
-NSUN5P2	0,505093708
-ANKRD10	0,505841449
-LOC339047	0,506042447
-LRRC1	0,506594446
-CUX1	0,507257715
-SRRT	0,508240438
-MAF	0,508625791
-EBLN2	0,509549245
-NM_017618	0,510705903
-RBM4B	0,51138423
-FBXW12	0,511744983
-ATP8B1	0,511969804
-NM_024978	0,512045897
-KCNMB4	0,512142959
-CLMN	0,512461537
-LOC100132540	0,512589899
-SERPINH1	0,513136463
-RHBDF2	0,513703735
-PCF11	0,514081494
-HAUS2	0,514694211
-TECPR2	0,514970535
-TNIP2	0,515014912
-AUP1	0,516155581
-KIAA0101	0,516801916
-N35922	0,51703624
-STK38	0,517483454
-AZGP1P1	0,518047589
-C13orf15	0,518310047
-PRR11	0,518691616
-PDCD6	0,51972326
-AFF1	0,520716014
-AF222691	0,521107674
-BE045142	0,521502008
-PACS2	0,521749261
-PSRC1	0,522634606
-ZNF358	0,523463012
-MAPKBP1	0,523696079
-S100A4	0,524041412
-MYO1C	0,524902669
-IRF3	0,52538788
-TOB2	0,526119659
-KLHL21	0,527145117
-PGF	0,527713686
-LOC399491	0,528407104
-ARAP1	0,528556373
-AZGP1	0,528659072
-SIRT7	0,528927974
-C16orf53	0,529668261
-KLHL2	0,533153888
-AK022213	0,533802801
-ANKRD28	0,534099367
-TF	0,536170201
-MAVS	0,53636005
-MSX1	0,536723495
-C12orf35	0,537890473
-AA554945	0,538449904
-SUN2	0,539191173
-RBM6	0,54218394
-AL080112	0,542349721
-SORT1	0,542569398
-AL049285	0,542660805
-FOXO4	0,542834527
-ABCA8	0,543725594
-RING1	0,54468938
-KCNE4	0,546337688
-TAZ	0,546506594
-DIP2A	0,546907877
-CLK4	0,548788669
-ZNF277	0,549312201
-MUS81	0,551193399
-DBT	0,556696292
-EMP3	0,557013195
-DDIT4	0,557077384
-RUFY1	0,557170712
-MYST3	0,559285285
-PRPF4B	0,559881298
-LOC100132247	0,562956585
-HSPB1	0,56508456
-CHD7	0,566776564
-CHORDC1	0,566831861
-COBL	0,569205746
-STAG2	0,569603186
-CTDSP2	0,570069613
-ZNF160	0,572703009
-PDE4C	0,574535337
-WWC3	0,575159977
-BMI1	0,576213767
-CRYAB	0,577245348
-AHCTF1	0,577515066
-ADIPOR2	0,5780263
-CASC3	0,57815663
-MUTYH	0,579456271
-AK023783	0,580340854
-HIGD1B	0,583663012
-PLOD1	0,587347495
-PRR14	0,587364521
-SH3BP4	0,58788373
-C19orf28	0,587956493
-NDRG1	0,588555643
-HIST1H1C	0,591446402
-TCF12	0,592176798
-MPST	0,593408757
-SEPP1	0,593935425
-DNAJB6	0,595685757
-SIRPA	0,596218961
-FLT1	0,597923318
-MYOT	0,598968138
-HIST1H2AC	0,600586387
-HBP1	0,600714263
-KAZ	0,601415288
-PTBP1	0,602313539
-NSUN5P1	0,603090503
-GUSBP3	0,604393039
-KCNJ2	0,616084197
-KAT2A	0,620256502
-MCM7	0,622618327
-FBXW4	0,627081137
-MKNK2	0,628440154
-IL17RB	0,631530593
-CLK1	0,632420317
-LRP4	0,632833859
-FAM53B	0,641895571
-JMJD6	0,64411039
-TYK2	0,644727629
-PLOD3	0,644893842
-CXXC1	0,650530485
-AK024136	0,659066605
-PAN2	0,66036619
-NPTX2	0,665210794
-SPEN	0,669461617
-SETD5	0,670191692
-STX10	0,674048462
-CDK2AP2	0,67411425
-PPM1B	0,68382966
-SLCO4A1	0,685048974
-GLT25D1	0,706365388
-ZC3H11A	0,716021559
-ZBTB16	0,720405109
-ZNF692	0,720940567
-NUPR1	0,724120307
-FLCN	0,747339708
-NFASC	0,755177517
+name	value
+GBE1	-0,943978048
+SLC18A2	-0,941309505
+KCNJ6	-0,894120983
+DLK1	-0,887122171
+PTDSS1	-0,851959645
+FGF13	-0,842876271
+PCDH8	-0,83524894
+ZNF226	-0,82900335
+SLC6A3	-0,824713365
+PIP5K1B	-0,812285785
+DENR	-0,81101551
+TPBG	-0,806963209
+PRKAR2B	-0,805288865
+OSBPL10	-0,80406299
+ALDH1A1	-0,795042129
+GGCX	-0,795035797
+ACP2	-0,794853979
+SLITRK5	-0,793842132
+FAM70A	-0,793715412
+HPRT1	-0,792370336
+CCNH	-0,790971864
+MYRIP	-0,78490295
+TUBB2A	-0,783142444
+ACTR10	-0,782043082
+BASP1	-0,778702387
+CADPS2	-0,777552826
+PID1	-0,775106213
+SV2C	-0,774895093
+RBM3	-0,77091551
+REEP1	-0,770000111
+RIMBP2	-0,766421185
+CNIH3	-0,765790316
+DMXL2	-0,765309344
+LOC10431	-0,762992699
+SV2B	-0,759985564
+AGK	-0,756506198
+RCAN2	-0,753762002
+LPPR4	-0,753018962
+RALYL	-0,75270126
+L1CAM	-0,751978689
+BCAS2	-0,751241508
+LOC100131795	-0,750350108
+TH	-0,748260596
+AV756161	-0,747351587
+TRIM36	-0,746057792
+MPPED2	-0,743864716
+NELL2	-0,742513977
+MAGED1	-0,739190733
+LRRC49	-0,738776851
+SYNGR3	-0,734846774
+ERC2	-0,734619705
+VBP1	-0,73223558
+UQCC	-0,729749962
+DCLK1	-0,725139215
+GSS	-0,724321987
+OPA1	-0,723790592
+PPP2R2B	-0,720892147
+COPS4	-0,720599852
+NSF	-0,720580224
+DLD	-0,72035948
+DYNC1I1	-0,719837984
+GABARAPL3	-0,717235008
+GPRASP1	-0,71302626
+NAP1L2	-0,712876929
+AMPH	-0,711957162
+PNMAL1	-0,70952389
+RGS6	-0,706463
+LDB2	-0,704777497
+TTC19	-0,704232585
+SCN3B	-0,703738866
+ATPIF1	-0,702603531
+BEX1	-0,700382911
+LMO3	-0,699029823
+TBC1D9	-0,698189481
+NDUFS1	-0,697230219
+INSM1	-0,696524737
+PARL	-0,696362568
+MRPL15	-0,688780959
+C3orf14	-0,687875821
+C19orf62	-0,687403479
+PCYOX1L	-0,686812669
+VRK1	-0,685016241
+MDH2	-0,684889561
+SMYD3	-0,684642724
+ASAH1	-0,68459801
+GSTA4	-0,684021936
+NDUFA9	-0,683116722
+ATP5C1	-0,682289667
+DDX25	-0,681511867
+GNG3	-0,681122999
+MUDENG	-0,67996077
+SCG2	-0,679728044
+MOAP1	-0,679575281
+SYT1	-0,678979261
+ATP6V1H	-0,6786546
+SHOC2	-0,677754756
+PCSK1	-0,677441918
+LBH	-0,67710638
+HK1	-0,676818391
+KIAA0319	-0,676346138
+SMAP1	-0,67618103
+EHBP1	-0,675429621
+RAP1GAP2	-0,673705297
+FABP7	-0,673485271
+LRRN3	-0,6731503
+AHNAK2	-0,672875949
+DHDDS	-0,671959403
+SNAPC5	-0,670824633
+C17orf108	-0,670563093
+AL390170	-0,67026906
+PTS	-0,669577055
+NUDT11	-0,668061506
+HMP19	-0,66794356
+IMMT	-0,667541939
+RGS4	-0,667109174
+RET	-0,667088994
+PBLD	-0,666164981
+AP3M2	-0,666056972
+WDR7	-0,665751643
+ATP6V0D1	-0,665487037
+RTF1	-0,664652469
+TUBB3	-0,664644351
+CHCHD2	-0,664529051
+DYNLT3	-0,663584428
+RAB6B	-0,662755469
+CHGB	-0,661865706
+NGFRAP1	-0,659441958
+AZIN1	-0,659394366
+EN1	-0,659313013
+SNX10	-0,659251628
+MIA3	-0,65882244
+ANK1	-0,657621479
+NR4A2	-0,65598531
+ANAPC13	-0,655864214
+RGS7	-0,654445938
+NME5	-0,652754395
+TXNDC9	-0,652019899
+PPIP5K2	-0,651763237
+RFK	-0,651442652
+BE674466	-0,651048329
+PEG10	-0,650932122
+PIAS2	-0,650823358
+CUX2	-0,649970555
+SEPT6	-0,649422911
+FKBP1B	-0,649416387
+C12orf10	-0,648407487
+HMGCS1	-0,648164918
+WDR61	-0,648133373
+GFPT1	-0,647751981
+MLLT11	-0,647471245
+AGTR1	-0,645674318
+CSNK1D	-0,645408463
+WDR47	-0,64495088
+PSMD14	-0,644669314
+CISD1	-0,643780748
+PSMD11	-0,642982055
+KCNS3	-0,642919136
+TIMM8B	-0,642730563
+RUNDC3B	-0,641744336
+ANKRD6	-0,640032629
+MDH1	-0,639623665
+STMN2	-0,639070421
+BAI3	-0,638894116
+STX12	-0,638382169
+NECAP1	-0,638376593
+NIT2	-0,638223243
+CIRBP	-0,637859912
+XK	-0,636787355
+KIAA1797	-0,636384728
+ICMT	-0,636379567
+GALT	-0,636138691
+SPINT2	-0,635454321
+PAIP1	-0,634724103
+TAGLN3	-0,63459569
+CADPS	-0,634245008
+GALNT11	-0,634168707
+SLC9A6	-0,632805526
+ANKRD34C	-0,63217094
+COPG2IT1	-0,63213856
+VPS4B	-0,63135628
+ATP6V0E2	-0,631164455
+SC5DL	-0,631137699
+CNPY2	-0,630875303
+GCC2	-0,630691438
+CRYZL1	-0,63015348
+MOBKL3	-0,630076244
+SNCA	-0,629316875
+STAM	-0,628134338
+TUBA4A	-0,627764216
+MAK16	-0,627148096
+FRY	-0,626684765
+UBE2V2	-0,626378865
+RWDD2B	-0,626170788
+FBXO9	-0,62572532
+FLJ41278	-0,6251633
+SLC30A9	-0,624759053
+LOC100132015	-0,623179237
+EXOG	-0,622056922
+RAP1GAP	-0,618803848
+DYNC1LI1	-0,618641756
+HARS	-0,618639749
+NDUFA5	-0,618245275
+SPCS1	-0,618130333
+PSMB7	-0,618122572
+NETO2	-0,618103081
+ATP5G3	-0,617855025
+UCHL1	-0,617452524
+FAM127A	-0,616124191
+TSSC1	-0,615619431
+CBLN1	-0,615519237
+CYB5R1	-0,615294192
+PSMG1	-0,61487171
+AKAP12	-0,614821543
+CYB561	-0,614281499
+KCND3	-0,613554227
+GABRB1	-0,613364723
+SLIT1	-0,613251897
+HN1	-0,612796898
+F8	-0,612749576
+VSNL1	-0,611517123
+ATP5A1	-0,611141848
+ARMCX5	-0,610703909
+AI097640	-0,610659067
+CERK	-0,610508368
+TMX4	-0,610174408
+TSPAN13	-0,609932725
+CAMLG	-0,609409157
+NDUFA7	-0,609351405
+STRAP	-0,609237631
+RTCD1	-0,607502869
+ORC5L	-0,606910471
+SCG5	-0,606870723
+HSPA12A	-0,606863939
+VAV3	-0,606070683
+TUBB2C	-0,60582666
+DCTN2	-0,605238426
+OCRL	-0,604661192
+HPCAL4	-0,604023171
+ARL1	-0,604008234
+CDK14	-0,603712397
+TLK1	-0,603591955
+BLVRA	-0,603201697
+NEFL	-0,602887281
+SLC25A32	-0,602708801
+ATXN10	-0,602624835
+UQCRC2	-0,601726567
+SLC25A3	-0,601470752
+MYL12B	-0,601373186
+CDS2	-0,601292766
+DDC	-0,601079077
+BSCL2	-0,6009448
+CACNB3	-0,598982611
+RIMS3	-0,598771066
+LASS6	-0,598387226
+FIBP	-0,598382328
+LRPPRC	-0,598144321
+PYROXD1	-0,598012671
+MAP3K9	-0,597438703
+CHL1	-0,5969101
+FJX1	-0,596748319
+PFN2	-0,596551333
+ATMIN	-0,59649395
+LIN7B	-0,596058244
+AV704232	-0,595274626
+PPP2R5C	-0,594797769
+SNAP91	-0,59414072
+AKT3	-0,593859242
+NDUFAB1	-0,593111219
+CCDC28A	-0,59307395
+GLOD4	-0,592429097
+STXBP1	-0,591440124
+HLTF	-0,591296161
+CRMP1	-0,590916915
+KIAA0513	-0,590696005
+GHITM	-0,590624599
+ATP6V1B2	-0,590367192
+USP14	-0,589739205
+RNFT2	-0,589705749
+SCG3	-0,589375952
+ATP5B	-0,588999541
+FAM136A	-0,588982627
+UBE2N	-0,588308222
+ANXA6	-0,588071667
+MRTO4	-0,58799806
+SNRK	-0,587183425
+CACNA2D2	-0,587134808
+IFT57	-0,586933566
+PPP3CB	-0,586906049
+RICH2	-0,586554767
+ME3	-0,586514247
+THOC7	-0,585617181
+FAM188A	-0,584083221
+EIF2B3	-0,582997986
+CNTNAP1	-0,582856877
+SCRN1	-0,582791752
+ACAT1	-0,582760841
+IDI1	-0,582694626
+PBX1	-0,582658829
+CDC42	-0,582658446
+NBEA	-0,582614884
+PPP1R2	-0,581839918
+ACTR6	-0,581817384
+TAF9	-0,581794162
+NIPSNAP1	-0,581711722
+SEC61A2	-0,58139821
+WDR37	-0,581272248
+VWA5A	-0,581248993
+CDC27	-0,580500838
+MYT1L	-0,580491453
+PSMC1	-0,580473356
+KATNB1	-0,578133005
+ZWINT	-0,577661475
+C12orf24	-0,577181135
+SLC25A46	-0,577144749
+DOLK	-0,576794187
+APOO	-0,576716633
+GCH1	-0,576494714
+TBC1D30	-0,575582077
+DCTN3	-0,575526778
+FBXL2	-0,575141782
+KIFAP3	-0,574923419
+CMAS	-0,574834972
+C18orf10	-0,574780811
+PNMA2	-0,574504978
+PDHX	-0,574434123
+SAMM50	-0,574204311
+NDUFA2	-0,574087728
+NPTN	-0,573534504
+HIGD1A	-0,573110642
+CYC1	-0,573010558
+HMGCR	-0,572959475
+TRAPPC2L	-0,572517332
+IMPA1	-0,572397104
+IMPACT	-0,572070372
+KIAA0802	-0,572067617
+DSTN	-0,571964512
+C5orf44	-0,571958339
+CCK	-0,571148184
+OGDHL	-0,571078621
+TCP11L1	-0,570951095
+RNF14	-0,569913578
+IARS	-0,569079443
+CDH8	-0,569072707
+RNF41	-0,568830451
+SCN3A	-0,568276898
+PSMD12	-0,567936617
+TNFRSF21	-0,567631199
+FIG4	-0,566751868
+DDX24	-0,566446037
+MARK1	-0,566206858
+ATP8A2	-0,565754513
+ACLY	-0,565055263
+DDX42	-0,564984354
+KIF3C	-0,564949485
+PIN1	-0,564290859
+PSEN2	-0,564206755
+TERF2IP	-0,564084181
+VDAC3	-0,563895581
+B3GNT1	-0,563686309
+CHN1	-0,563660153
+GLO1	-0,561564055
+RAB11A	-0,561549092
+PRPS1	-0,561391557
+MAP2	-0,561080301
+NHP2	-0,56096586
+DNAJA2	-0,560780556
+NDRG4	-0,560771764
+HNRNPA0	-0,560406816
+NDUFV2	-0,559975953
+ADH5	-0,559909821
+FAM3C	-0,559672666
+COPS7A	-0,559265307
+SULT4A1	-0,558733244
+MATN3	-0,558346148
+TMEM14A	-0,557817575
+HRASLS	-0,557799459
+TMEM14B	-0,557593404
+TTC1	-0,557573183
+R3HDM1	-0,557428266
+AUH	-0,55725646
+C5orf22	-0,55714645
+TUBB	-0,557095971
+C5orf13	-0,55663948
+COX7A2L	-0,556219721
+POMP	-0,556110434
+ATP5J2	-0,555267292
+ZNF204P	-0,555121445
+INA	-0,554984251
+NUP93	-0,55488654
+STAU2	-0,55454534
+VAT1	-0,554180752
+DDB1	-0,554146967
+THY1	-0,554057809
+SRPRB	-0,553818923
+IMP4	-0,553554219
+SRP19	-0,552319097
+FUCA1	-0,551919323
+PRKCZ	-0,551777138
+CD2BP2	-0,55167071
+C12orf43	-0,551436389
+SUSD4	-0,55137396
+W88821	-0,551080268
+LSM4	-0,550328209
+SNAP25	-0,550276399
+ACSL6	-0,549806401
+MYH10	-0,549550685
+DDHD2	-0,548942799
+PRKACA	-0,548422775
+CHRNB3	-0,547701041
+NEFM	-0,547618123
+PLD3	-0,547495065
+GSPT2	-0,547329995
+ATP6V1E1	-0,546911033
+GABBR2	-0,546899558
+IPW	-0,546596796
+SCAMP5	-0,546380917
+RFPL1S	-0,545994554
+BSN	-0,545979557
+MAGI1	-0,54490486
+DRG1	-0,544733954
+PITPNB	-0,544704547
+LETMD1	-0,544636809
+AI263044	-0,544470885
+STOML1	-0,544383238
+GBAS	-0,544103215
+RAB3GAP1	-0,543092086
+ACTG1	-0,54300405
+PPME1	-0,542943175
+AFG3L2	-0,542490245
+DNAJC6	-0,541912283
+TUBA1B	-0,541625287
+ABCE1	-0,541581351
+ARF3	-0,541401116
+SRSF3	-0,54134715
+NEFH	-0,540578844
+ADK	-0,540377244
+TIMM17A	-0,540158649
+ELOVL6	-0,540054201
+FAM189A1	-0,539987546
+ATP6V1A	-0,539816156
+OAT	-0,53960074
+KIAA0284	-0,539436564
+SLC25A12	-0,538986194
+AP3D1	-0,538816413
+ISCU	-0,53848727
+CDH10	-0,538458105
+APEH	-0,538385859
+TMEM35	-0,537944022
+NDFIP1	-0,537769873
+U79277	-0,537586945
+SYNGR1	-0,53757151
+MEAF6	-0,537175986
+DNM1	-0,536361784
+DEF8	-0,536162488
+PDXK	-0,536128962
+RIT2	-0,536060129
+AACS	-0,535868362
+RAB3A	-0,535840143
+LXN	-0,535676847
+CCBL2	-0,53559953
+ATXN7L3B	-0,535570224
+RCN2	-0,535264733
+SDC2	-0,535187449
+NRXN3	-0,534911729
+SDC1	-0,534748047
+PSMD1	-0,534162775
+UBA5	-0,534098166
+PEX11B	-0,533915774
+RAP1GDS1	-0,533764019
+NUPL1	-0,533680375
+ARMCX1	-0,533607326
+SDHAP1	-0,533209621
+PJA2	-0,532853246
+ACOT7	-0,532662038
+SEZ6L	-0,532618647
+CELF2	-0,532603645
+CXorf40A	-0,532513065
+NDUFB5	-0,532279155
+GARS	-0,532224902
+NRG1	-0,532009485
+SEC31B	-0,53180843
+ME1	-0,531466374
+PSMD8	-0,531445018
+MSL1	-0,531268404
+PCLO	-0,531166247
+RAB14	-0,531006634
+MAGED2	-0,530858407
+EIF3K	-0,530846086
+MMD	-0,530845303
+MYO5A	-0,530805656
+NCRNA00094	-0,530597959
+KIAA1107	-0,53057188
+KIAA0564	-0,530294183
+PSMB2	-0,530140819
+C1orf114	-0,530111522
+GCLM	-0,529867963
+NDN	-0,529086871
+SRD5A1	-0,528786683
+DNAJB9	-0,528374918
+SLC7A8	-0,528181836
+CLIP3	-0,527794519
+NDUFB1	-0,527724864
+CLSTN2	-0,52726691
+C14orf156	-0,527148764
+CIAPIN1	-0,527136633
+ATP5F1	-0,527047789
+PSMB5	-0,526841307
+FAM32A	-0,526499611
+KIAA1644	-0,526147045
+RTN1	-0,526062751
+EXOSC9	-0,525622526
+PFKM	-0,525053758
+TCF25	-0,524910517
+ATP5O	-0,524889972
+PTPRN2	-0,524794642
+SNX4	-0,524373257
+ATP6V1G2	-0,524016622
+SLC35E3	-0,523930118
+SLC2A6	-0,52364368
+SUCLA2	-0,523588063
+PLCB1	-0,523263994
+TMEM30A	-0,521872901
+PDE4D	-0,521870014
+RAB5A	-0,521632556
+MAPK9	-0,521572661
+CAP2	-0,521120749
+RPS6KA3	-0,520660932
+GNAO1	-0,520506337
+PSMD6	-0,520132666
+TBCE	-0,519679173
+C9orf125	-0,519623009
+MN1	-0,51937171
+MFSD1	-0,51842841
+KIF3A	-0,518357676
+SHFM1	-0,517546292
+NRIP3	-0,516545986
+ANKMY2	-0,516365077
+CDK5	-0,516196782
+REEP5	-0,516165841
+SLC1A1	-0,516141732
+UBE2K	-0,516036367
+SMEK2	-0,515537555
+PI4K2A	-0,515462049
+TTC39A	-0,514924765
+GUCY1B3	-0,514788287
+QPCT	-0,514170797
+ST6GALNAC5	-0,514077764
+ATP6V1F	-0,513941613
+HSD17B12	-0,513489073
+PPFIA2	-0,51321383
+PLCH1	-0,512855521
+CNTN6	-0,512564243
+ENTPD6	-0,512350634
+ALAS1	-0,512141897
+RUNDC3A	-0,511994377
+PCMT1	-0,511547085
+IDS	-0,511290223
+PLEKHB2	-0,510964275
+CDO1	-0,510668427
+NDUFB6	-0,510219117
+COX6C	-0,509869079
+OPTN	-0,509603205
+PSMA1	-0,509510596
+STS	-0,509361214
+TIMM10	-0,509318807
+C1D	-0,509252454
+GAP43	-0,509215292
+CCDC6	-0,509150548
+TRIM37	-0,509012308
+ATP2B2	-0,508803511
+PGAM1	-0,50863259
+GGNBP2	-0,508616013
+SRP72	-0,508482078
+TCEAL2	-0,508464868
+SV2A	-0,508330914
+CDK5R2	-0,508227652
+FHOD3	-0,508155146
+FECH	-0,508046235
+ATP2A3	-0,507932978
+SUB1	-0,507787459
+ACO2	-0,507726776
+C20orf3	-0,507526055
+SEC22B	-0,507453281
+VPS35	-0,507278509
+MRPS33	-0,507141908
+TXNL4A	-0,50704416
+ARHGEF9	-0,506224253
+RBM9	-0,506096633
+TMEM135	-0,506088817
+UHRF1BP1L	-0,505757524
+ME2	-0,505446593
+BZRAP1	-0,505378895
+MCAT	-0,50534007
+AKAP6	-0,505213579
+COPS3	-0,505110121
+MRPS35	-0,505107922
+YWHAB	-0,505015581
+PEX7	-0,504955276
+COPS8	-0,504746043
+OXCT1	-0,504643125
+MAD2L1	-0,504589351
+MCTS1	-0,504510155
+LGALS8	-0,50448664
+ACP1	-0,504339709
+MX1	-0,50393674
+NCALD	-0,50389725
+TASP1	-0,503797818
+AGTPBP1	-0,503605082
+RNF128	-0,503554068
+PSMD13	-0,503503704
+TXN	-0,50336484
+NHLH2	-0,50325399
+USP12	-0,503149229
+PFDN4	-0,502988386
+NAP1L3	-0,502893901
+MRPL20	-0,502624211
+ACSL3	-0,502355771
+MTPAP	-0,502307088
+PMPCB	-0,502239978
+SH3GL3	-0,502227406
+API5	-0,502196949
+CAPNS1	-0,5020898
+YWHAZ	-0,501747483
+TOMM70A	-0,501591565
+STX18	-0,501503813
+HNRNPK	-0,501464694
+LRP1B	-0,501433491
+CDC123	-0,500993468
+DCTN6	-0,500740808
+VAPB	-0,500599356
+CCDC56	-0,499906136
+GOT2	-0,499477446
+RHEB	-0,499343134
+PSMD2	-0,499333749
+YPEL5	-0,49910251
+ATP5G1	-0,499077107
+TUBA1A	-0,498949544
+GSTM3	-0,498766376
+EPB41L1	-0,498605796
+EPS15	-0,498447403
+ENO2	-0,498261848
+ASMTL	-0,498100631
+FH	-0,498098378
+CLTC	-0,497596743
+PSMA3	-0,497405846
+UROS	-0,497291028
+OLFM1	-0,496832922
+ATP6V1G1	-0,496818916
+B3GALNT1	-0,496135395
+PHLPP2	-0,496077027
+TSPYL1	-0,495383913
+SERINC1	-0,49538338
+RPL15	-0,495355843
+ITFG1	-0,495195881
+PDHB	-0,494999933
+RABL3	-0,494855325
+TMEM22	-0,49462563
+MCFD2	-0,494506103
+GABARAPL1	-0,494373853
+MAGEL2	-0,493987847
+VPS33B	-0,493750355
+CDIPT	-0,493440531
+ATP6V0B	-0,493438352
+CLGN	-0,493358721
+SEC23A	-0,493255831
+C7orf43	-0,49286586
+ARL3	-0,492481932
+SLC12A5	-0,492392187
+LAPTM4B	-0,492348426
+LOC285359	-0,492290998
+LARP1	-0,49192011
+YME1L1	-0,491725992
+RAB2A	-0,491586306
+SPATA20	-0,490991626
+ASH2L	-0,490785052
+PTBP2	-0,490747846
+WTAP	-0,490599757
+NANS	-0,490410248
+SCFD1	-0,490269997
+EPB49	-0,489916122
+TUFT1	-0,489843226
+POP4	-0,489594415
+CACNA1G	-0,489236615
+PRPF19	-0,48917604
+NCOA4	-0,488872014
+C1orf216	-0,488856307
+TXNL1	-0,488777426
+AMPD2	-0,48875487
+ASL	-0,488300478
+PFDN1	-0,48807629
+EXTL2	-0,488020888
+RPA3	-0,48773487
+ACVR1B	-0,487609726
+ANKRD46	-0,487476076
+GRIA1	-0,48726366
+PSMB6	-0,487099126
+CAPRIN2	-0,486969775
+SRGAP3	-0,48684289
+ARPC5L	-0,486786621
+PSME3	-0,486309204
+NME2	-0,486066455
+ISCA1	-0,485683262
+ZNF365	-0,485504618
+PINK1	-0,485341061
+RWDD2A	-0,48504437
+EXOC1	-0,484927354
+ECE2	-0,484617735
+WDR77	-0,484600271
+AI890972	-0,484490353
+ERBB4	-0,484253264
+PSMD4	-0,483962197
+RAB6C	-0,483864006
+CSTF3	-0,483798153
+NIPA2	-0,483638091
+AK5	-0,483482302
+C17orf91	-0,483141592
+INPP4B	-0,482534933
+PJA1	-0,482372063
+BE551361	-0,482367089
+B4GALT5	-0,48224903
+MTX2	-0,481915827
+MGST3	-0,481667788
+TRMT11	-0,481613419
+PTPRN	-0,481522612
+DNAJC12	-0,48150495
+FTSJ2	-0,481162212
+CCT8	-0,48112028
+PGAP1	-0,481030935
+SLC25A44	-0,480898127
+AMIGO2	-0,480319409
+SCAMP1	-0,480275681
+RBKS	-0,480222
+SYN1	-0,48014199
+APEX1	-0,479680328
+AL157484	-0,4790893
+PAK3	-0,479026618
+SLC25A13	-0,478484409
+EIF1B	-0,478403329
+DLAT	-0,478235597
+AI375694	-0,47804406
+PMS2L1	-0,477748782
+DYNC2LI1	-0,477528415
+RANBP9	-0,477445784
+PTPN20A	-0,476653786
+ZMYM4	-0,476508652
+UQCRQ	-0,476353248
+EXOSC7	-0,476299374
+NDUFB3	-0,476207507
+LCMT1	-0,476121484
+ZNF547	-0,47597802
+TBCA	-0,475802982
+MAPK8IP3	-0,475554385
+N80935	-0,475378775
+SLC4A3	-0,475327531
+AASDHPPT	-0,475086681
+CAND2	-0,475049952
+CXorf40B	-0,474988185
+FXYD6	-0,47456179
+RNF10	-0,474499733
+ELOVL4	-0,474412575
+AAK1	-0,474378982
+SEH1L	-0,474159291
+PTPRU	-0,473978747
+LPGAT1	-0,473432618
+VPS24	-0,473360696
+MCF2	-0,473341916
+FAR2	-0,473007144
+CKMT1A	-0,472884518
+TMED3	-0,472883274
+RNASEH1	-0,47283341
+NDUFA3	-0,472657747
+GLS	-0,472644869
+FAM168A	-0,472617309
+KLHDC10	-0,472577269
+GLRX5	-0,472478522
+SYT17	-0,472292582
+PAM	-0,472018566
+CLTB	-0,471770785
+COPS2	-0,470912718
+DDA1	-0,470419616
+PCSK2	-0,470372976
+SLC25A6	-0,470332168
+TPI1	-0,470300584
+MECR	-0,47026417
+ORC4L	-0,47025895
+ITPR1	-0,470228063
+HMG20A	-0,470060529
+GNB5	-0,470039178
+TMEM208	-0,469963608
+NCAPG	-0,469752447
+GLRB	-0,469638821
+ATP6V1D	-0,469577982
+AKAP11	-0,469501191
+SH3GL2	-0,46948768
+NISCH	-0,469445416
+SIPA1L1	-0,469275377
+PFKP	-0,469125064
+LYRM4	-0,469088537
+SLC4A1AP	-0,46898494
+AP2A2	-0,468669242
+CX3CL1	-0,46850557
+WBP11	-0,468444743
+LASP1	-0,468444317
+GOT1	-0,468375399
+C6orf120	-0,468133996
+SPAG7	-0,468070563
+SERGEF	-0,467688975
+TFB2M	-0,4675501
+AP3B2	-0,467537408
+PAFAH1B1	-0,467362101
+BPGM	-0,467130793
+CRAT	-0,466839519
+DDX1	-0,466770911
+ADAM23	-0,46652833
+ASB6	-0,466473575
+PCDHA1	-0,466456945
+TUSC3	-0,465574044
+TCEA2	-0,465512943
+SMARCA4	-0,4653413
+DAPK1	-0,465142929
+DBNDD1	-0,464965333
+NDUFC2	-0,464959656
+IDH3B	-0,464778307
+CDC37L1	-0,464692992
+WDR11	-0,464429092
+CD200	-0,464378251
+TUSC2	-0,464289641
+IRGQ	-0,464009317
+CALY	-0,463919598
+NNT	-0,463872117
+MSH2	-0,463745236
+GYG1	-0,463657489
+FAM134C	-0,463380379
+RTN2	-0,463379977
+RBM12	-0,463289569
+SYNJ1	-0,463207762
+ABCA5	-0,462881594
+ENTPD4	-0,462777994
+MAP2K4	-0,462732144
+AIMP2	-0,46256199
+PITPNA	-0,462484131
+BNIP3	-0,461982272
+COPS5	-0,461956463
+BRE	-0,461910476
+MIR21	-0,461667267
+ATP5S	-0,46152488
+SIN3B	-0,461515059
+NAT10	-0,461457105
+MTCH2	-0,461117099
+ACHE	-0,461032229
+PSD3	-0,46079613
+UCHL3	-0,460466303
+SMPX	-0,459975528
+USP11	-0,459753441
+RNF187	-0,459566796
+AAGAB	-0,458932639
+ENY2	-0,458770966
+NDEL1	-0,458614173
+FAM184A	-0,458384449
+TOX4	-0,458204483
+SLC25A15	-0,458110832
+SACM1L	-0,458050139
+ADARB1	-0,458034616
+SPHK2	-0,457781426
+CES2	-0,457687554
+CYFIP2	-0,457201169
+KPNA2	-0,457034156
+ACTR1A	-0,456856222
+SLC25A22	-0,456321526
+DPYSL3	-0,456025294
+PRKAR1A	-0,455984698
+SIDT1	-0,455560984
+TIPRL	-0,455474112
+EIF5	-0,455347544
+C16orf58	-0,455176502
+RAB7A	-0,454946879
+MFSD6	-0,454914435
+NDUFS2	-0,454605666
+APOOL	-0,454580027
+GNB1	-0,454284789
+SARS	-0,454282127
+PIK3R3	-0,454240907
+SERINC3	-0,454097365
+ST3GAL5	-0,45407104
+DHRS11	-0,453695947
+NEDD8	-0,45367218
+RAB15	-0,453664346
+HSPA13	-0,453577406
+OLA1	-0,453153228
+C3orf18	-0,45312023
+AF131844	-0,453027105
+C12orf52	-0,452914604
+ACBD3	-0,452894377
+PCIF1	-0,452240197
+BMP2K	-0,451224584
+TSPYL5	-0,450674174
+SEC63	-0,450642641
+C7orf44	-0,450408444
+PWP1	-0,450360796
+SLC25A14	-0,45012674
+SYP	-0,449768016
+PRKCB	-0,449564151
+KIF2A	-0,449276369
+PEX26	-0,449100108
+SDHA	-0,448617251
+PITRM1	-0,448602767
+PPA2	-0,448269554
+MAN2A2	-0,448177121
+FAM49A	-0,448170721
+KCTD9	-0,448062861
+REEP2	-0,44801948
+NDUFS3	-0,447803075
+CHGA	-0,447356315
+UBE2E3	-0,447311178
+LOC595101	-0,447006376
+RNF170	-0,446698112
+TMCO1	-0,446651514
+PCCB	-0,446640741
+RAB1A	-0,44645249
+ATP1A1	-0,446309137
+KIAA1045	-0,446174802
+CASD1	-0,445992918
+C3orf37	-0,445975885
+RAD17	-0,445659766
+BBS4	-0,445631347
+TBC1D19	-0,445509157
+TSG101	-0,445289202
+DKK3	-0,445181251
+KCNQ2	-0,444911548
+EIF4E	-0,44477948
+LOC100134209	-0,444742688
+OSTF1	-0,444651424
+PPCS	-0,444330494
+ATP13A2	-0,443924538
+DHRS7B	-0,443866868
+TSN	-0,443785273
+AI201594	-0,443780197
+UBE2J1	-0,443536878
+C12orf51	-0,443320039
+INPP5F	-0,44324612
+KIAA0391	-0,443138749
+NDUFB8	-0,442168118
+COX8A	-0,442151263
+PLCB4	-0,442128902
+UQCRC1	-0,442055114
+RNMT	-0,442010619
+PSMB4	-0,441631296
+ATP9A	-0,441570839
+COMMD8	-0,441419712
+STX7	-0,441415012
+UQCRFS1	-0,441387219
+ARMC8	-0,441335025
+USP33	-0,441131902
+SC4MOL	-0,441051846
+AVL9	-0,440604375
+CORO1C	-0,440555184
+ATP6V0A1	-0,440500219
+AKTIP	-0,440321706
+C11orf49	-0,440065839
+ACCN1	-0,439959618
+DYNC1H1	-0,439954428
+RTN4	-0,439926435
+IFT52	-0,439664934
+ARIH1	-0,439616652
+SLC23A2	-0,439279622
+FDPS	-0,439263979
+ZW10	-0,439088192
+C6orf211	-0,438493952
+CAPZA2	-0,438442617
+TRIM9	-0,43841496
+PANK2	-0,438226487
+SLC25A36	-0,437878589
+TM7SF2	-0,437751686
+GPD1L	-0,437274057
+TM2D3	-0,437156245
+TBC1D22A	-0,436837159
+AFF2	-0,436678505
+PSMA4	-0,43652406
+SCAPER	-0,436328183
+KPNB1	-0,43624217
+C8orf33	-0,436164892
+RRAS2	-0,435924543
+PNMA1	-0,435862986
+DRD2	-0,435854058
+CCDC92	-0,435740221
+CYB5B	-0,435703661
+DNM1L	-0,435497666
+FAM98A	-0,435109538
+CYCS	-0,43500707
+UBE2B	-0,434857087
+DCTPP1	-0,434751269
+ENC1	-0,434576571
+SAP18	-0,434463135
+MED7	-0,43446171
+UBXN6	-0,433506891
+MAEA	-0,433493136
+C20orf27	-0,433220759
+ARFGEF2	-0,4331108
+FKBP9	-0,433030189
+COQ10B	-0,432955202
+SNRNP25	-0,432902395
+PHKB	-0,432809153
+CETN2	-0,432732838
+PIK3R4	-0,432641256
+EFR3A	-0,432263211
+FAM162A	-0,432255742
+LOC732160	-0,432226821
+SRPK2	-0,432044566
+USP9X	-0,431489845
+DENND2A	-0,431031563
+PPP2CA	-0,430950806
+CHST1	-0,430892555
+OSBPL9	-0,430720865
+TPM3	-0,430527364
+UGP2	-0,430314768
+AL049387	-0,430134526
+ARHGDIG	-0,429952838
+GPR161	-0,429932801
+HGSNAT	-0,429440496
+TCEAL4	-0,429402449
+KHDC1	-0,429285977
+SPATA7	-0,428924113
+NIPSNAP3B	-0,428922472
+NHP2L1	-0,42870798
+BZW2	-0,428685674
+BZW1	-0,428658261
+ABCF3	-0,428526247
+PEX19	-0,428349422
+POLR2K	-0,42820853
+FAM134B	-0,428156057
+TUBGCP4	-0,428150919
+CSNK2A1	-0,427824997
+PPP2R5D	-0,427719013
+CEND1	-0,427667723
+RNF11	-0,427514623
+EBNA1BP2	-0,427275229
+SDHC	-0,42690156
+ATP6AP2	-0,426823582
+MAPK1	-0,426681157
+YTHDC2	-0,425950246
+ACTR3B	-0,425721173
+LRRC47	-0,424928312
+ANO10	-0,424906321
+MORF4L2	-0,424702281
+NAE1	-0,424669605
+GRSF1	-0,424576498
+UBE3C	-0,42455123
+RRM1	-0,424268285
+IARS2	-0,424201991
+HINT1	-0,423973896
+B4GALT7	-0,423964657
+OBSL1	-0,423852756
+RPH3A	-0,423713255
+PTPRM	-0,423526608
+TRAP1	-0,423405292
+GSTO1	-0,423136683
+PGK1	-0,423107749
+KCTD2	-0,423033005
+AKAP9	-0,423014145
+KIAA0090	-0,422971022
+NIF3L1	-0,422805913
+SAE1	-0,422487927
+TRAPPC4	-0,422454822
+UBE3B	-0,422322842
+MRPL13	-0,422291395
+ARF1	-0,422218883
+NCKAP1	-0,421739152
+COX11	-0,421717769
+XPA	-0,421552598
+FKBP11	-0,421544606
+ZFAND1	-0,42136139
+RUSC1	-0,421250909
+PSMC2	-0,42099626
+MCM4	-0,420976269
+HEXA	-0,420954607
+PDE4A	-0,420795908
+VPS45	-0,420785909
+OGFOD1	-0,420640442
+ADPGK	-0,420505817
+AP2M1	-0,420467875
+PSMD5	-0,420139323
+PGRMC1	-0,420109613
+CLASP2	-0,419942702
+CAMTA1	-0,419843296
+COX5A	-0,419753275
+BCAP29	-0,419678508
+C21orf59	-0,419586484
+INSIG1	-0,419347593
+NDUFAF1	-0,419256514
+SNCG	-0,419205938
+NCAN	-0,418993508
+SLC24A3	-0,418714364
+MAP2K1	-0,418679322
+BRCC3	-0,418660516
+MYCBP2	-0,418420128
+PREPL	-0,41818051
+TUFM	-0,418149804
+LYRM2	-0,41810337
+ORC3L	-0,417994092
+TSR2	-0,417894679
+SLC41A3	-0,41774061
+DZIP3	-0,417712026
+MRPS11	-0,417644175
+B4GALT6	-0,41761846
+CHD5	-0,417472
+TUBA1C	-0,417351982
+OTUB1	-0,41729395
+DCAF6	-0,417154254
+UQCR10	-0,417021115
+BEX4	-0,416948363
+RTN3	-0,416868526
+GOLT1B	-0,416408995
+MRPL3	-0,416396676
+DDX19A	-0,416375948
+C4orf41	-0,416356919
+SEMA3G	-0,416349944
+TUBA3D	-0,416216957
+B4GALNT1	-0,415958605
+TOR1A	-0,415819164
+SUPT16H	-0,415597727
+ACTR3	-0,415469056
+ABCB9	-0,415410201
+SERF1B	-0,415262572
+PSMC6	-0,415072747
+GALNT2	-0,414525722
+ARF5	-0,414370994
+TCEB1	-0,414262524
+FEN1	-0,414164817
+HS2ST1	-0,413801139
+FBXL15	-0,413238338
+ANAPC10	-0,413161353
+MAPK10	-0,413048251
+FGF12	-0,412576909
+GTF2B	-0,412561968
+CALM3	-0,412474461
+C12orf5	-0,412385409
+BTRC	-0,412323302
+UBXN8	-0,411884422
+G6PC3	-0,411853401
+MARK4	-0,411850043
+SDHB	-0,411814414
+FXC1	-0,411804756
+KIAA1467	-0,411406746
+COL4A3BP	-0,411372338
+MADD	-0,411317373
+SLC25A11	-0,411257994
+APBB3	-0,411242683
+LDHB	-0,411172229
+ENTPD3	-0,410988615
+CAMK2B	-0,410817586
+C15orf24	-0,410807275
+RAB11FIP5	-0,410722406
+C18orf1	-0,410410534
+IL13RA2	-0,410393436
+TMEFF1	-0,40994415
+TAX1BP1	-0,409905258
+ABHD11	-0,409662969
+SETD4	-0,409479623
+NARS	-0,409352949
+LOC441259	-0,409193342
+SMAD2	-0,408937637
+MAGEH1	-0,408820062
+LPIN2	-0,408744346
+WRB	-0,408371938
+HSPB11	-0,408269901
+COMMD9	-0,407620354
+RMND1	-0,407542555
+RBP1	-0,407484296
+TSPAN7	-0,407465467
+YKT6	-0,407243851
+ATP5L	-0,407238078
+STAT1	-0,407123963
+SPTAN1	-0,407085674
+SLBP	-0,407034029
+FAM115A	-0,407018502
+ATP1B1	-0,407007242
+GIN1	-0,406994648
+SLC25A4	-0,406703055
+RPAP3	-0,40653888
+ELAVL4	-0,406510215
+LDHA	-0,406394191
+GABRG2	-0,406143723
+ACOT1	-0,406088493
+LZTFL1	-0,406077259
+LARP4	-0,406073312
+PTPRG	-0,405852123
+DIRAS2	-0,405793372
+SNCB	-0,405789504
+CDS1	-0,405765281
+ARL2BP	-0,405758176
+BCL2L13	-0,405729545
+STAT4	-0,405634359
+C17orf75	-0,405632179
+ELAVL2	-0,405590653
+DNM3	-0,405342092
+SNX16	-0,404866663
+TACO1	-0,40485549
+HPGD	-0,404805074
+CHMP2B	-0,404775945
+DPP8	-0,404495701
+SYBU	-0,403649563
+CHP	-0,403478973
+GTF2H5	-0,403475179
+PPP2R5B	-0,403191055
+TRAK1	-0,402996995
+ACSL4	-0,402921692
+RABGAP1L	-0,402883713
+PSMB3	-0,402864552
+ASTN1	-0,402784524
+TIMM23B	-0,402679864
+NDUFC1	-0,402669713
+GPM6A	-0,402645229
+NCDN	-0,402391637
+TMEM183A	-0,402206694
+LACTB2	-0,402125728
+SFPQ	-0,401934429
+SLC1A4	-0,401903736
+LOC731884	-0,401617561
+TTC3	-0,401599425
+APBA1	-0,401587582
+FAM20B	-0,401527926
+ISOC1	-0,401479145
+TMEM70	-0,401425176
+GLUD1	-0,401204073
+NDUFA4	-0,401152135
+SHANK2	-0,401076931
+NDUFA6	-0,400922451
+FAM128A	-0,400907344
+TSNAX	-0,400758374
+BLCAP	-0,400561763
+WASF3	-0,400514139
+MTMR6	-0,400412018
+CBARA1	-0,399961135
+SMCR7L	-0,399645568
+REXO2	-0,399637796
+ASTN2	-0,399013865
+FBXO31	-0,398919379
+MRPS10	-0,398754479
+GNAL	-0,398117434
+RDH11	-0,398104472
+ANKH	-0,398086916
+EPHA5	-0,397910595
+DPY19L2P2	-0,397861593
+NRXN1	-0,39777997
+FOXA1	-0,397622781
+AGGF1	-0,397583973
+CLCN6	-0,397581706
+PRKAG1	-0,397496639
+GRM5	-0,397456403
+BCAT1	-0,397331444
+MAP1LC3B	-0,397317027
+HMGCL	-0,397130437
+IFIT5	-0,397045055
+FAM82B	-0,397007464
+TMEM189-UBE2V1	-0,39671729
+TMEM160	-0,396535704
+PIGZ	-0,396390486
+VDAC2	-0,3962914
+BCAP31	-0,396227306
+CUL2	-0,395939867
+C5orf30	-0,395902062
+VAMP4	-0,395520757
+CLTA	-0,395495699
+NOS1AP	-0,395452681
+YWHAH	-0,395414553
+AGL	-0,39537715
+PPIA	-0,395286888
+POLR2E	-0,395239973
+FAM190B	-0,395231307
+CAND1	-0,395218949
+DIABLO	-0,395167608
+FAM155A	-0,395099838
+FAM174B	-0,394929763
+ABCA11P	-0,394841999
+LMF1	-0,394801997
+EIF3I	-0,394774336
+RRAGA	-0,39363313
+SLC25A5	-0,39336993
+BTBD3	-0,393323586
+SLC38A6	-0,393193457
+TSPYL4	-0,39289974
+NDUFA8	-0,392898828
+ERI3	-0,392853573
+CDH11	-0,392815946
+VPS11	-0,392712183
+RPP40	-0,39270293
+SMS	-0,392616216
+USP4	-0,39251437
+RAN	-0,392486577
+SYT11	-0,392234251
+SEC23IP	-0,392233152
+SUPV3L1	-0,392124663
+TOX3	-0,392048323
+OSBPL3	-0,391742979
+ATP5J	-0,391738382
+APC	-0,391687772
+EIF2AK2	-0,391678642
+MPPE1	-0,391534871
+CHD3	-0,391021702
+BE858194	-0,390954653
+GPN2	-0,390821549
+TMEM97	-0,39059622
+BRF2	-0,390477924
+NSDHL	-0,390017568
+LOC654342	-0,389476483
+SATB1	-0,389035394
+RPP14	-0,388984247
+C16orf68	-0,388858051
+PHF14	-0,388842446
+CKAP5	-0,388699527
+MMADHC	-0,388406258
+MEST	-0,388313548
+UQCRH	-0,387974488
+GBAP1	-0,387823169
+PMPCA	-0,387778282
+TMEM41B	-0,387668262
+SCLY	-0,387620138
+OXA1L	-0,387520115
+CLPX	-0,387517816
+EML1	-0,387443167
+DPP6	-0,387318033
+FBXO3	-0,387294212
+GAPDH	-0,386769027
+ATP6V1C1	-0,386766958
+PRAF2	-0,386484628
+NAA35	-0,386425969
+EIF4H	-0,386302469
+SGSH	-0,386196526
+CLCN3	-0,386084887
+SMARCA1	-0,385880429
+FAM158A	-0,385760557
+AP3S2	-0,385712457
+EIF1AX	-0,385367803
+RNF115	-0,385287305
+GPI	-0,385266179
+SEC62	-0,385020013
+G3BP2	-0,384968143
+NDUFV1	-0,38487232
+C19orf42	-0,384758261
+BEND5	-0,384699839
+KCNAB2	-0,384620267
+EVL	-0,384619104
+MTMR9	-0,384460721
+SIRT3	-0,384239932
+CNIH	-0,383916854
+TOLLIP	-0,383913386
+C11orf2	-0,383735535
+NUDCD3	-0,383703548
+MED4	-0,383545823
+RABGEF1	-0,38353381
+PTN	-0,383407974
+GBF1	-0,383365739
+C1orf163	-0,383317238
+LOC100129361	-0,383315417
+CUL4B	-0,383032231
+OXR1	-0,382758654
+TRIM33	-0,382726006
+GPC5	-0,382713696
+C11orf51	-0,382673891
+MAN1C1	-0,382595078
+FGF9	-0,382294616
+SPOCK2	-0,382267861
+GLMN	-0,382038722
+MPP1	-0,381567886
+KIF21B	-0,381555674
+RND1	-0,381481938
+PEX1	-0,381462705
+C2orf34	-0,381417191
+OTUD3	-0,381344145
+MSRB2	-0,381206334
+CCDC85B	-0,38118283
+RGS3	-0,380621769
+SERPINI1	-0,380596066
+C14orf2	-0,380470075
+IDH3G	-0,380458518
+POLR2C	-0,380378788
+CTNNA2	-0,380377628
+XRCC6	-0,380295972
+EIF3A	-0,380281294
+CRBN	-0,380214781
+RPS6KC1	-0,3801397
+NUDT2	-0,380057201
+GOLPH3L	-0,379823471
+CSNK1A1	-0,379812095
+NDUFB2	-0,379757693
+FTO	-0,37940886
+SLC6A15	-0,379271656
+PCP4	-0,379256762
+NIT1	-0,37912136
+CCNC	-0,378699092
+DGKB	-0,378485235
+RANBP6	-0,377965444
+DNAJC8	-0,377764456
+MAPRE2	-0,377675379
+ARFGAP2	-0,377574006
+BDNF	-0,377511436
+HSD17B10	-0,376728332
+AKAP7	-0,376531212
+EHD1	-0,376479944
+PSMD10	-0,376243528
+FABP5L2	-0,376090187
+VAMP7	-0,376017526
+WBP4	-0,375749974
+MAP1B	-0,375485017
+SMPDL3A	-0,375390185
+GPR89C	-0,375362209
+SEPT2	-0,37512019
+GPX3	-0,374915078
+AARSD1	-0,374664572
+HSPA9	-0,37466397
+MAP1A	-0,374598439
+C16orf62	-0,374459363
+CARKD	-0,374388504
+ASS1	-0,374197776
+WDR12	-0,374046313
+ABHD14A	-0,37397421
+SPIN2B	-0,373568971
+RAB6A	-0,373528481
+PTPRF	-0,373483075
+RRAGB	-0,373427062
+STK39	-0,373365187
+COX7B	-0,373307822
+PDCL	-0,373110957
+ATP2A2	-0,373066228
+PPM1E	-0,37285382
+TRMT61B	-0,372798595
+C21orf33	-0,372766056
+MGMT	-0,372730061
+LPHN3	-0,372647138
+WBP2	-0,372385809
+ACSBG1	-0,372296169
+PGRMC2	-0,372287654
+LRRC20	-0,372239514
+AGA	-0,372171162
+NRCAM	-0,372117405
+FUT9	-0,372053568
+C22orf28	-0,371916518
+MRPS15	-0,371914782
+UFM1	-0,371876489
+CAMK2G	-0,371790847
+AVPI1	-0,371692415
+MAST2	-0,371637676
+PPP1R7	-0,371553142
+EEF1A2	-0,371514176
+ATP5D	-0,371416456
+EEF1E1	-0,37139203
+NLRP1	-0,371368381
+PMS2CL	-0,371209965
+CDK5R1	-0,371120209
+C2orf72	-0,371108998
+OAZ2	-0,3710748
+AL109698	-0,37073584
+INPP4A	-0,370700597
+ERH	-0,370513944
+CAMK1G	-0,370474818
+MED24	-0,370430566
+DMXL1	-0,370287216
+COMMD4	-0,370258812
+NOMO3	-0,370043447
+MORF4	-0,369691968
+ZNHIT3	-0,369651044
+GDPD5	-0,369635923
+CUL5	-0,369519961
+AP1B1	-0,369511443
+YARS	-0,369387873
+ABHD10	-0,36913324
+KCNB1	-0,369083149
+SKP1	-0,369015624
+FBXO28	-0,368924883
+ATR	-0,368436696
+TMED2	-0,368132686
+ARPC1A	-0,367983188
+PHYH	-0,367958422
+MRPL22	-0,367879083
+SRRD	-0,367868238
+WDYHV1	-0,367821841
+EIF3CL	-0,367732775
+HMGB3	-0,367450086
+DENND1B	-0,36732795
+ALDH5A1	-0,367318431
+CCNA1	-0,367103911
+FAM134A	-0,367014983
+DZIP1	-0,366778091
+WASF1	-0,366602553
+ATXN3	-0,366426778
+CCDC25	-0,3658102
+ERP29	-0,365799413
+IVD	-0,365499555
+SNX24	-0,365222253
+CDK20	-0,365176415
+TTC9	-0,365148586
+RBM8A	-0,36488846
+AMACR	-0,364562114
+TBPL1	-0,364450426
+PTPMT1	-0,364434415
+CANX	-0,364232908
+ELAC2	-0,364131757
+EIF2S1	-0,364109368
+AKR1B1	-0,363915593
+ACADM	-0,363858719
+RGS16	-0,363795844
+SLC20A1	-0,363602798
+MTUS2	-0,363384151
+ZMIZ2	-0,363364816
+NDUFS4	-0,363146027
+AW242701	-0,363104323
+SNAPC3	-0,363053639
+ENOPH1	-0,362868334
+LYRM1	-0,362706602
+TRMT12	-0,362561085
+BAALC	-0,362539013
+CHMP1B	-0,362404908
+ATP1A3	-0,362300724
+TOMM20	-0,362192747
+PEX14	-0,362047536
+EIF2AK1	-0,361934247
+CNNM2	-0,361790716
+PPOX	-0,361753445
+TAC1	-0,361655557
+GLRX3	-0,361266708
+OBFC1	-0,360197329
+MFN2	-0,360036589
+DGCR14	-0,359808857
+FAM175B	-0,359691136
+PARP2	-0,359639462
+GPR107	-0,359495249
+TUBGCP5	-0,35920098
+ENSA	-0,359186957
+UMPS	-0,358973056
+SSBP1	-0,358916914
+PFDN2	-0,358707301
+IFFO1	-0,35859667
+CCT2	-0,358497035
+PSMA5	-0,358414139
+ZC3H15	-0,358397302
+EPHX2	-0,358269729
+CALB1	-0,358259257
+POP7	-0,358253841
+MRPL12	-0,357874032
+DFNA5	-0,357815106
+PIAS1	-0,357740062
+ARL4C	-0,35770713
+HRAS	-0,357592893
+CEP68	-0,35754909
+SNRPA1	-0,357535253
+SCP2	-0,357518758
+C4orf27	-0,356816465
+TMEM185B	-0,35662055
+SPAG16	-0,356585241
+ESYT1	-0,356493695
+PTP4A1	-0,356347412
+PDLIM2	-0,356333479
+MSRA	-0,355999453
+UAP1	-0,355870622
+CDK16	-0,355785531
+MBOAT7	-0,355761708
+FARSA	-0,355610517
+MRPS7	-0,355424517
+EPHB2	-0,355389176
+LOC729991-MEF2B	-0,355378273
+PDHA1	-0,355252318
+ACTL6B	-0,355166654
+SAR1A	-0,355144478
+KDM1A	-0,355067715
+PRDX3	-0,354963773
+ETF1	-0,354759299
+ARMCX2	-0,354758912
+IQSEC1	-0,35395949
+TIMM13	-0,353925241
+AP2B1	-0,353904118
+STYK1	-0,353863363
+CDK7	-0,353806664
+DLG3	-0,353783905
+SEPHS2	-0,353722454
+MTOR	-0,353463273
+PPIH	-0,353351383
+GRPEL1	-0,353254529
+C9orf91	-0,353075824
+RGS17	-0,353023569
+NTSR1	-0,352789658
+HNRNPH2	-0,352751195
+HCCS	-0,3526918
+C2orf3	-0,352661516
+TFDP2	-0,352647453
+GOSR2	-0,352396188
+PSMB1	-0,352279045
+MPI	-0,35224609
+DUSP26	-0,351953212
+HERC1	-0,351631367
+SORD	-0,351295095
+TUBB2B	-0,351140866
+LPCAT4	-0,351128323
+CFL1	-0,351124653
+ARPP19	-0,350935095
+MTMR4	-0,350923479
+COX7A2	-0,350878835
+PGM1	-0,350865278
+RHOQ	-0,350802567
+CCDC53	-0,350756677
+UQCRB	-0,350742301
+NAPA	-0,350657124
+CSDC2	-0,35061274
+BECN1	-0,350596093
+GYG2	-0,350535323
+GPKOW	-0,35045328
+FXYD7	-0,350387292
+CYLD	-0,349973469
+CSPG5	-0,349825086
+TTC15	-0,349816074
+ILF2	-0,349761198
+STOML2	-0,349586681
+CACNB2	-0,349516102
+VARS	-0,349372141
+ZSCAN18	-0,349241937
+PTRH2	-0,349224021
+P2RX5	-0,349175679
+RALB	-0,349042784
+NUBPL	-0,348899542
+NCBP2	-0,348786336
+DKFZp434H1419	-0,348772873
+UFSP2	-0,348370783
+ARHGEF17	-0,348050229
+FXR2	-0,34801331
+INSIG2	-0,347755165
+XRCC5	-0,347746659
+CLTCL1	-0,34759935
+TMEM177	-0,347585446
+VAMP2	-0,347189398
+EML2	-0,347084746
+SNUPN	-0,346850632
+GPX4	-0,346688538
+RASA1	-0,346685342
+USP46	-0,346590476
+LSM5	-0,346546029
+SEC31A	-0,34652486
+PALM2-AKAP2	-0,346447335
+CKAP2	-0,346385113
+ELOVL5	-0,346375127
+PMS2L3	-0,346133275
+PAQR3	-0,346117871
+ST8SIA3	-0,34604187
+FDX1	-0,34603415
+C12orf4	-0,345989709
+COQ7	-0,345988262
+UROD	-0,345987158
+RPE65	-0,345902642
+DCK	-0,345889475
+RARS	-0,345819092
+CAPZA1	-0,345775372
+NRN1	-0,345693574
+RNF7	-0,345545425
+ABAT	-0,345474072
+CRY2	-0,345467057
+HR	-0,345290796
+CACNA2D3	-0,345213407
+TWIST1	-0,345148814
+P4HTM	-0,345112277
+GDI1	-0,344731063
+GRIA3	-0,344721718
+D4S234E	-0,344715573
+TMEM151B	-0,344385728
+MPHOSPH6	-0,344298044
+PYGB	-0,344201683
+MARCH6	-0,344086188
+AL050136	-0,343680587
+NDUFS6	-0,343667551
+TRAPPC9	-0,343555476
+PYGL	-0,343533875
+EFNB3	-0,343417492
+SCD	-0,343398039
+TFG	-0,342863204
+PPFIA3	-0,342761025
+SENP6	-0,342750174
+KCMF1	-0,342689973
+GNAS	-0,342684217
+MAPK6	-0,342588157
+PRMT5	-0,34246621
+SEPT11	-0,342460355
+MEIS3P1	-0,342265108
+FABP3	-0,3421554
+YIPF6	-0,3420929
+FABP6	-0,342074193
+SRSF9	-0,341825092
+AP1AR	-0,341737984
+PKNOX2	-0,341609179
+PAK6	-0,341535575
+PRKAA1	-0,341378959
+UBA3	-0,34130955
+OAZ1	-0,341251276
+EID1	-0,340941987
+MRPS28	-0,340842312
+AA890010	-0,340724739
+OSBP	-0,340497775
+ATP6V0C	-0,34047911
+ARHGAP24	-0,340414643
+PNKP	-0,340118439
+PSMD7	-0,340085658
+IPO9	-0,340071575
+ARF4	-0,339993296
+TERF2	-0,339818219
+SRSF2	-0,339525933
+PSMC5	-0,33950993
+TM9SF1	-0,339389717
+ACAT2	-0,339093022
+CDK8	-0,33909169
+KIAA0196	-0,338987444
+TFPT	-0,338941882
+TRPC4AP	-0,338718194
+TUBG1	-0,338211067
+SCN2B	-0,338080627
+MTHFD1	-0,338071854
+ATPAF2	-0,338050158
+IGSF1	-0,337997383
+RGPD6	-0,337877048
+C16orf45	-0,33773508
+C10orf76	-0,337659307
+UBE2A	-0,33762595
+PQLC1	-0,337612976
+SOD1	-0,337454918
+ARPC2	-0,337418781
+MEMO1	-0,33728488
+CSDE1	-0,337036578
+PHYHIP	-0,336992273
+LYPLA1	-0,33698776
+NDUFA1	-0,336883322
+MARCKSL1	-0,336747008
+DCTN1	-0,336745427
+COX6A1	-0,336728807
+DPM1	-0,336614034
+ELP3	-0,336602956
+LOC653566	-0,336555692
+COX7BP1	-0,336528019
+CAPZB	-0,336348777
+DCUN1D4	-0,335942405
+UCHL5	-0,335933871
+PSIP1	-0,335684272
+MRS2	-0,335589123
+RABGAP1	-0,335570544
+KCNA6	-0,335454989
+RAC1	-0,335429141
+ZMYM2	-0,33542626
+MRPL17	-0,335371398
+MLF1	-0,335274724
+RFC3	-0,33507418
+ARMCX3	-0,335005795
+GMDS	-0,334931775
+KIAA0317	-0,334922749
+CAMSAP1	-0,334678333
+LSG1	-0,334628714
+PNPO	-0,334625052
+THOC5	-0,334532053
+C11orf58	-0,334154436
+MTCH1	-0,334038037
+KAL1	-0,333848755
+OMG	-0,333590731
+KLHL7	-0,333537148
+TTPAL	-0,333489991
+GLA	-0,333336937
+SEZ6L2	-0,333262252
+SNURF	-0,333035272
+ARL6IP1	-0,332988884
+BFSP1	-0,332976059
+MAPKSP1	-0,332894473
+HABP4	-0,332672498
+SLC8A2	-0,332645114
+CKAP4	-0,332543738
+NPM1	-0,332250102
+CLSTN3	-0,332157745
+RUSC2	-0,33210981
+RCHY1	-0,331805148
+CACNA1D	-0,331681156
+ZFAND5	-0,331302172
+TACC2	-0,331046487
+CHCHD3	-0,331008486
+RGS2	-0,330792786
+LDOC1	-0,330775706
+BTN2A1	-0,33075204
+WDR45	-0,330593865
+W87688	-0,330499179
+YWHAQ	-0,330473094
+RAB3GAP2	-0,33029144
+HTRA2	-0,330240669
+SNRPD1	-0,330240562
+ANXA7	-0,330030639
+KIAA1024	-0,329770804
+RAD51C	-0,329735785
+PRPF18	-0,329474331
+CCT6B	-0,329361737
+ABCD3	-0,329205796
+PARN	-0,329139621
+APOL2	-0,328983174
+MRPS18A	-0,32863432
+RASL10A	-0,328581006
+COG8	-0,328398026
+ZNF512B	-0,327877848
+ATP5H	-0,327758416
+PRDM4	-0,327710757
+TSPAN3	-0,327644045
+EPB41L3	-0,327416874
+APLNR	-0,327394979
+TFR2	-0,327337619
+GADD45A	-0,327012981
+POLR3F	-0,326871651
+FASTKD3	-0,326789822
+TCERG1	-0,326746174
+VPS41	-0,326459968
+C17orf101	-0,325979143
+EXOC3	-0,325763291
+SLC25A17	-0,325666279
+GDAP1L1	-0,325526797
+HCFC1R1	-0,325022815
+SF3B5	-0,324878766
+TEX10	-0,324812522
+PSMA7	-0,324673715
+TCTN3	-0,324389244
+NOVA1	-0,32437578
+RABEPK	-0,324366299
+ALG5	-0,324335095
+ENOSF1	-0,32427768
+SH3BGRL3	-0,32409913
+CTNND2	-0,324002004
+NKRF	-0,323983769
+SLC6A1	-0,323833407
+MAPK1IP1L	-0,323722226
+RAB22A	-0,323713658
+GRP	-0,323354345
+SDS	-0,323335387
+IBTK	-0,323304602
+CARS	-0,322679359
+WWP1	-0,322463311
+ARL8B	-0,322442301
+SLC19A2	-0,322361872
+F8A3	-0,322202521
+LPHN1	-0,322183082
+SMARCD3	-0,322148361
+GPN1	-0,322024809
+FAF2	-0,322014431
+SLC35B1	-0,321878066
+MPV17	-0,321698226
+TOM1	-0,321634922
+NEDD4L	-0,321518057
+MRFAP1L1	-0,321393672
+C6orf62	-0,321303598
+POLR3B	-0,321247444
+HTR2A	-0,321189596
+CUL3	-0,321141566
+PSMD9	-0,321108014
+LRP3	-0,32099653
+TMEM62	-0,320873847
+PLS3	-0,320803014
+SUMO1	-0,32076762
+DLG4	-0,320617015
+ANKRD17	-0,320557554
+ARFIP2	-0,320500236
+HMGN4	-0,320196335
+PRKAG2	-0,319945607
+STAR	-0,319749743
+NF1	-0,319726773
+ATOX1	-0,31967306
+UBE2M	-0,319629201
+NDRG3	-0,319446308
+SNPH	-0,319396594
+TPD52	-0,319178712
+PLK2	-0,319120325
+C1QBP	-0,318975829
+SRSF8	-0,318843616
+USP22	-0,318806098
+GPD1	-0,318728943
+MAPK8IP2	-0,318691894
+USP20	-0,318610382
+RPA2	-0,31845096
+CCPG1	-0,318358561
+NQO2	-0,318256129
+POLR3C	-0,318231923
+HBXIP	-0,318079181
+MRPS31	-0,318018334
+SNRPB2	-0,31801084
+CACNG3	-0,317104885
+CCNE1	-0,316783937
+NDUFAF4	-0,316755785
+GRK6	-0,316405946
+ZER1	-0,316363024
+CHCHD7	-0,316179658
+C20orf29	-0,315860291
+AI693193	-0,315746456
+TPMT	-0,315745725
+TPPP3	-0,315557058
+CTH	-0,315210231
+HSDL2	-0,31516145
+MAPRE3	-0,314964867
+NLE1	-0,314918022
+ARHGEF4	-0,314777145
+STK19	-0,314737564
+AW503390	-0,314280211
+KIAA1279	-0,314104435
+CA14	-0,313849822
+CYP2E1	-0,313441486
+FHL1	-0,313417456
+MYL6B	-0,313075964
+PACRG	-0,3129322
+SCN2A	-0,312912414
+POLR3G	-0,312898745
+MED6	-0,312862133
+PCSK1N	-0,312861133
+FLJ10038	-0,312756044
+PHTF1	-0,312716368
+PRPF4	-0,312654478
+RPRD1A	-0,312642779
+HLF	-0,312545473
+MTMR1	-0,312535102
+MFN1	-0,312461722
+C1orf50	-0,312398425
+QPRT	-0,312349796
+ZDHHC6	-0,31229266
+ITGAE	-0,311863717
+SLC18A1	-0,311739998
+CD83	-0,311711539
+GGCT	-0,311631664
+KIAA0100	-0,311503156
+OPN3	-0,311374884
+SSX2IP	-0,311111099
+NUCB2	-0,31105706
+UTP11L	-0,311015852
+GOLGA8B	-0,310924837
+UST	-0,310734373
+PRKCI	-0,310493775
+AP2S1	-0,310480065
+WBSCR22	-0,310476192
+PPP3CA	-0,310434457
+PDSS2	-0,310396648
+PEG3	-0,310335546
+ATP5E	-0,310319916
+GABRA5	-0,310200087
+AGPAT4	-0,310173061
+PDCD10	-0,310157516
+DDOST	-0,310094837
+RPL23	-0,309992315
+HOMER1	-0,309485866
+C1orf123	-0,309187816
+POLE3	-0,309012195
+DDX41	-0,308923345
+HSD17B8	-0,308824584
+GMPR2	-0,308792858
+SCARB2	-0,308695909
+DGUOK	-0,308606021
+MAGEF1	-0,308535371
+FOXA2	-0,308348483
+GLS2	-0,308287643
+TBCC	-0,308286536
+FBXO41	-0,308255485
+SLC12A1	-0,308214984
+PELO	-0,308137793
+KCNE1L	-0,30811412
+RBBP4	-0,308007454
+UBL5	-0,307720013
+KLHL12	-0,307571676
+FTSJ1	-0,307464516
+ZFYVE16	-0,307366442
+PPT1	-0,3073579
+ZC3H13	-0,307293327
+DYRK1A	-0,307183877
+PHACTR2	-0,306935621
+SLITRK3	-0,306872073
+PI4KA	-0,306770561
+RNPS1	-0,306364972
+RALGAPB	-0,306086767
+BRP44	-0,305953308
+BNIP1	-0,305883874
+SUPT4H1	-0,305675152
+BCKDK	-0,30566687
+PLAA	-0,305619464
+ACTR2	-0,305363631
+PION	-0,305054773
+NFU1	-0,305010295
+CCT6A	-0,304801168
+KIAA0427	-0,304585348
+EHD3	-0,304533089
+FAM63B	-0,304437794
+STK25	-0,304425083
+POLB	-0,304419007
+MRPL35	-0,304416576
+UBE2Z	-0,3043165
+GSTZ1	-0,304133065
+AP3S1	-0,30395899
+SPATS2L	-0,303776395
+LOC729580	-0,303766036
+RALGAPA1	-0,303697943
+PUF60	-0,303647762
+DAP3	-0,303640732
+AHI1	-0,303570806
+UBE2NL	-0,303361552
+TMEM164	-0,303165514
+DOCK3	-0,303099341
+CADM3	-0,303050893
+ZNF219	-0,302968533
+PRKAR1B	-0,302898104
+DOK5	-0,302798088
+ORMDL2	-0,302372011
+ACVR2A	-0,302331205
+ALDOA	-0,30171568
+ATRN	-0,301666345
+COX7C	-0,301597748
+PRKDC	-0,301229867
+GNG10	-0,300757182
+SNX17	-0,300752701
+RBMS1	-0,300466996
+AJAP1	-0,300458474
+PREP	-0,300414848
+ALDOC	-0,300361514
+LAMA4	-0,300246196
+PI4KAP1	-0,300223018
+TMEM222	-0,30010369
+PIGB	-0,299980372
+SSSCA1	-0,29997354
+DCUN1D1	-0,299517655
+DLSTP1	-0,299414392
+ITM2B	-0,299325985
+AK025651	-0,299260618
+ACOT13	-0,299073057
+ZNF593	-0,298588283
+LOC100129250	-0,298385026
+H2AFY	-0,298292243
+IGF1	-0,298232454
+KIAA0368	-0,29819687
+FKBP3	-0,298122528
+C12orf49	-0,297820161
+PRKRIR	-0,297808472
+GLUD2	-0,297805688
+NBL1	-0,297799978
+PTPN4	-0,297657679
+LOC644617	-0,297586698
+IL33	-0,297538719
+CUL4A	-0,29730361
+SIP1	-0,297199387
+POLDIP2	-0,297140479
+EBP	-0,297109427
+FASTKD2	-0,296665172
+SMPD1	-0,296658212
+FAM55C	-0,296650198
+TRPV2	-0,296465177
+DOPEY1	-0,29633822
+SCYL3	-0,296201386
+UBL3	-0,296188632
+STK38L	-0,296164266
+APITD1	-0,296017845
+SFXN1	-0,295918484
+CPT1A	-0,295754312
+USP8	-0,29570338
+MRPS30	-0,295702739
+ATG7	-0,295335659
+C10orf88	-0,29514056
+PIPOX	-0,295018193
+RAC3	-0,294600261
+CIAO1	-0,294564961
+KLC2	-0,294523931
+LEPROTL1	-0,29448316
+ENDOD1	-0,294147277
+FEM1B	-0,294007766
+IRS1	-0,293342341
+CYP51A1	-0,293155923
+DYNLRB1	-0,292974645
+TOM1L2	-0,292906836
+TDP2	-0,292808809
+MRPL49	-0,292778686
+LRP8	-0,292767989
+MOSPD1	-0,292730297
+C6orf134	-0,29255632
+TRPC1	-0,29249815
+RASL11B	-0,292459191
+AL109671	-0,292334441
+TTC37	-0,292136499
+ODZ4	-0,292070818
+KIN	-0,291741417
+KPNA1	-0,291721639
+CAST	-0,291558763
+NDUFA13	-0,291524477
+AKR1A1	-0,29149158
+QARS	-0,29146477
+MRPS22	-0,29145846
+MMACHC	-0,291414294
+UBQLN2	-0,291358191
+PIK3CB	-0,291242041
+COX6B1	-0,291081182
+PDK2	-0,290962723
+RABGGTB	-0,290962562
+SR140	-0,290943983
+ATF2	-0,290881352
+FADS1	-0,290820194
+SRP14	-0,290691218
+RAD23B	-0,290632171
+AHCY	-0,290521401
+RINT1	-0,290502144
+SRP54	-0,290224786
+COX5B	-0,289972152
+NBN	-0,289962803
+DDX50	-0,289845246
+NUFIP1	-0,289611609
+HDGFRP3	-0,289540354
+HBA2	-0,289412602
+SRP9L1	-0,289377441
+ARFGEF1	-0,289327503
+FAM13B	-0,289118442
+DIMT1L	-0,288943725
+LPO	-0,28888192
+VPS28	-0,288730564
+SSR3	-0,28867602
+SEPT7	-0,288663677
+NARS2	-0,288651232
+EMG1	-0,288493971
+HSPA8	-0,288488899
+TBC1D13	-0,288209587
+TTC35	-0,288076299
+GTPBP4	-0,287916733
+SPG7	-0,287774853
+PAFAH1B3	-0,28772138
+MAPT	-0,28765216
+RERGL	-0,287509361
+HNRNPD	-0,287438947
+PLCL2	-0,287391702
+HLA-DPA1	-0,287200849
+CD55	-0,286966384
+IDH3A	-0,286870398
+STXBP5L	-0,286801199
+MAP3K12	-0,286334641
+PPP2R1A	-0,286259611
+TMEM126B	-0,286136364
+CDKN3	-0,286064506
+ABCC5	-0,286013319
+TMEM127	-0,285913561
+DNAJC2	-0,285585137
+SEC61G	-0,285583827
+SSR1	-0,285489405
+AIMP1	-0,285281231
+YTHDF2	-0,285194578
+FAM86B1	-0,285046154
+CTBP1	-0,285027477
+CHRFAM7A	-0,285001423
+SSBP3	-0,284934817
+MRPL46	-0,284930449
+TSPAN6	-0,284861931
+MYST2	-0,284824247
+GGH	-0,284817124
+PRKACB	-0,2847024
+C2orf47	-0,284692381
+NLK	-0,284579832
+ASNS	-0,28445955
+EXOC5	-0,28439526
+OAZ3	-0,284379411
+CTNNBIP1	-0,284364924
+PVR	-0,284070802
+C16orf80	-0,284019987
+UBE3A	-0,283816198
+EAPP	-0,28376748
+IGSF3	-0,283764031
+KCND2	-0,283569047
+FOXK2	-0,283286684
+SLC35A2	-0,283204451
+TBCB	-0,283168385
+SLC38A1	-0,283158141
+ACCN2	-0,283147998
+FAM149A	-0,283126904
+TIMM22	-0,283102824
+EIF4ENIF1	-0,28310048
+THSD1P1	-0,282819454
+MAGED4	-0,282562753
+CLASP1	-0,282510547
+C1orf61	-0,282424601
+C6orf106	-0,282397365
+WDR44	-0,282155933
+GNL3	-0,282115302
+RCBTB1	-0,28192202
+OSTM1	-0,281535242
+AGPAT5	-0,281510168
+PRNP	-0,281405094
+APPBP2	-0,281330465
+GAD1	-0,281295305
+NECAB3	-0,281056363
+ABCF1	-0,280961256
+DNAJC7	-0,280750506
+EPHB1	-0,280596899
+GPRC5A	-0,280368026
+HSPA14	-0,280049432
+CLPTM1	-0,280042656
+SGPP1	-0,27999737
+ABCG4	-0,279891909
+GFRA1	-0,279146972
+ATP5SL	-0,278849245
+CTSO	-0,278677227
+DCTN4	-0,278556645
+MAP2K2	-0,278535478
+ZNF423	-0,278503712
+FUS	-0,278285124
+ACTR8	-0,278282163
+PRR13	-0,278189761
+ZNF329	-0,278179162
+RNASEH2B	-0,278151755
+LOC284244	-0,278099761
+FAM117A	-0,277715513
+MREG	-0,277651168
+C2orf18	-0,277609469
+AW612311	-0,277599115
+SYNRG	-0,277434047
+SMARCE1	-0,277346186
+DNAJA3	-0,277188103
+PPP2R5E	-0,2770317
+TMCO6	-0,276951805
+C6orf35	-0,276886272
+DDX18	-0,276619655
+TTLL1	-0,276373935
+LANCL1	-0,276361838
+SNRPE	-0,276287655
+DTX4	-0,276233703
+IDH2	-0,276017451
+SACS	-0,275814599
+ABHD2	-0,275491786
+VAMP1	-0,275092752
+AGPAT1	-0,27504004
+TYMS	-0,274913065
+ZDHHC3	-0,27479568
+LMO1	-0,274566957
+UVRAG	-0,274559415
+HBB	-0,274385467
+PSMA2	-0,274273938
+CD24	-0,27422103
+GRAMD1B	-0,27394685
+PRC1	-0,27393137
+YARS2	-0,27376193
+SIGMAR1	-0,273597834
+CPEB3	-0,273534888
+ARMC9	-0,273442678
+DNAJC10	-0,273369377
+TM9SF4	-0,27326642
+RBX1	-0,273166064
+C13orf1	-0,273151402
+PDCD4	-0,273130523
+LUZP2	-0,272843047
+APLP2	-0,272609838
+USO1	-0,272598741
+SH3BP5	-0,272512602
+PPP1R11	-0,272494252
+PEMT	-0,272485616
+CDC16	-0,272287144
+LCMT2	-0,272235596
+DCX	-0,271983078
+DDAH1	-0,271924121
+UBE2D2	-0,271815552
+TANK	-0,271664689
+AW974666	-0,271662837
+USH1C	-0,271630244
+BDH1	-0,271624449
+B9D1	-0,271589518
+BRD9	-0,271105209
+USP7	-0,271052865
+TRIM2	-0,270764995
+PARK7	-0,270634786
+NSFL1C	-0,270597248
+COQ2	-0,269953826
+HNRPDL	-0,269787459
+NOV	-0,269731303
+SLC25A28	-0,269706278
+EXT2	-0,26958066
+VLDLR	-0,269148459
+SLC4A4	-0,268895862
+SMURF1	-0,268798637
+ORC2L	-0,268275919
+ZC4H2	-0,268056536
+SDHAF1	-0,267985583
+VDAC1	-0,267895013
+ALDH1A3	-0,267738476
+PNPLA4	-0,267586498
+HAGH	-0,267406111
+CNTNAP2	-0,267355858
+KPNA3	-0,267278305
+LRBA	-0,267216793
+DPYSL4	-0,267150239
+MCCC2	-0,26714725
+KBTBD4	-0,267031071
+DCTD	-0,267005887
+C1orf21	-0,266982234
+C2orf43	-0,26679916
+SF3A3	-0,266732334
+PTPN3	-0,266674559
+FBXO21	-0,26664933
+CCT7	-0,266615147
+CLNS1A	-0,266539743
+HAPLN1	-0,266160364
+SYT13	-0,26591944
+SENP5	-0,265695364
+HMGB2	-0,265556554
+CANT1	-0,265168032
+CGREF1	-0,265157579
+GRM1	-0,26510368
+ZFHX4	-0,265049797
+PVRL3	-0,264999073
+ADAR	-0,264636454
+TRIM3	-0,264561355
+ANP32E	-0,264413865
+PDLIM7	-0,264406742
+MLH1	-0,264377914
+PRKCA	-0,264376056
+CYB5R3	-0,264120933
+PDE1A	-0,263919942
+LOC100127998	-0,263915362
+WSB2	-0,263691169
+RPF1	-0,263404659
+CXCL12	-0,26333499
+TMEM66	-0,263285506
+EIF6	-0,263232223
+NFE2L1	-0,262789646
+KLHL20	-0,262772392
+PPM1H	-0,262689193
+PIN4	-0,262483899
+TUBA4B	-0,26241982
+ECT2	-0,262276809
+MGC5566	-0,261888759
+C9orf116	-0,261830489
+ASB1	-0,261751394
+ABCC8	-0,261735107
+ELOVL2	-0,261638578
+PHB2	-0,261466477
+ZNF580	-0,261379751
+DNAJC24	-0,261364702
+PSMB10	-0,261344946
+CSE1L	-0,261292597
+ANKRD27	-0,261154598
+TUBG2	-0,261047779
+C6orf162	-0,261001828
+AL034399	-0,260886813
+GLT8D1	-0,26052144
+SRR	-0,260520305
+MCC	-0,260395686
+COX4I1	-0,260324715
+SEP15	-0,260222524
+RNF103	-0,260210477
+ZNF576	-0,260159221
+MGEA5	-0,260092677
+RSL24D1	-0,259958151
+USP13	-0,25969613
+MLLT3	-0,259631882
+SRI	-0,259268888
+NCS1	-0,259133737
+MAPKAPK5	-0,259103348
+IQCG	-0,25908825
+FN3KRP	-0,258914892
+BCKDHB	-0,258870249
+GOLGA5	-0,258736414
+RDBP	-0,258483881
+SUPT7L	-0,258355414
+METTL1	-0,258206012
+CREB3	-0,258159408
+TMEM111	-0,258136123
+NRSN2	-0,257397396
+CNTN1	-0,257314074
+COX10	-0,257277055
+SERPINB9	-0,257269621
+MTF2	-0,256976969
+EDNRB	-0,25676028
+HSF2	-0,25652969
+POLR2L	-0,256424652
+TRIM58	-0,256294322
+DACH1	-0,256241463
+UEVLD	-0,256239024
+ATP1B3	-0,256215499
+SAP130	-0,256053262
+TRPC6	-0,255890704
+HERC6	-0,255794959
+NAV3	-0,255707496
+GOSR1	-0,25567987
+CNR1	-0,255506006
+PSME4	-0,25522233
+CAMKV	-0,254605479
+ADSL	-0,254512794
+BCS1L	-0,254298738
+CCNB1	-0,253924801
+SNX2	-0,253887319
+ASAP2	-0,25387509
+WDR70	-0,253565737
+PTPRE	-0,253309549
+SEPT5	-0,253058348
+SCML1	-0,253051964
+BCR	-0,252946659
+MAGOH	-0,252829021
+SEMA4F	-0,25277628
+CLIP1	-0,252764211
+JMJD4	-0,252747043
+ZMYND11	-0,25273006
+CPSF6	-0,252574141
+PTPRA	-0,252430519
+PLA2G12A	-0,252393049
+MXRA5	-0,252290125
+RFX5	-0,252264534
+WARS	-0,252174212
+HUS1	-0,252166663
+VCAM1	-0,251733145
+CEACAM21	-0,25171453
+RHOT1	-0,251514974
+EMD	-0,251327933
+TSPYL2	-0,251307071
+THNSL1	-0,25130438
+NDUFB4	-0,251250318
+CHMP5	-0,251232028
+SKAP2	-0,251185084
+LRPAP1	-0,251070101
+COMMD3	-0,251069448
+ROGDI	-0,250917557
+PPAP2B	-0,25089017
+ADSS	-0,250852878
+LGI2	-0,250809779
+CBX6	-0,250671998
+NELF	-0,250584567
+DENND5B	-0,250357567
+ATP2C1	-0,239139672
+SUMO2	-0,233193565
+KRAS	-0,208565613
+PEX3	-0,200767265
+PRDX2	-0,195371323
+PDCD2	-0,194653063
+TM2D1	-0,189207426
+KHDRBS1	-0,16653347
+KLC1	-0,156510024
+ANK2	-0,155852142
+HBS1L	-0,155006259
+NTRK3	-0,121314135
+PTPRO	-0,110200451
+PLEKHA5	-0,10184855
+GCOM1	-0,091608137
+TIMM8A	-0,084179504
+MKRN1	-0,074942655
+PLA2G4B	-0,068760926
+RUFY3	-0,059042335
+RIMS2	-0,057507607
+C21orf2	-0,054091983
+METAP2	-0,053236401
+LRRC40	-0,040678287
+RPL10	-0,034862755
+RIOK3	-0,033313025
+SYNCRIP	-0,027340658
+UNC45A	-0,021866459
+MPZL1	-0,020796077
+RANBP1	-0,01610173
+ITGB1BP1	-0,011025016
+UBC	-0,009666523
+RER1	-0,007044099
+PDS5B	-0,005231512
+NCAM1	-0,004638056
+LIMCH1	0,003894784
+VPS13D	0,014841215
+WDFY3	0,017457694
+MRP63	0,023151675
+TSR1	0,064261585
+GRB10	0,066410415
+FAM128B	0,074972161
+PAK2	0,079518764
+PKP4	0,080237181
+TMEM144	0,083124821
+C3orf63	0,086752023
+DDAH2	0,250378216
+AF238870	0,250544885
+PTMS	0,250667518
+JAG1	0,250675664
+RPL32	0,25075902
+UXT	0,250812127
+HSP90B1	0,250888984
+SS18	0,250904748
+RND2	0,250918958
+CLEC4M	0,250931594
+AU147194	0,251115897
+IL1RAPL1	0,251119435
+EPB41L2	0,251131328
+TFDP3	0,251241244
+GAL3ST4	0,251281983
+EDN2	0,251371356
+SFTPC	0,251372616
+TRMT61A	0,251534845
+GPR4	0,251535902
+KEAP1	0,251692277
+RNF122	0,251718243
+NOTCH2	0,251745042
+WDR1	0,251871256
+NFX1	0,252023298
+DOHH	0,252100123
+NES	0,252167647
+SRSF10	0,252172984
+AQP3	0,252182392
+LOC728412	0,252404082
+RCN3	0,252455902
+CSNK1G1	0,252462493
+KCNS1	0,252601737
+CCDC71	0,252614101
+JUND	0,252645305
+LYST	0,252718314
+TPCN1	0,252770336
+MTA1	0,252823052
+RIN1	0,252841454
+ATHL1	0,252944239
+FTSJ3	0,253136044
+SERPINA1	0,253202139
+STARD7	0,2533744
+MRPL34	0,253425868
+PPID	0,25344089
+SH3PXD2A	0,253534644
+UBA7	0,253547625
+RUNX1	0,253686159
+ARNTL	0,253823553
+STAT6	0,253840779
+CASKIN2	0,25393147
+NFATC4	0,253965486
+LILRB2	0,254041373
+PPP1R13L	0,254173566
+RAP1A	0,254249533
+OTUD4	0,254380531
+ZNF516	0,254390037
+ZC3H14	0,254430628
+BTD	0,254441889
+ABHD4	0,254494909
+MT3	0,254554667
+PTCH1	0,254572046
+CDC42EP3	0,254591236
+LOC150776	0,254715807
+PTGES	0,254816225
+TPM2	0,254867646
+TAGLN	0,254960085
+AL050032	0,254984309
+HPN	0,25500915
+FLNC	0,255046574
+GJB3	0,255060346
+RAB40B	0,255071999
+CST1	0,255226531
+FGF21	0,255229382
+AW574933	0,255334628
+FGF5	0,255461872
+CLCN7	0,2555275
+BAHCC1	0,255618646
+FANCA	0,255627746
+CYBA	0,255682121
+TIE1	0,255683605
+ANKHD1-EIF4EBP3	0,255707685
+CDV3	0,255740411
+COL9A1	0,255878907
+TTC31	0,256049153
+ZIC1	0,256075896
+CCDC121	0,256090992
+FUT4	0,256155794
+UCP3	0,256197327
+AU146391	0,25625958
+MMP2	0,256269664
+STXBP2	0,256386629
+TMEM87A	0,2564575
+FXR1	0,256493521
+RDX	0,256507051
+HPS1	0,256516919
+TRAM2	0,256517872
+HYAL2	0,256778041
+TNFRSF14	0,256783849
+NEK7	0,256861333
+AGRN	0,256876471
+SMC4	0,256895131
+GAS7	0,256949822
+PDE4B	0,256950938
+CHD4	0,256970114
+SPP1	0,257084517
+HECA	0,257172806
+NXF2B	0,257181225
+LILRA5	0,257188463
+SCAP	0,257267679
+SNX1	0,257354288
+GIGYF2	0,257400552
+CELF1	0,257407908
+HSD17B14	0,257420303
+DUOX1	0,25770603
+MRM1	0,257826185
+NBR2	0,257852879
+FAM176B	0,257955278
+SYNPO	0,257997864
+GPRIN2	0,258040238
+IER3	0,25816919
+ZNF506	0,258198461
+NM_016414	0,25824817
+VPS53	0,258358594
+PGPEP1	0,258378109
+GNL1	0,25847832
+OGFR	0,258496938
+CXCR2	0,258632799
+C1orf38	0,258857462
+RPL22	0,258901214
+NM_018041	0,259005358
+MYOF	0,259133176
+NGB	0,259197495
+CLIC4	0,259260666
+TBC1D9B	0,259295717
+KCND1	0,259337213
+RNASET2	0,259420675
+EXT1	0,259568659
+AQR	0,259572114
+VWA1	0,259618684
+MUC3A	0,259647513
+CAV1	0,259682957
+IRF4	0,259719685
+OR7C1	0,259728956
+SETDB1	0,259737838
+E2F6	0,259867146
+TFEB	0,259924981
+CPSF3L	0,26005015
+MARCH8	0,260576922
+MFSD11	0,260945964
+ETAA1	0,260954881
+SMARCD2	0,260999203
+RGS12	0,261024661
+CCNG2	0,261112401
+RPS8	0,261183649
+IL17RA	0,261275371
+NUDC	0,261284708
+ZNF133	0,261329337
+ATP13A1	0,261543252
+PICK1	0,26166607
+C20orf117	0,261682534
+GIPR	0,261728602
+HIST2H4B	0,261730186
+S100A11P1	0,261732522
+MARCH3	0,26174629
+ZBED4	0,261794357
+KHK	0,261822851
+SCAMP2	0,26194666
+AF070579	0,261954742
+TECR	0,261998101
+AK024915	0,262016665
+CASP7	0,262240261
+PDK4	0,262293861
+MYO7A	0,262479993
+TUBBP5	0,262483574
+TMEM143	0,262491406
+NAP1L1	0,262524812
+PLEKHB1	0,262542861
+ING1	0,262679424
+SPSB3	0,262786186
+C9orf167	0,262955615
+NTM	0,262977412
+FIP1L1	0,263199662
+FYCO1	0,26321575
+GGT1	0,263227324
+ALG12	0,263240056
+IGL@	0,263282588
+PPBP	0,263290228
+SNX13	0,263292989
+SRSF4	0,263309909
+CYTH1	0,263721364
+AL050035	0,263831657
+TRMU	0,263920451
+TIMP1	0,263959235
+RFNG	0,263965598
+HIP1R	0,264033626
+NR1H3	0,264039538
+NT5C2	0,264091319
+FNTB	0,264115077
+SAR1B	0,264175117
+GIT1	0,26420824
+RRAGD	0,264311012
+HAP1	0,26435511
+FLT3LG	0,264378926
+NM_018612	0,264421364
+SLC7A9	0,26447762
+GLTSCR2	0,264541217
+SUN1	0,264635751
+CEP152	0,264663399
+MBTD1	0,264688291
+SYT12	0,264690461
+ACTR5	0,264835312
+EIF4A1	0,264933012
+COX7A1	0,26511391
+CMTM6	0,265385079
+FAM102A	0,265449454
+AW970584	0,265532869
+FMO5	0,265619005
+N4BP2L1	0,26587536
+SPAG11A	0,265939376
+TGFBI	0,265987004
+RYK	0,266131346
+SERBP1	0,266135884
+AK021988	0,266152576
+NCAM2	0,266199101
+AK024995	0,266233606
+RAB9A	0,266259326
+SYNJ2	0,266313048
+PHLDB1	0,266315252
+PKN1	0,266439146
+MFAP3L	0,266558078
+PPFIBP2	0,266640652
+WBP5	0,266861878
+TMX1	0,266949292
+SLC6A12	0,267009029
+C3AR1	0,267017849
+CSRP2	0,267020264
+SP3	0,267034674
+ATN1	0,267069634
+GNB3	0,267107148
+TIAL1	0,267113358
+GPATCH8	0,267177985
+PMEPA1	0,267182372
+MAP2K3	0,267199274
+NM_018033	0,267304029
+WWTR1	0,267350058
+SEMA6A	0,267400431
+RBPJ	0,267426168
+AL049279	0,267438916
+IL1RN	0,267473934
+QKI	0,267577841
+SOX15	0,267588393
+DMTF1	0,267672579
+RPL19	0,267821304
+TRIM39R	0,267839755
+SLC26A6	0,267879749
+NM_025056	0,267969441
+BBS9	0,267969882
+M85256	0,26799656
+ADORA3	0,268097905
+TMEM176B	0,268515164
+SECTM1	0,268600799
+ST14	0,268612452
+ARHGEF18	0,268652414
+SIRT5	0,268726991
+MYBPC1	0,268763379
+RPL15P22	0,268793196
+SIGLEC15	0,268860828
+DNAJA1	0,26890035
+LMBR1L	0,269042598
+GIMAP4	0,269074847
+MFAP3	0,269075993
+ABCA6	0,269120338
+AW836210	0,26919833
+LOC100133772	0,269228182
+CHST4	0,269387102
+RNASEH2A	0,269387986
+RPL18	0,269450865
+RPLP2	0,269486597
+MEPE	0,269489799
+FAM106A	0,269545639
+GATAD1	0,269621956
+PPP2R3A	0,269725552
+MASP2	0,269836416
+MYO10	0,26992164
+PIGG	0,269941407
+SMG5	0,269952017
+IFI30	0,269956381
+AK025180	0,269971157
+AMD1	0,269982316
+LMOD1	0,270125966
+SNX15	0,270191178
+SCARB1	0,270338985
+SERTAD3	0,270373355
+MBD5	0,270430073
+SLC2A5	0,270454389
+ITCH	0,270468949
+ADA	0,270490353
+PWP2	0,270541137
+ARHGEF1	0,270572389
+C2CD2	0,270675538
+EIF1	0,27071329
+C1orf35	0,270772513
+IFI16	0,270855012
+LOC285830	0,270905428
+IL10	0,271025993
+MORC4	0,2712707
+CA11	0,271346355
+C5orf54	0,271348162
+C14orf93	0,271428228
+RPL17P7	0,271481741
+TMEM161A	0,271564557
+LRCH3	0,271627825
+DFFB	0,271779652
+BAZ1B	0,271859723
+DKFZp547G183	0,271894591
+RAB11FIP2	0,271895928
+PCK1	0,27194659
+TMPRSS5	0,27195628
+TIPARP	0,272078235
+UBE2L3	0,272125747
+ZNF672	0,272142507
+GALNT10	0,272151507
+EXD2	0,272173543
+KAT2B	0,272322281
+RPS11	0,27237174
+POLR2H	0,272422791
+IGLL3	0,272574443
+AA554430	0,272578205
+DOCK10	0,272578712
+DMC1	0,272606886
+CD40	0,272762332
+CDK11A	0,272811711
+UCKL1	0,272898303
+FAM125B	0,273084179
+UBXN7	0,273084433
+SMA4	0,273204796
+DYNLT1	0,273349219
+CTTNBP2NL	0,273380758
+HSPH1	0,273396703
+CYP39A1	0,273418193
+HOMER3	0,273432217
+RRBP1	0,273480926
+ATAD2B	0,27361049
+LGALS3	0,273847411
+LASS2	0,273913098
+ZNF451	0,273935073
+NXPH4	0,27404559
+C22orf46	0,274118605
+KDM4B	0,27422483
+GPNMB	0,274363725
+CYHR1	0,274415705
+CCDC9	0,274487483
+WWC2	0,274522318
+ZNF652	0,274533788
+ILK	0,274538403
+CTDP1	0,27455992
+LOC51152	0,274810051
+AL442084	0,274963062
+CPNE7	0,275259638
+CENPB	0,275294531
+TCIRG1	0,275300556
+PRPF40A	0,275423637
+ARHGAP17	0,27552534
+LOC100133811	0,275961848
+ADAM17	0,276019886
+CRISPLD2	0,276144309
+IFIH1	0,276175289
+LOC440434	0,276293985
+DCLK2	0,276369722
+MS4A6A	0,276482788
+VASH1	0,276499979
+SRSF7	0,276513035
+B3GAT3	0,276752575
+CALHM2	0,276762436
+MAP4	0,276867434
+DULLARD	0,27687625
+CTSS	0,276943812
+BAG3	0,277040195
+KRT8P12	0,277155277
+POLR2F	0,277193722
+CD14	0,277207134
+SF3B1	0,277255775
+EZH1	0,277320185
+MBD1	0,277342685
+MITF	0,277407356
+BAIAP2	0,277445862
+FCGR2B	0,277531437
+PAQR4	0,277547889
+NFATC2IP	0,277597337
+CAT	0,277600148
+TJP2	0,277610024
+CCNA2	0,277687494
+GEM	0,277887602
+C2orf54	0,277935237
+HIRIP3	0,278018588
+MCM3APAS	0,278082892
+CFB	0,278130274
+TAGLN2	0,278365668
+AK024851	0,278382784
+HGD	0,278585783
+NR2E1	0,278716062
+SEC61A1	0,278797194
+PDE4DIP	0,278806635
+FRMD4A	0,278822955
+RHOC	0,278842121
+UBTF	0,278963815
+NCOR2	0,279024257
+PPP6R3	0,279218049
+ALAS2	0,279327775
+SPSB1	0,279537438
+SGMS1	0,279545277
+TEAD4	0,279565374
+AK024897	0,27961031
+IRS2	0,279708094
+TRIM62	0,279977776
+AF308291	0,279984986
+AK022362	0,280079092
+KIAA0495	0,280115197
+CUL7	0,280170918
+PARD3	0,280192562
+NUP98	0,280376383
+DHRS4L2	0,280391865
+AK024093	0,280444114
+VEGFB	0,280560816
+PTEN	0,280592383
+NBPF10	0,280620974
+CASP1	0,280699269
+AK2	0,280734467
+MLX	0,280792537
+GNG11	0,280826824
+HNRNPM	0,280968313
+IL12RB2	0,28098376
+CDK18	0,28098866
+RARA	0,280998983
+GYPC	0,281028129
+PAK4	0,28104576
+SEMA3F	0,281239182
+BAT2L2	0,281335934
+BRD4	0,28139016
+PAOX	0,281415979
+SMAD3	0,281446531
+PIK3R2	0,281480063
+IFT122	0,281682471
+IRAK4	0,281825175
+RASSF2	0,281825652
+RPL13A	0,282085077
+ZNF22	0,282127023
+KDM4A	0,282136199
+CPM	0,282150511
+EIF2S2	0,282316006
+USP48	0,282335945
+CLCNKB	0,282422648
+C11orf61	0,282474246
+ANKRD11	0,282516441
+PTTG1IP	0,282619596
+SEC14L1	0,282620994
+DOCK6	0,282646645
+CARHSP1	0,28271852
+RRAS	0,282814195
+TRIM38	0,283129972
+PLA1A	0,283206252
+GAB1	0,283220235
+PDLIM1	0,283254227
+SSH3	0,283308195
+KLF9	0,283315657
+N4BP2L2	0,283629404
+TNS4	0,283667599
+C15orf28	0,28383226
+ANXA11	0,283988681
+TAF12	0,283993401
+SLC39A1	0,284190806
+SAP30	0,284320416
+RNASE4	0,284337811
+RPS28P6	0,28438483
+DDR2	0,284449824
+BMP4	0,284614799
+CEPT1	0,284615091
+ITPKB	0,284650775
+PLEKHF2	0,284678379
+AW974812	0,284683098
+PTCRA	0,284827371
+SETMAR	0,2848555
+SOCS3	0,284925858
+NM_014129	0,284930906
+MYO1D	0,285094554
+RBL1	0,28514691
+HN1L	0,285254673
+LASS4	0,285307965
+RPS21	0,285547221
+PPP2R1B	0,285765143
+NEO1	0,285937917
+SEC24C	0,286013109
+BCL3	0,286014454
+KCNMA1	0,286080656
+AL137590	0,286198689
+EDIL3	0,286207431
+ARHGEF16	0,286210956
+HCK	0,286227266
+GSTA1	0,286246055
+SLA	0,286356975
+UNG	0,286379363
+SP100	0,286388329
+PRSS53	0,28642638
+MYL6	0,286728542
+CDH5	0,286728949
+C10orf116	0,286730624
+GTF2IRD1	0,286882519
+POLH	0,286995879
+SFRS16	0,287066034
+TPM4	0,28709233
+ABCD4	0,287100216
+GLT25D2	0,287127854
+COL18A1	0,287131911
+NPIPL3	0,287424398
+C1orf69	0,287453135
+MTF1	0,287488427
+IGF2BP2	0,287555495
+PALLD	0,287872078
+RPS16	0,287887395
+CYP2C9	0,287955438
+SC65	0,288029122
+CRYBG3	0,288096904
+SHC2	0,288312879
+FLNA	0,288339801
+NM_014486	0,288348194
+ISYNA1	0,288383809
+PNO1	0,288506351
+GZMK	0,2886543
+ATG13	0,288748426
+NCOR1	0,288772721
+ZSWIM1	0,288892162
+GPM6B	0,28893274
+SNTA1	0,289049438
+RHOBTB1	0,289064808
+GGA1	0,289073087
+ATXN2L	0,289088819
+FAM46A	0,289172187
+ZNF532	0,289393934
+CD40LG	0,289400418
+ZCCHC11	0,289421485
+WDR5B	0,289498086
+EPN2	0,289629137
+WNK1	0,289684816
+ZNF408	0,289721753
+LHFPL2	0,290003635
+NARG2	0,290029081
+STYXL1	0,29008917
+YY1AP1	0,290249669
+CPOX	0,290281635
+IL11RA	0,290333682
+PAXIP1	0,290387596
+ZNF282	0,290414378
+C11orf95	0,290643441
+MERTK	0,290681835
+VPS13C	0,29069039
+RPS17	0,290756898
+NEIL1	0,290762184
+ZNF292	0,290850132
+NOSIP	0,290873511
+DNAJB2	0,290950763
+INPPL1	0,29102828
+ZFX	0,29106383
+SETX	0,291138151
+SLC25A37	0,291207794
+PCDHGA8	0,291472818
+TXNIP	0,291962928
+DDX27	0,291971417
+BG389073	0,29216848
+JTB	0,292275569
+RBM10	0,292352574
+RASGRF1	0,29242252
+SYNM	0,292474024
+EXPH5	0,292481151
+NPL	0,292494012
+CHKA	0,292519533
+MGA	0,292564204
+SOX10	0,292580481
+AK024185	0,292975066
+FAM120A	0,292996604
+PLXNB1	0,293000141
+BDH2	0,293071563
+JRK	0,293136106
+SLC11A1	0,293139917
+TM4SF1	0,293242649
+EDA	0,293286441
+CDK10	0,293299298
+HLA-E	0,293305618
+LOC642846	0,293349826
+GFPT2	0,293396887
+SENP3	0,293408144
+RPS3AP44	0,293415546
+C16orf88	0,293431615
+FAM60A	0,293472328
+RPL36A	0,293501288
+SERPINA5	0,293547044
+CNOT8	0,293568161
+KDM4C	0,293620372
+POU2F2	0,293815578
+C14orf139	0,293870806
+ZNF217	0,293937173
+NM_025042	0,294034268
+NNMT	0,294200775
+VEZT	0,294224684
+KIAA0754	0,294307773
+RBM28	0,294637248
+ITPR2	0,294711729
+PPPDE1	0,294796015
+KLHL28	0,294874305
+MGP	0,294956866
+LOC729602	0,295016892
+SRSF5	0,295036903
+ROCK1	0,295267164
+SS18L2	0,295271871
+LMNA	0,29532356
+ESRRA	0,295387708
+SNHG3-RCC1	0,295411716
+TAL1	0,295434654
+SQRDL	0,295470062
+TARDBP	0,295665655
+LMAN2L	0,295705138
+RIN3	0,295771443
+PSPH	0,29602696
+DGKD	0,296027908
+WHSC1	0,296067068
+SPRY4	0,296068122
+ADARB2	0,296162399
+ELF3	0,296200778
+TLE1	0,296292637
+ACAN	0,296375799
+AK022038	0,296556116
+IL1RL1	0,296721787
+OR2A9P	0,296898432
+NCRNA00260	0,296954725
+CAD	0,296976627
+PNRC2	0,297129071
+IQCK	0,297134521
+ACOX2	0,297377087
+APOC4	0,297497329
+DGKA	0,297541846
+ZBTB1	0,297547513
+PUS1	0,297622568
+C7orf64	0,297653213
+FBLN1	0,297723957
+SBF1	0,297752819
+TMF1	0,298582891
+IL1R1	0,298701666
+LILRB3	0,298823808
+FLAD1	0,298825369
+CD163	0,299040686
+TCL6	0,299056301
+FADS3	0,299096634
+LBR	0,299180453
+AL162044	0,299184427
+ZNF337	0,299271736
+AHNAK	0,299352615
+YY1	0,299417937
+HIPK2	0,299439852
+NAT15	0,299519834
+ANKZF1	0,299817611
+NECAP2	0,299838267
+MAP3K7	0,299838407
+SAMD4A	0,299863792
+WDR8	0,300094232
+ZNF24	0,300179611
+NR3C1	0,300200063
+FGF1	0,300357727
+NPC1	0,300564708
+LMO4	0,300573598
+TTLL5	0,300853453
+AL050053	0,300945526
+RSU1	0,300958049
+C15orf39	0,301123219
+SLC14A1	0,301147038
+ELAVL1	0,301190126
+SLC17A4	0,301215925
+FANCC	0,301274346
+LRCH4	0,301338927
+EGFL7	0,301340052
+C9orf3	0,301357727
+SRGN	0,301411135
+PLCL1	0,301576339
+MAN1A1	0,301613058
+S100A8	0,301917937
+W86781	0,301984854
+HIP1	0,302012828
+OR7A5	0,302027387
+PPP1CC	0,3020408
+CGGBP1	0,302058231
+CYP3A4	0,302333153
+GALNS	0,302376776
+NR0B1	0,302394827
+SMNDC1	0,302468654
+MGST2	0,302482901
+RPL12	0,302658969
+DMPK	0,302955014
+TNRC6B	0,30299615
+PPM1D	0,303104009
+EED	0,303134999
+STAG3L1	0,3031801
+TMCC1	0,303195736
+RPL13	0,303245467
+RBPMS	0,30326423
+ARHGAP10	0,303298204
+PLCB3	0,303300054
+XPO1	0,303410309
+MYO1F	0,30341788
+SRPK1	0,303531642
+ZCWPW1	0,303562617
+MTHFD2L	0,303678034
+FAM111A	0,303798707
+TTC38	0,304186409
+COL7A1	0,304295553
+C4orf19	0,304312458
+NGLY1	0,304332742
+HTATIP2	0,304339936
+IFNAR2	0,304414877
+CXorf1	0,304737703
+UNC5B	0,304789798
+YAP1	0,30479215
+PHC2	0,30485466
+FBL	0,304914384
+CDH2	0,304939032
+FXYD2	0,304942957
+ANKRD36	0,305000603
+KRT8	0,305028726
+DSCAM	0,30505625
+SMO	0,305151387
+FCGRT	0,305420183
+PAIP2B	0,305483478
+PABPC1	0,305528523
+PIGV	0,305604211
+BACH2	0,305697602
+PLGLA	0,305722503
+MORC3	0,305845022
+DIDO1	0,305996983
+PRPF38B	0,306041882
+TRMT1	0,306054262
+NFATC1	0,306233076
+AK021495	0,306242002
+GPR1	0,306335484
+STARD13	0,306369109
+CELSR2	0,306371185
+ZNF193	0,306396574
+ABHD6	0,306458055
+PLCXD1	0,306486283
+RPAP1	0,306695411
+AL050122	0,306737964
+DHRS3	0,306750918
+C1QA	0,306800137
+AF009267	0,30681596
+SETD2	0,307047565
+STX6	0,307184977
+TMEM204	0,307304516
+SMYD2	0,307490131
+BF942161	0,307560212
+SLC44A1	0,307685609
+ELF2	0,307698089
+AATF	0,307770923
+AV761453	0,307800442
+ACTN1	0,307927265
+AI523613	0,307943372
+SOLH	0,307971092
+ZNF410	0,308222237
+GOLGA4	0,308250269
+FLJ21369	0,308352331
+FCGR2A	0,308469725
+BRD7	0,308638563
+TLR2	0,308769609
+FTHL5	0,308790654
+SPOCK1	0,308861441
+LSM14A	0,308907157
+USF2	0,309161806
+TENC1	0,309220224
+EMP2	0,309252571
+BSDC1	0,309299474
+ZNF701	0,309462113
+PLIN3	0,309516744
+SORBS1	0,309562012
+FTL	0,309588981
+AGFG2	0,309634949
+UBR5	0,309647344
+MMP14	0,30965745
+SFRS8	0,309923113
+ITPR3	0,309975876
+PLK3	0,310097184
+NUP188	0,310124261
+CROCC	0,310245563
+CHSY1	0,310328559
+CTCF	0,310675097
+EDC4	0,310685915
+NFE2L2	0,31069885
+LILRA6	0,311008878
+SATB2	0,311055754
+GTPBP6	0,311254994
+TSPAN14	0,311316513
+C10orf18	0,31133762
+SECISBP2	0,311419174
+DHX34	0,311443077
+LSS	0,311450185
+CHI3L1	0,311532669
+PDGFC	0,311715929
+BMP7	0,311741682
+MBNL1	0,311755686
+DNA2	0,311841432
+COMT	0,312081286
+LOC100133005	0,312165679
+PTOV1	0,312192713
+LCAT	0,312407744
+LRRFIP2	0,312480817
+UCN	0,312589312
+AK024606	0,312655002
+MICAL3	0,312700621
+ROM1	0,31291043
+MED12	0,312925796
+CPNE1	0,313173908
+GBP2	0,313262095
+PELI2	0,313279559
+MLL	0,313398121
+HIF3A	0,313438743
+ST18	0,313449639
+AF131777	0,313643716
+CATSPER2P1	0,313785721
+ZNF302	0,314066212
+APBB2	0,314110219
+KIAA0907	0,31421022
+ZNF592	0,314679884
+HNRNPA1	0,314773035
+TSC2	0,314882123
+SFRS15	0,314884343
+ZNF835	0,314920694
+WDR6	0,314979423
+LOC729143	0,315037798
+PPARD	0,315048839
+U2AF2	0,315118843
+MGAT1	0,315269456
+ZNF44	0,315270856
+RPL36	0,315475789
+GRAMD3	0,315513449
+PTPN2	0,315554784
+AL080072	0,315635626
+C19orf2	0,315918303
+DNAH3	0,315930745
+ZNF146	0,316341954
+SMEK1	0,316538461
+MLXIP	0,31681421
+NMT2	0,316848231
+G3BP1	0,316864559
+DDX3Y	0,316997159
+STEAP1	0,317082981
+BC002629	0,317231764
+KDM2A	0,317406731
+TMEM39A	0,317430306
+C15orf29	0,317437851
+MACF1	0,317513626
+LOC391020	0,317572673
+SETD1A	0,317586539
+KTN1	0,317889697
+RUNX3	0,31809511
+NINJ1	0,318107478
+ARMC7	0,318150459
+BMP1	0,318194029
+DKFZP586I1420	0,318199121
+JARID2	0,318226296
+AW972351	0,318303541
+PAPSS2	0,31841091
+ELTD1	0,31845583
+ETS2	0,318667898
+CREB3L2	0,318705762
+DFNB31	0,31892768
+SERHL2	0,318966243
+C10orf26	0,319058163
+NM_030892	0,319421731
+WRAP53	0,319795295
+UBQLN4	0,319828198
+RALGDS	0,319938162
+PRKCH	0,320101043
+AU146983	0,320105843
+SLC5A3	0,32021553
+DUSP1	0,320239212
+NKX2-2	0,320312108
+C1orf183	0,320387827
+PCM1	0,320482282
+THRA	0,320531901
+NM_025028	0,320726138
+SIVA1	0,320736787
+TTR	0,320757249
+IKBKB	0,320778441
+ARID1A	0,321020715
+HDAC4	0,321059842
+ZFP36L2	0,321167918
+TMEM212	0,321179342
+AA443771	0,321214505
+AGAP5	0,32125931
+PIGA	0,3216713
+SFRS12	0,321704401
+LDLRAP1	0,321832456
+CCDC21	0,321857948
+SSFA2	0,321990716
+RAMP1	0,322050077
+FLJ10357	0,322160744
+LAD1	0,322322766
+RACGAP1	0,322340831
+NPIPL2	0,322616655
+CEP350	0,322648588
+CRLF1	0,322735059
+IGSF9B	0,322744338
+PLXND1	0,322801951
+MCL1	0,322913781
+ALMS1	0,32297709
+ZNF768	0,323059066
+RSL1D1	0,323228527
+C4orf34	0,323582139
+PNPLA6	0,323738553
+MAST4	0,323801655
+NME3	0,323835175
+SNHG3	0,32391938
+S100A12	0,324014586
+PPP4R1	0,32409634
+PLD1	0,324165096
+POLG	0,324186823
+NKTR	0,324203565
+ST3GAL4	0,324231325
+TMEM63A	0,324243134
+ST20	0,32438459
+RNF114	0,324406844
+HYI	0,324468621
+DUSP6	0,324699964
+NR1H2	0,324884332
+DVL2	0,324900869
+SRSF11	0,324979841
+CLK2	0,325170283
+MKLN1	0,325287178
+SCRIB	0,325320413
+KIAA0467	0,325541973
+DMWD	0,325745064
+KLHL23	0,32579572
+RPS6	0,325948088
+ZBTB17	0,326014408
+RAI14	0,326038467
+UBE2G2	0,326143089
+ZNF562	0,326186073
+EZR	0,326282578
+TRPS1	0,326283144
+HFE	0,326390644
+MED23	0,32658232
+DDX11	0,326766632
+SHMT2	0,326784725
+LRP5	0,326954416
+PTH1R	0,327100265
+LOC731602	0,327131294
+AA401963	0,327241371
+CDK5RAP2	0,327276136
+SERP1	0,327279991
+SLC1A5	0,327303416
+BGN	0,327370767
+HSD17B1	0,327475971
+AL390143	0,327497051
+DIAPH2	0,327617697
+PITPNC1	0,327719899
+SPRY2	0,327767132
+FZD7	0,327974293
+MAP4K4	0,328171238
+TNS1	0,328369107
+ZNF783	0,328517049
+M78162	0,328518574
+ADAMTS1	0,32853944
+FKBP5	0,328911405
+AGAP8	0,329115979
+PLEKHF1	0,329179433
+DNAJB1	0,329339376
+RBMS2	0,329438459
+HNRNPH1	0,329454824
+ULK2	0,329496298
+PAPD7	0,329501864
+SURF1	0,329547559
+W61005	0,329673439
+ZNF862	0,330131081
+GNA15	0,330266409
+CHD9	0,330273108
+DLC1	0,330294104
+TMEM2	0,330321664
+AK024879	0,330353812
+N4BP1	0,330435804
+SERF2	0,330633507
+SNRPA	0,330957742
+IRF8	0,33098543
+ABCA2	0,331251046
+NPFF	0,331328402
+CP	0,331565597
+AU144887	0,331713137
+AW851559	0,33185735
+TCF4	0,332062967
+ZNF354A	0,332076549
+TMEM92	0,332352956
+NFATC3	0,332386137
+SSRP1	0,332529738
+TCF7L2	0,332651908
+PIM1	0,332716071
+PIP4K2A	0,332914219
+EIF4EBP1	0,332959146
+LOC100132863	0,333054912
+MMRN2	0,333075923
+AU147295	0,333342973
+VIM	0,333356286
+C2orf67	0,333469715
+DNMT1	0,333550022
+CEP110	0,333679402
+BAZ2B	0,33371151
+KDELR2	0,333939841
+L3MBTL	0,334448273
+CDK19	0,334505985
+CYorf15B	0,334832089
+DDX17	0,334839203
+FKBP4	0,335166906
+STOM	0,335173644
+U82303	0,335241438
+LOC202181	0,335841121
+ATM	0,335893127
+STK3	0,335957389
+MID1	0,336166241
+IGFBP5	0,336454348
+PARP4	0,336459483
+EXOC7	0,336479503
+FANCG	0,336652927
+PHF2	0,336678654
+FBRS	0,33674511
+ANP32B	0,336836072
+NCK2	0,336876937
+CASP6	0,336920233
+ZBTB3	0,337122586
+DHFR	0,337448147
+APOLD1	0,337464001
+STAG1	0,337490482
+NM_024305	0,337551103
+SIGLEC8	0,337608204
+ERLIN1	0,337809212
+POLDIP3	0,337889824
+SPTLC2	0,33799094
+C7orf26	0,338204972
+UBE2D4	0,338265561
+MAP2K7	0,3384787
+MECOM	0,338508564
+DOCK1	0,339029429
+HS1BP3	0,339148762
+PRKY	0,339216015
+GOLGA1	0,33927478
+XPC	0,339433169
+PHF3	0,33953002
+HIC2	0,339768003
+C9orf7	0,340519877
+CTDSPL	0,340591645
+ZNF83	0,34077157
+PHGDH	0,340889735
+TMEM165	0,340978736
+CLN3	0,341078466
+AU147983	0,34113627
+PATZ1	0,341151411
+DIP2C	0,341390806
+RECK	0,341533646
+EWSR1	0,342003886
+SMAD7	0,342182186
+MTRF1L	0,34225773
+TJAP1	0,342452426
+PRKD2	0,342725824
+SPOP	0,343019265
+HLA-J	0,343028528
+PLXNB2	0,343103735
+FBXL14	0,343454364
+LAMA2	0,343637649
+RNF220	0,343845541
+CLK3	0,344164444
+STARD3	0,344187457
+OGT	0,345118989
+IFITM3	0,345141829
+HMOX1	0,345196784
+EIF2C2	0,34557825
+CCND3	0,345663426
+TGFBR3	0,345676022
+POLR2J3	0,345712548
+BCAR3	0,345713549
+C14orf147	0,34610842
+CLDN15	0,34616346
+TOP1	0,346179876
+RASL12	0,346286134
+MED13L	0,346369067
+SOS2	0,346799305
+SERPING1	0,347144597
+IER5	0,347279068
+TLE2	0,347426427
+LLGL2	0,347448236
+TMCC2	0,347500013
+PHF20	0,347602909
+SIRT4	0,347862165
+OSGIN1	0,348060574
+H2BFS	0,348076316
+NM_017756	0,348230007
+NCRNA00115	0,348422218
+MT1E	0,348733923
+NACC2	0,3488369
+NFIB	0,348943619
+AKR1C3	0,349206923
+ARPC1B	0,349407208
+NIPBL	0,349628117
+RPL11	0,349803207
+MSH6	0,350014407
+PTDSS2	0,350073646
+AL050145	0,350120404
+FAM107A	0,350271118
+CHN2	0,350358174
+DAPK2	0,350378033
+DLG5	0,350436992
+OPHN1	0,350596034
+C20orf11	0,351010126
+SLC35D1	0,35135795
+SELL	0,35142274
+FAM193B	0,351790995
+NM_024880	0,352020901
+RASGRP2	0,352114346
+CAPN3	0,352194849
+THOC1	0,352289646
+TAOK3	0,352396226
+FBXO42	0,352613215
+LARP6	0,352692849
+KLKB1	0,352702835
+METTL7A	0,352961228
+STIP1	0,352968743
+WIPF2	0,353085817
+FOXD1	0,353404764
+HSPB2	0,35378232
+ENGASE	0,353978221
+LAT2	0,354239264
+HIST1H2AH	0,354250391
+GSDMD	0,354483715
+TRA2A	0,354674037
+C19orf29	0,354762053
+BRPF1	0,355002213
+NUMA1	0,355146564
+SNW1	0,355320637
+SMARCC1	0,355374541
+ZNF175	0,35555253
+BATF3	0,355680727
+HIST1H2BC	0,35575565
+ERN2	0,356098991
+ZFR	0,356185362
+AW301806	0,356253591
+SMTN	0,356289422
+RPS6KA2	0,356774064
+MIIP	0,35685635
+ARGLU1	0,356919378
+CTNNAL1	0,357152141
+PCDH9	0,357228835
+LAS1L	0,357263917
+DOK1	0,358029668
+AFTPH	0,35852635
+ZNF143	0,358674337
+C11orf71	0,35888557
+MICALL2	0,359221642
+KDM6A	0,359260932
+CFH	0,359284568
+CEBPB	0,359516672
+MTUS1	0,359547348
+AW973791	0,359548173
+SERTAD2	0,359684853
+FGFR1	0,359721729
+KPTN	0,360479451
+NR2F2	0,361169645
+RGL2	0,361384531
+NM_014120	0,361482036
+TAF5	0,361611903
+ZC3HAV1	0,362177526
+BEST1	0,362248528
+TNFRSF1A	0,362724804
+CLIP2	0,363062238
+EHMT2	0,363078239
+IFITM1	0,363162265
+GCFC1	0,363190607
+PECAM1	0,363227012
+YES1	0,363556218
+ZFP36L1	0,363744573
+SBNO2	0,364095165
+RMND5A	0,364201024
+IL10RB	0,364481295
+CBS	0,364486163
+TBC1D2B	0,364503601
+C10orf10	0,36458821
+AU144530	0,365137826
+ZNF500	0,365202134
+ATP6V0E1	0,36527949
+SEPT8	0,365711052
+VCAN	0,365762437
+RPL36AP51	0,366073863
+RPL31	0,36613283
+TAOK1	0,36613666
+GCN1L1	0,366181489
+CALCOCO1	0,366300689
+GNA11	0,366387362
+SH2B2	0,366425408
+RREB1	0,367259867
+SLC35E1	0,3672965
+GPRC5B	0,367311931
+TCF7	0,367371063
+PDIA4	0,367810651
+ZNF34	0,367845233
+MBD3	0,36793004
+CXCR4	0,368041224
+C9orf114	0,368120984
+IFITM2	0,368313531
+ZNF665	0,368328536
+ZCCHC24	0,368368275
+LOC100133944	0,369022431
+CSDA	0,369150342
+AU148255	0,369666508
+CIZ1	0,369704457
+CRTC3	0,369792369
+CTNNA1	0,369962411
+RARRES2	0,37011032
+NM_025033	0,370246707
+VSIG4	0,370274949
+FAM48A	0,370421427
+ZDHHC11	0,370675656
+NPAS2	0,370715345
+ADH1B	0,370935809
+ACSL1	0,371025369
+C1orf63	0,371083889
+TYMP	0,371266716
+LEPREL1	0,371463494
+LAMB2	0,371472469
+MAFB	0,371542293
+AW971248	0,371589606
+BC003629	0,371603781
+FAM63A	0,371786321
+ABCA1	0,371992682
+IGF2R	0,37211512
+SOX13	0,372131188
+WAPAL	0,372391179
+ZFC3H1	0,372437982
+ZNF710	0,372493324
+HSPA6	0,37258644
+CCDC101	0,372823539
+BAZ1A	0,372824952
+AXL	0,372842922
+NPIPL1	0,372916072
+HDGF	0,372923023
+KHDRBS3	0,373093219
+MT1X	0,373144553
+MTMR15	0,373164421
+AF257099	0,373262757
+AEBP1	0,37342966
+KLHL25	0,373672957
+GJB4	0,37372121
+LUC7L3	0,374023648
+U79248	0,374142769
+LOC653562	0,374188384
+RBM4	0,374375075
+ABCC10	0,374890625
+CXorf21	0,374896996
+DAXX	0,374917403
+C1R	0,375063944
+TPST2	0,375279072
+KLHL24	0,375307199
+C7orf68	0,375539219
+ZCCHC8	0,375600764
+CASP4	0,375605037
+ETV1	0,37597402
+BIN1	0,376340315
+RGS19	0,376617752
+PKNOX1	0,377091746
+CTTN	0,377173864
+TRIP10	0,377452782
+ANGEL1	0,377498562
+PLIN2	0,377879768
+NM_025007	0,377942771
+PTMA	0,378229214
+S100A11	0,378255627
+AXIN1	0,378580893
+NPRL3	0,378633074
+PNN	0,378695864
+AV727934	0,378843386
+ANGPT2	0,37912784
+AK023918	0,379250766
+CNPY3	0,37927474
+AF130051	0,37947818
+TLE4	0,379880985
+PAPOLA	0,379974199
+ITGB5	0,380683545
+FAM38B	0,380693638
+PABPN1	0,380909515
+SLC6A8	0,38116858
+RYBP	0,38121367
+NASP	0,381229843
+FGR	0,381246748
+PER1	0,381695992
+CDR2L	0,381867955
+LRRFIP1	0,382075479
+HMHA1	0,382282948
+KIAA0485	0,382313718
+GUSB	0,38235255
+RPS17P5	0,38240934
+FXYD5	0,382563723
+RBL2	0,382697586
+RANBP10	0,382980904
+NEDD9	0,383084673
+MSL2	0,383144236
+FAM50A	0,383317183
+AL080232	0,383323554
+SPG21	0,383712061
+TPD52L1	0,384098652
+H2AFX	0,384141378
+SWAP70	0,384225003
+IVNS1ABP	0,384369268
+KDELC1	0,384542393
+MYL12A	0,384757468
+FOXO3	0,384856157
+MED13	0,385128516
+AL049252	0,38560217
+AF007147	0,385820993
+PAX6	0,385884587
+DNASE2	0,38591545
+SLC12A9	0,386200858
+SIRT1	0,38637719
+ARID5B	0,386492868
+MT2A	0,38656824
+SLC38A2	0,386710042
+GNG5	0,386756333
+SRRM2	0,386841072
+SERPINB6	0,386985458
+CC2D1A	0,387023088
+LRRC37A2	0,387067777
+CSF1	0,387071999
+RPL29P11	0,38708859
+SFRS14	0,387094074
+MYO9B	0,387103012
+AW972855	0,387241981
+TRIP4	0,387728627
+ZBTB40	0,387827711
+STARD8	0,387863703
+WBSCR16	0,387992811
+NXF1	0,388021286
+CTDSP1	0,38803541
+RSAD1	0,388042285
+SUV420H1	0,38833134
+CDKN1C	0,388508896
+NM_016415	0,388588403
+E2F4	0,388673603
+KANK2	0,388702219
+ZC3H7B	0,388980025
+ANGPTL4	0,389035415
+CRY1	0,389801967
+KIAA0556	0,389845114
+TBC1D16	0,390016803
+TCOF1	0,390109025
+ZFYVE26	0,390278079
+IFRD1	0,39034324
+EIF4B	0,390385914
+SMC1A	0,390525141
+SCIN	0,3907272
+MARS	0,391061966
+PTRF	0,391089965
+POLR2J	0,391514571
+APAF1	0,391530483
+ITPK1	0,3915415
+PNRC1	0,392133859
+CLIC2	0,392140808
+KIAA0913	0,392243895
+PRKAR2A	0,392619325
+PRKX	0,392750502
+SYDE1	0,392957216
+ACSL5	0,393140899
+LRP10	0,393162277
+LPP	0,393214983
+SNTB2	0,393383504
+NADK	0,393882671
+PCBP2	0,394206896
+N51370	0,394562467
+CLIC1	0,394663761
+CTBP2	0,394785714
+PHB	0,394929787
+BCL2	0,395102709
+TAF4	0,395492947
+LOC652607	0,395562084
+YBX1	0,396079328
+PRPF3	0,396609142
+SLC38A10	0,396741732
+ERBB2IP	0,396808535
+CFLAR	0,396840203
+TNFRSF10B	0,397091951
+PHC1B	0,397196351
+ARL17A	0,397406114
+ZBTB20	0,397424403
+REPIN1	0,397830532
+BE466926	0,397930108
+MT1P2	0,398055653
+ZNF778	0,398225613
+DICER1	0,398300689
+NM_018603	0,398329284
+RAF1	0,398631868
+MXD4	0,398685167
+FBXL7	0,398770393
+CALD1	0,399121196
+GSDMB	0,399246982
+ZCCHC2	0,399293751
+PODXL	0,399691684
+ACACB	0,400136922
+VEZF1	0,400413083
+PLEKHM1	0,401187317
+CSPG4	0,401646086
+ID3	0,40170175
+RBM41	0,401719975
+KDM6B	0,401885964
+PHF15	0,402522419
+LAMP2	0,402538077
+CDC14B	0,402583482
+HNRNPL	0,403044314
+SLC4A2	0,403448509
+DDX23	0,403953946
+TUBD1	0,40407115
+SLC16A3	0,404204458
+CAPN2	0,405022548
+CBFA2T2	0,40560438
+TCEB2	0,405769952
+HNRNPF	0,406126644
+MORC2	0,406182732
+FOXO1	0,406430281
+AI962978	0,406538883
+HP1BP3	0,406567553
+CBFB	0,406789498
+RBM14	0,406886421
+SFI1	0,407058786
+ZHX3	0,407089165
+KDM3A	0,407233406
+SIRT2	0,407341821
+ANKS1A	0,407373917
+TCF3	0,407442968
+NOTCH2NL	0,407672378
+EEF1D	0,407830724
+SOX12	0,408065349
+SLCO1A2	0,40820492
+HNRNPA3	0,408299868
+GTF2H3	0,408624789
+FZD9	0,408729069
+SAFB2	0,408755308
+APBA3	0,408834306
+ASCL1	0,409161488
+CG012	0,409559201
+WDR59	0,409606436
+LAMA5	0,409632505
+ZNF276	0,409730125
+ZNF395	0,410080702
+TIMM44	0,410223052
+BGLAP	0,410749324
+ZHX2	0,411039562
+CARS2	0,411302016
+SLCO3A1	0,411338796
+LOC442497	0,411765627
+FRYL	0,411842495
+CYP2J2	0,412070197
+ABL1	0,412522321
+INF2	0,412975218
+SGK1	0,413352645
+SFTPB	0,413789208
+TIGD1L	0,41383023
+RBCK1	0,414019825
+TRAPPC10	0,414285862
+DUSP7	0,414641136
+WSCD1	0,415016303
+DCP1A	0,415308358
+LPAR1	0,415365439
+RBBP6	0,415730871
+DONSON	0,416255506
+C16orf5	0,416258918
+NCOA1	0,416350707
+CFHR1	0,416440287
+AA126763	0,416566153
+LRRC32	0,416765832
+CP110	0,41732481
+LTBP3	0,417338221
+TDRD3	0,417356196
+HMG20B	0,417456909
+CDC42EP2	0,417645635
+TAF1C	0,417736819
+NM_013344	0,41778911
+VGLL4	0,417820331
+PHKA2	0,417904785
+KDSR	0,418009802
+RELA	0,418064238
+TBL1X	0,41814877
+SIAH2	0,418727849
+MYO1E	0,418747589
+HIST1H2BD	0,419127582
+AI744451	0,419208355
+PTMAP7	0,419537834
+ARID5A	0,419593497
+CYP27A1	0,420064872
+RAB13	0,420441013
+CPSF7	0,420526378
+CPT1B	0,420770156
+LRDD	0,420794327
+PILRB	0,421599366
+STAB1	0,421733406
+FCHO1	0,422126906
+ZNF32	0,422311821
+TBC1D3H	0,422328806
+C1orf66	0,42292679
+NM_025032	0,423323973
+AI732802	0,423584905
+PCID2	0,423787762
+POGK	0,423912669
+TMEM140	0,424587207
+TMC6	0,424604298
+AL080160	0,42490597
+AK021505	0,425024442
+SCD5	0,425610027
+RAD52	0,425956612
+AF116715	0,425960499
+DCI	0,425967692
+SFRS18	0,426091505
+HCG2P7	0,426136765
+ADORA2A	0,426366158
+NM_021651	0,426442506
+MID1IP1	0,426940092
+HNRNPC	0,427103695
+NM_025024	0,427155973
+AK024315	0,427460397
+AK021514	0,427966252
+SLC29A3	0,428138792
+NSUN5	0,428255135
+PHF10	0,428599049
+DAPP1	0,428626141
+TMEM109	0,428647746
+LOC91316	0,428742129
+ITGB4	0,42956266
+SLC30A1	0,429998682
+AW150065	0,430129937
+ZCCHC6	0,430267528
+ARHGEF2	0,430371137
+AK027193	0,43049002
+TRIM52	0,430535815
+MT1G	0,430767233
+NOTCH1	0,430849119
+ZRSR2	0,43114681
+RPS6KA1	0,43184981
+KANK1	0,432456197
+FURIN	0,432618855
+APOBEC3C	0,432749845
+ANKRD40	0,432772877
+TRIOBP	0,432900403
+ZNF384	0,433116555
+CDKN1A	0,43319672
+BTG1	0,433570541
+EPHX1	0,433658916
+CNOT6	0,434207544
+HSPA1L	0,434322364
+PKD1	0,434547199
+WAS	0,434717417
+RPL23AP32	0,434993767
+P4HA1	0,434997425
+MAX	0,435160002
+UIMC1	0,435278167
+NM_025120	0,435322168
+NCOA6	0,435700178
+TPD52L2	0,435768747
+BCL6	0,435938226
+AK024108	0,436355329
+C7orf23	0,436800978
+CDC42BPA	0,437074951
+CD59	0,437137855
+POLR1B	0,437227618
+TLR5	0,437498143
+HDAC1	0,437993569
+ARHGEF7	0,438071237
+AA045174	0,438161955
+TBC1D17	0,438488128
+PRELP	0,438518539
+GTF2H2B	0,438525643
+HIST1H2BK	0,43866778
+AU147851	0,438979485
+RBM39	0,439661925
+IQGAP1	0,439786742
+RPL18AP3	0,440613252
+LTBR	0,440721546
+RPL35A	0,441136859
+ARAP2	0,441441928
+ARAF	0,441560027
+MT1H	0,441587824
+LOC441258	0,442117007
+ZCCHC14	0,442132801
+IRF7	0,442147625
+NOL12	0,442203671
+PTPLB	0,442541309
+AI683552	0,442752948
+MYST1	0,442881562
+MXI1	0,443040642
+AW974910	0,443299524
+C1orf144	0,443500279
+KRCC1	0,444417306
+PIAS4	0,444438643
+SRSF1	0,444637015
+LRP2	0,444740953
+ZDHHC18	0,445392541
+SPN	0,445443935
+ST13	0,446667878
+PHF17	0,446746739
+NACA2	0,446876872
+SASH1	0,447285208
+CD22	0,44772036
+CSNK1E	0,447902552
+COL5A3	0,447933631
+MAT2A	0,448695587
+EFHD1	0,448820126
+MAP3K3	0,448963961
+BIN3	0,449317201
+LUC7L	0,449469644
+KIF1C	0,449622117
+RNF144A	0,450034368
+TULP3	0,450626451
+CDKN2C	0,450879897
+HSD17B7	0,451226227
+ACIN1	0,451331774
+PABPC3	0,451363083
+PHF21A	0,45139036
+HNRNPH3	0,451480034
+HIST2H2BE	0,452219911
+RRP1B	0,452597128
+SOX2	0,453132172
+ZNF444	0,453296716
+FAM13A	0,453547738
+JUP	0,453753674
+PODNL1	0,453854292
+MAML1	0,453885
+SNRNP70	0,45408945
+SDCCAG3	0,45464357
+PLGLB1	0,454722494
+CDH19	0,454754165
+HSPA1B	0,455063205
+ARHGEF10	0,455229121
+NFIL3	0,455469821
+NFKBIA	0,455577982
+XRCC2	0,455670024
+ACTN4	0,455764555
+PDS5A	0,456071133
+POU2F1	0,456120351
+VPS54	0,456318614
+BANF1	0,456451252
+PGCP	0,456765652
+RPL28	0,456867479
+ICAM2	0,457066169
+SNAP23	0,457069788
+SART1	0,457941993
+AK023891	0,458253977
+BANP	0,458588544
+MAP3K11	0,458968207
+EPOR	0,459463669
+FKSG49	0,459538011
+MT1F	0,459638951
+NM_014128	0,460468204
+AP1G2	0,460676306
+GAS2L1	0,461632768
+PHIP	0,462053958
+NOL8	0,462387404
+NM_017932	0,462395281
+RNF130	0,462894529
+ZMYND8	0,463309493
+AK024525	0,463401166
+TRIM28	0,463454342
+BCAT2	0,463509769
+TYRO3	0,463574548
+PHLPP1	0,463738295
+BST2	0,465024297
+PDGFRB	0,465034704
+AL049987	0,465336929
+AKAP8L	0,466278804
+TGM2	0,467555999
+CREBBP	0,467899354
+KIAA0894	0,468325808
+DDX39	0,468959477
+NCAPD2	0,468959537
+ALPK1	0,469621875
+TGIF1	0,469902489
+PPP1R14B	0,470121069
+PNMT	0,470291567
+NAA16	0,470467422
+ZNF611	0,470526774
+ZRSR1	0,470857426
+NPIP	0,472818474
+RBM38	0,473036567
+USP34	0,473278809
+TGFB3	0,474067001
+ITSN2	0,475328182
+CEBPD	0,475754278
+MCM3AP	0,476296498
+HAPLN2	0,476718109
+POGZ	0,477224004
+NR2F1	0,477556735
+GAS1	0,478628972
+SLTM	0,478903701
+ECE1	0,479007813
+CALCOCO2	0,47910558
+RXRA	0,479821295
+MEIS2	0,480178943
+CLEC2B	0,481843785
+AL049260	0,482481089
+CHST3	0,48259726
+COL16A1	0,483094975
+SLC25A16	0,483255606
+LHPP	0,48421483
+AF010144	0,484619234
+GTSE1	0,484629217
+MUM1	0,484956644
+TNXB	0,485246904
+PRINS	0,486032909
+ANKRD49	0,486282532
+PTPRK	0,486899575
+PPAP2C	0,487395433
+C22orf9	0,488987561
+KHNYN	0,489026627
+RAPGEF3	0,489474077
+AF078844	0,489716822
+MAN2A1	0,489875474
+IFT20	0,490824284
+USP21	0,490859618
+NOP2	0,491526918
+LOC440248	0,491905455
+LOC647070	0,493492979
+MAFF	0,494072026
+BG251521	0,495196452
+C6orf145	0,496322836
+MLL4	0,496324893
+ATF4	0,49676781
+RELN	0,497310216
+PELI1	0,497491599
+P2RX7	0,497499324
+CNOT2	0,498172475
+FAM38A	0,498599859
+DCLRE1C	0,498693515
+INSR	0,502304787
+MAPKAPK2	0,502573806
+NDE1	0,50267356
+MT1M	0,502716901
+CDK5RAP3	0,504041432
+SULT1A4	0,504805398
+NSUN5P2	0,505093708
+ANKRD10	0,505841449
+LOC339047	0,506042447
+LRRC1	0,506594446
+CUX1	0,507257715
+SRRT	0,508240438
+MAF	0,508625791
+EBLN2	0,509549245
+NM_017618	0,510705903
+RBM4B	0,51138423
+FBXW12	0,511744983
+ATP8B1	0,511969804
+NM_024978	0,512045897
+KCNMB4	0,512142959
+CLMN	0,512461537
+LOC100132540	0,512589899
+SERPINH1	0,513136463
+RHBDF2	0,513703735
+PCF11	0,514081494
+HAUS2	0,514694211
+TECPR2	0,514970535
+TNIP2	0,515014912
+AUP1	0,516155581
+KIAA0101	0,516801916
+N35922	0,51703624
+STK38	0,517483454
+AZGP1P1	0,518047589
+C13orf15	0,518310047
+PRR11	0,518691616
+PDCD6	0,51972326
+AFF1	0,520716014
+AF222691	0,521107674
+BE045142	0,521502008
+PACS2	0,521749261
+PSRC1	0,522634606
+ZNF358	0,523463012
+MAPKBP1	0,523696079
+S100A4	0,524041412
+MYO1C	0,524902669
+IRF3	0,52538788
+TOB2	0,526119659
+KLHL21	0,527145117
+PGF	0,527713686
+LOC399491	0,528407104
+ARAP1	0,528556373
+AZGP1	0,528659072
+SIRT7	0,528927974
+C16orf53	0,529668261
+KLHL2	0,533153888
+AK022213	0,533802801
+ANKRD28	0,534099367
+TF	0,536170201
+MAVS	0,53636005
+MSX1	0,536723495
+C12orf35	0,537890473
+AA554945	0,538449904
+SUN2	0,539191173
+RBM6	0,54218394
+AL080112	0,542349721
+SORT1	0,542569398
+AL049285	0,542660805
+FOXO4	0,542834527
+ABCA8	0,543725594
+RING1	0,54468938
+KCNE4	0,546337688
+TAZ	0,546506594
+DIP2A	0,546907877
+CLK4	0,548788669
+ZNF277	0,549312201
+MUS81	0,551193399
+DBT	0,556696292
+EMP3	0,557013195
+DDIT4	0,557077384
+RUFY1	0,557170712
+MYST3	0,559285285
+PRPF4B	0,559881298
+LOC100132247	0,562956585
+HSPB1	0,56508456
+CHD7	0,566776564
+CHORDC1	0,566831861
+COBL	0,569205746
+STAG2	0,569603186
+CTDSP2	0,570069613
+ZNF160	0,572703009
+PDE4C	0,574535337
+WWC3	0,575159977
+BMI1	0,576213767
+CRYAB	0,577245348
+AHCTF1	0,577515066
+ADIPOR2	0,5780263
+CASC3	0,57815663
+MUTYH	0,579456271
+AK023783	0,580340854
+HIGD1B	0,583663012
+PLOD1	0,587347495
+PRR14	0,587364521
+SH3BP4	0,58788373
+C19orf28	0,587956493
+NDRG1	0,588555643
+HIST1H1C	0,591446402
+TCF12	0,592176798
+MPST	0,593408757
+SEPP1	0,593935425
+DNAJB6	0,595685757
+SIRPA	0,596218961
+FLT1	0,597923318
+MYOT	0,598968138
+HIST1H2AC	0,600586387
+HBP1	0,600714263
+KAZ	0,601415288
+PTBP1	0,602313539
+NSUN5P1	0,603090503
+GUSBP3	0,604393039
+KCNJ2	0,616084197
+KAT2A	0,620256502
+MCM7	0,622618327
+FBXW4	0,627081137
+MKNK2	0,628440154
+IL17RB	0,631530593
+CLK1	0,632420317
+LRP4	0,632833859
+FAM53B	0,641895571
+JMJD6	0,64411039
+TYK2	0,644727629
+PLOD3	0,644893842
+CXXC1	0,650530485
+AK024136	0,659066605
+PAN2	0,66036619
+NPTX2	0,665210794
+SPEN	0,669461617
+SETD5	0,670191692
+STX10	0,674048462
+CDK2AP2	0,67411425
+PPM1B	0,68382966
+SLCO4A1	0,685048974
+GLT25D1	0,706365388
+ZC3H11A	0,716021559
+ZBTB16	0,720405109
+ZNF692	0,720940567
+NUPR1	0,724120307
+FLCN	0,747339708
+NFASC	0,755177517
diff --git a/console/testFiles/pd_full/PD_160714_2/layouts/ageing.txt b/console/testFiles/pd_full/PD_160714_2/layouts/ageing.txt
index 952e851c76..d5c8ec23b4 100644
--- a/console/testFiles/pd_full/PD_160714_2/layouts/ageing.txt
+++ b/console/testFiles/pd_full/PD_160714_2/layouts/ageing.txt
@@ -1,416 +1,416 @@
-# VERSION=1.0
-# NAME=Ageing brain
+# VERSION=1.0
+# NAME=Ageing brain
 # DESCRIPTION=Differential transcriptome expression from post mortem tissue. Source: Allen Brain Atlas datasets, see PMID 25447234.
-name	value
-ELMO2	-0.547404913905166
-RGS1	0.664905640201586
-GSTT1	-0.630503181260422
-SDPR	0.576954531502211
-KCNJ2	-0.389733143810031
-DLG2	-0.622560222549952
-C2orf46	0.306481308387015
-YPEL1	-0.110679998012662
-AFF2	-0.580887248407995
-TCP11L2	-0.446138772716671
-TYROBP	0.0965004216809888
-PCK1	0.583148947380073
-C3	-0.229405245486493
-BLOC1S2	-0.501156113973434
-LPAR5	-0.252012578774993
-ACAD11	0.484415314534294
-CALB1	-0.585051808236823
-GNG2	-0.514333881323537
-GRIN3A	-0.54737874801763
-BLNK	-0.23678687239484
-SMARCD1	-0.480222958914743
-ARMC9	0.512102956486084
-CX3CR1	-0.300766155352383
-SLC31A2	-0.502055753854611
-AGPAT3	-0.413409719893933
-EFNB3	-0.382400551167611
-ELMOD2	0.402518685883201
-PRKCG	-0.34345444223993
-LAPTM5	-0.136628457581106
-IQUB	0.562346209462303
-STAM	-0.566262263187017
-OR11A1	0.178234692397988
-ZDHHC9	-0.520488129277965
-C11orf9	-0.511135500492906
-KLF4	0.640024343756592
-SYCP2L	0.555576793235834
-C20orf112	-0.63210679508749
-AP3M1	-0.436291767005889
-ALMS1P	0.310301539060874
-GREM1	-0.101042197816266
-HLCS	-0.404869146774348
-CARNS1	-0.358503492948689
-TSHZ2	-0.370201532555949
-CDKN1A	0.37878581767329
-CNDP1	-0.387074241865627
-C1orf161	0.408555295769768
-DOK6	-0.552556377657443
-C12orf43	-0.345533858224805
-SIPA1L2	-0.469893969573457
-FLJ40712	0.248899115372987
-TREM2	0.326657235461902
-MS4A6A	0.333196279374371
-RASGRF1	0.18816869654076
-RNF26	-0.576816063125611
-C7orf68	0.551320218061987
-DPP7	0.601525547176648
-OMD	0.556147496355725
-SNAI2	-0.402803074931945
-COL21A1	0.475584827359055
-APBB1IP	-0.510593783545533
-PRKCQ	-0.625167167620313
-PDGFRA	-0.593141766545025
-SLCO2B1	-0.20664851085323
-LPCAT3	-0.457401881600448
-CD37	-0.225548512842192
-IRF8	-0.513003936776053
-CSF1R	-0.17710132121375
-CD74	0.0263995452022326
-CHI3L1	0.637898420604861
-SELPLG	-0.165789940031603
-CDH8	-0.544872582360693
-CXCL12	-0.350721988871356
-TOPBP1	-0.516846284550731
-SLC16A10	0.372816060474775
-PCDHB9	-0.583344609658305
-HLA-DRA	0.249881965203208
-OLR1	0.105145169714195
-ADORA3	0.352457579745827
-ALOX5AP	0.094898490604102
-HLA-DOA	0.0912244782358314
-ZNF519	0.242878217518759
-FCER1G	0.122597294910367
-MT1H	0.274901514766897
-MFSD2A	0.12726693788776
-AIF1	-0.0853762046815476
-CTSH	0.324179727747488
-C3AR1	0.00893654957093225
-FCGR2A	-0.0476956544487118
-CXCL16	0.0931434603948185
-EVI2B	-0.236921572611684
-BACE1	-0.616602739604107
-OR1E1	0.491889127463635
-CLK1	0.423619868541565
-FLJ13197	0.340321509869536
-WBP2NL	0.590401706468574
-UGT8	-0.444926073295334
-HSD17B14	0.614959487312916
-GRIK3	-0.628539434045017
-MT1G	0.569589804148072
-BAIAP3	0.50915236570152
-TJAP1	-0.211899568999271
-PIP4K2C	-0.546592244445733
-CAMK4	-0.62370886479691
-TMEM63A	-0.349108640870675
-CCDC45	0.470491672406875
-ERLIN1	-0.590064605968872
-ATP6V1F	0.31735684237396
-EPHB2	-0.492251103302591
-ANKRD11	-0.576352445468476
-PCDHB2	-0.56247030572076
-ACSL1	-0.580402201513607
-LGR5	-0.49666928921999
-PDE3B	0.561081934872393
-C1orf21	-0.433409479731833
-LRRTM1	-0.430851468978506
-GPR12	-0.285126298493215
-VSTM2A	-0.496505850586284
-ODZ1	-0.500803022233123
-CACNG2	-0.568038440978143
-SMPD3	-0.448297258958326
-SORBS2	-0.652515435812272
-DCAF7	-0.561122254419525
-GJD2	-0.500391756170096
-PEG10	-0.529984214958046
-A2M	-0.0956498395825097
-THRB	-0.278461084991876
-C11orf24	-0.519543924524242
-TFG	-0.340307925442264
-MAMLD1	-0.389582104545406
-ASPHD2	-0.44086160208266
-ANKRD37	0.644400268061014
-NCKAP1L	-0.38869429192758
-CAPN5	-0.568639095894228
-SERINC3	-0.473478678274642
-CEBPB	0.386715054596765
-PRDM10	-0.575525391963737
-HCN1	-0.384931312491389
-CAMTA1	-0.435666315274373
-KLHDC1	0.27598504319864
-DUSP1	0.576414053338242
-QRICH1	-0.533552393948272
-SH3KBP1	-0.391446975914019
-EBF1	-0.379385913897609
-PPP1R16B	-0.356903880861572
-BTBD3	-0.327196312551472
-NRXN2	-0.509283550099326
-KAZ	-0.541421535478964
-KIAA0317	-0.636085461640037
-NDST3	-0.426753877235142
-GMCL1	0.45632888308336
-P2RX5	-0.283914132520413
-IGFL3	0.297606727720448
-LOC286161	-0.366837279825892
-PLEKHM1	-0.408702703852517
-RIMS1	-0.372721943202267
-UBE2Q2P1	0.327173892822723
-TTYH2	-0.407525904378876
-DES	0.06209856553185
-DBNDD2	-0.30225683329951
-ENPP2	-0.409429156664166
-NTN4	0.494337823155339
-SUN2	-0.276353435973038
-ACTG2	-0.210220455726459
-CA2	-0.0242596436213912
-THBS1	-0.221580234422776
-LDLRAD3	-0.360622764104025
-SNX1	-0.0377961368749078
-ERBB3	-0.405973590470433
-TTN	0.391623015044573
-ATRN	-0.52540142288716
-NPC1	-0.267674240960311
-GNS	-0.181466206971045
-KLK6	-0.378431280290618
-FOS	0.360516377902882
-CD69	0.377148542537053
-LYVE1	0.138789282779698
-FTL	0.237591315022414
-JUNB	0.394473562572383
-GSTM5	0.217560993654354
-NR4A1	0.24427289755837
-PGAM2	0.551801840506397
-TMEM176A	0.537931366670412
-EGR1	-0.157019974633097
-GPR183	0.107180842069747
-CXCL11	0.395003724312407
-PLA2G12A	-0.18246216314499
-HLA-DMB	0.229795197318716
-CPNE8	0.0508489313725271
-ZFP36	0.42538436064968
-AGPAT4	-0.467855141787709
-HLA-DPA1	0.408536378107808
-PIK3C2B	-0.591780318571167
-CPNE6	-0.271576531727541
-PLD3	-0.200022062788495
-PVRL1	-0.555155906198138
-GGCT	-0.279243242312552
-P2RY13	-0.360442360434042
-CNTN5	0.00258913839174191
-MCM7	0.195233154899312
-GPR120	-0.199692500084005
-GABRE	0.0682190440098052
-LRRC39	0.498683033772744
-TLR7	-0.164697853025215
-RFC3	-0.486755240432686
-CD33	0.00184280522373291
-CA8	0.363290764959567
-MAS1	-0.492009752548035
-FBLN5	-0.511286958021381
-TMTC1	-0.332133706392934
-C1orf51	0.45497717618641
-RPL35	-0.0899084146126614
-DKK2	-0.38611669080376
-USP53	0.412868805138869
-CD177	-0.217675402988493
-ELAVL1	-0.579547221944692
-AIFM3	0.577935690502709
-ASCL1	0.37568323074867
-EXPH5	-0.575008199569129
-CBWD3	0.283287779368243
-PEPD	-0.0553830875558683
-GPNMB	0.364500938005497
-NEDD4L	-0.508710397589902
-CALB2	-0.425755713683833
-FAM49A	-0.447197463197697
-NT5DC3	-0.265234061560778
-HES6	0.347000889525298
-GDA	-0.336613721691585
-RASAL1	-0.344295261121664
-ANO3	-0.518790055621458
-C14orf145	0.508493948450919
-MSRB3	0.374050410076754
-CC2D2B	0.438851338613457
-FAM65B	-0.254284575986291
-KIRREL3	-0.539616579176257
-CKLF	0.222793814048359
-DNAJA4	-0.486836211576555
-BCOR	-0.579019889055718
-CBLL1	-0.642779519205918
-CACNG3	-0.428582206819538
-GRIN2B	-0.577739683994275
-LRRC67	0.341366642004448
-RELL2	0.405916058000189
-NUDT3	-0.340375787654433
-MAST2	-0.541618527665053
-S100A10	-0.105037624066791
-OR13C2	0.379430219617317
-HSPC157	0.570528832119166
-NOP10	0.322245514370384
-C6orf174	-0.338629613564291
-LRRC61	0.0251744454575518
-FOLR2	0.131043427693804
-DYRK2	-0.522163896119695
-CALHM2	0.169628414381558
-CST7	0.313658960797421
-DUSP7	-0.523627393294567
-MTMR10	-0.415446285885383
-PPM1G	-0.464776264617981
-ADCY1	-0.454137407761092
-RPL13	0.506459486318965
-RRN3P1	0.525814578931781
-CXCL2	0.3672098081501
-RXRG	0.0402026385616925
-SRGN	0.531671866088554
-HIST1H2AE	0.293542472070096
-CYP2B6	0.275105405791745
-HHIP	-0.466578712584274
-KIAA1324L	-0.40123393199988
-FLJ90757	-0.507490069062372
-MYT1L	-0.584482026813831
-EIF2C2	-0.484852873283777
-NKAIN2	-0.549382635628517
-EIF2AK2	-0.489504988062896
-KIF21A	-0.359563932905791
-CCT6A	-0.177223944265096
-CDV3	-0.391589063759768
-HIVEP2	-0.600071683037855
-SPATA1	0.543060390879784
-FKBP11	-0.615494036116273
-NDST1	-0.475889745275566
-ARHGEF10	-0.250541551205642
-ZHX1	0.482981433720838
-SLC10A7	-0.337979122832437
-JAKMIP2	-0.415964197082499
-NAV1	-0.510622036406541
-NDUFB2	0.377202661234421
-ZNF507	-0.468104205569414
-MGAT2	0.222876912868186
-TTR	0.346175361449992
-EPB41L3	-0.411485674977879
-CNTNAP2	-0.327376463196595
-HNRNPU	-0.346139332150707
-ZNRD1	0.194397447066282
-PMF1	0.232524370350156
-TNFRSF21	-0.387936336469165
-KCNB1	-0.405472129261546
-FOXG1	-0.471157786135538
-S100A13	0.557308910766736
-BRD4	-0.517114201471415
-TIGD6	0.442112009917649
-RSPH9	0.182331610189591
-RGS20	0.417845235693366
-ASAP1	-0.536170937682141
-SLC7A14	-0.280031937135622
-MGAT3	-0.448766981367882
-IFITM4P	0.485622606827836
-SFRS15	-0.542060168583627
-PITPNM3	-0.42639997101521
-PTPRE	-0.530218005259195
-ZEB1	-0.477757026844139
-KCNQ3	-0.429926385373833
-CRB1	0.536038063001376
-MAPT	-0.50877997133818
-ABCA3	-0.360772553926051
-NPAS2	-0.419863325483148
-CLIC2	0.498878325957547
-LARP1	-0.49884819681315
-NLGN2	-0.429454573027551
-ALS2CR11	0.294226279272528
-NAP1L2	-0.313096105976879
-SLIT1	-0.434411983489453
-PHB	0.00979800238909777
-ZNF587	-0.0136127665384343
-STRN4	-0.576565248356412
-DSCAML1	-0.596992679910324
-MBD2	-0.20298332637123
-CENPQ	0.422898511661338
-PHF10	0.395502631449537
-MAP3K9	-0.405184359146696
-XRCC1	-0.370898065524857
-AKR1C3	0.453192387807177
-TTC29	0.290819126414233
-ISG20L2	-0.428905666986556
-TMEM165	0.492824884935657
-C2CD3	-0.514182826428327
-DPP4	0.23910770529895
-CCDC92	-0.53622071697372
-EXT1	-0.382555479091514
-C1QL2	-0.201706565681442
-ABHD2	-0.301021168563018
-SMURF1	-0.635507196661467
-CSNK1G2	-0.414657842955022
-TSPO	0.312759943492922
-EFEMP1	0.418307207101287
-HIST1H2BC	0.155466056856681
-CACNA1G	-0.603776648047605
-FCGRT	0.35186075288181
-OR6N2	0.19188744379883
-LILRA4	0.402116115371683
-GRIA1	-0.509922904695054
-HOXD8	0.311094779788594
-UPP1	0.48025126950744
-C17orf88	0.245494799347336
-MKL2	-0.495926848441475
-TAB3	-0.397855481558619
-KRTAP19-5	0.333726211690568
-PCDHB3	-0.42089893790206
-KLRF1	0.238176912312437
-TLR4	0.293561440425403
-SEPT14	0.268206811480962
-BSN	-0.301460000103249
-GRLF1	-0.466342462809911
-C1orf61	0.409705166908955
-GSTM1	0.580671376408388
-SDCCAG3	0.339086319326061
-NHLH2	0.264436125619991
-CRTC1	-0.364358124950179
-ZNF701	0.262422484025346
-FTO	-0.484606564596535
-KIAA0430	-0.323429860829196
-HPSE2	0.444523469491999
-AAK1	-0.336960928171931
-ZNF592	-0.459711729876906
-INF2	-0.368727716463355
-UNC80	-0.203435560684691
-KCNJ9	-0.385326074668389
-CREBBP	-0.48479916887186
-TMEM187	0.353577074222219
-GIMAP6	0.196334054611495
-MSH4	0.495021650163618
-CYP2F1	-0.202379731783218
-WARS	-0.36956071999387
-EIF4H	-0.324258084689287
-LMF1	-0.465196534142832
-SLC9A11	0.380530864151023
-RPLP0	0.401187575431913
-SORCS3	-0.524716179920174
-SMPD1	-0.371378049257817
-MLL2	-0.382849048834827
-ACTA2	-0.351473562308814
-CD84	0.0440334284755635
-LRRC57	-0.0868790230732024
-ADAM28	-0.234050278113392
-FLJ37543	0.329929076805089
-NR4A2	-0.525703760298336
-METT11D1	0.315411883405057
-MEX3C	-0.570394569556345
-ST8SIA5	-0.525318796364569
-HRH1	-0.276472654345764
-RAB3IP	-0.23897971786832
-ETV6	-0.448657117826825
-LUZP2	-0.409590511647277
-TRIM44	-0.386063986999447
-MYH11	-0.280352372336459
-TPK1	0.485143439818794
-C1QC	-0.0250872517448672
-A2ML1	0.356485052871728
-ZNF365	0.476040462817264
-CCL2	0.160044975309114
-ADRA2A	-0.511689669158592
-TMPRSS5	0.299973105357606
-C5orf53	0.490994640268981
-MORC2	-0.41225212616417
+name	value
+ELMO2	-0.547404913905166
+RGS1	0.664905640201586
+GSTT1	-0.630503181260422
+SDPR	0.576954531502211
+KCNJ2	-0.389733143810031
+DLG2	-0.622560222549952
+C2orf46	0.306481308387015
+YPEL1	-0.110679998012662
+AFF2	-0.580887248407995
+TCP11L2	-0.446138772716671
+TYROBP	0.0965004216809888
+PCK1	0.583148947380073
+C3	-0.229405245486493
+BLOC1S2	-0.501156113973434
+LPAR5	-0.252012578774993
+ACAD11	0.484415314534294
+CALB1	-0.585051808236823
+GNG2	-0.514333881323537
+GRIN3A	-0.54737874801763
+BLNK	-0.23678687239484
+SMARCD1	-0.480222958914743
+ARMC9	0.512102956486084
+CX3CR1	-0.300766155352383
+SLC31A2	-0.502055753854611
+AGPAT3	-0.413409719893933
+EFNB3	-0.382400551167611
+ELMOD2	0.402518685883201
+PRKCG	-0.34345444223993
+LAPTM5	-0.136628457581106
+IQUB	0.562346209462303
+STAM	-0.566262263187017
+OR11A1	0.178234692397988
+ZDHHC9	-0.520488129277965
+C11orf9	-0.511135500492906
+KLF4	0.640024343756592
+SYCP2L	0.555576793235834
+C20orf112	-0.63210679508749
+AP3M1	-0.436291767005889
+ALMS1P	0.310301539060874
+GREM1	-0.101042197816266
+HLCS	-0.404869146774348
+CARNS1	-0.358503492948689
+TSHZ2	-0.370201532555949
+CDKN1A	0.37878581767329
+CNDP1	-0.387074241865627
+C1orf161	0.408555295769768
+DOK6	-0.552556377657443
+C12orf43	-0.345533858224805
+SIPA1L2	-0.469893969573457
+FLJ40712	0.248899115372987
+TREM2	0.326657235461902
+MS4A6A	0.333196279374371
+RASGRF1	0.18816869654076
+RNF26	-0.576816063125611
+C7orf68	0.551320218061987
+DPP7	0.601525547176648
+OMD	0.556147496355725
+SNAI2	-0.402803074931945
+COL21A1	0.475584827359055
+APBB1IP	-0.510593783545533
+PRKCQ	-0.625167167620313
+PDGFRA	-0.593141766545025
+SLCO2B1	-0.20664851085323
+LPCAT3	-0.457401881600448
+CD37	-0.225548512842192
+IRF8	-0.513003936776053
+CSF1R	-0.17710132121375
+CD74	0.0263995452022326
+CHI3L1	0.637898420604861
+SELPLG	-0.165789940031603
+CDH8	-0.544872582360693
+CXCL12	-0.350721988871356
+TOPBP1	-0.516846284550731
+SLC16A10	0.372816060474775
+PCDHB9	-0.583344609658305
+HLA-DRA	0.249881965203208
+OLR1	0.105145169714195
+ADORA3	0.352457579745827
+ALOX5AP	0.094898490604102
+HLA-DOA	0.0912244782358314
+ZNF519	0.242878217518759
+FCER1G	0.122597294910367
+MT1H	0.274901514766897
+MFSD2A	0.12726693788776
+AIF1	-0.0853762046815476
+CTSH	0.324179727747488
+C3AR1	0.00893654957093225
+FCGR2A	-0.0476956544487118
+CXCL16	0.0931434603948185
+EVI2B	-0.236921572611684
+BACE1	-0.616602739604107
+OR1E1	0.491889127463635
+CLK1	0.423619868541565
+FLJ13197	0.340321509869536
+WBP2NL	0.590401706468574
+UGT8	-0.444926073295334
+HSD17B14	0.614959487312916
+GRIK3	-0.628539434045017
+MT1G	0.569589804148072
+BAIAP3	0.50915236570152
+TJAP1	-0.211899568999271
+PIP4K2C	-0.546592244445733
+CAMK4	-0.62370886479691
+TMEM63A	-0.349108640870675
+CCDC45	0.470491672406875
+ERLIN1	-0.590064605968872
+ATP6V1F	0.31735684237396
+EPHB2	-0.492251103302591
+ANKRD11	-0.576352445468476
+PCDHB2	-0.56247030572076
+ACSL1	-0.580402201513607
+LGR5	-0.49666928921999
+PDE3B	0.561081934872393
+C1orf21	-0.433409479731833
+LRRTM1	-0.430851468978506
+GPR12	-0.285126298493215
+VSTM2A	-0.496505850586284
+ODZ1	-0.500803022233123
+CACNG2	-0.568038440978143
+SMPD3	-0.448297258958326
+SORBS2	-0.652515435812272
+DCAF7	-0.561122254419525
+GJD2	-0.500391756170096
+PEG10	-0.529984214958046
+A2M	-0.0956498395825097
+THRB	-0.278461084991876
+C11orf24	-0.519543924524242
+TFG	-0.340307925442264
+MAMLD1	-0.389582104545406
+ASPHD2	-0.44086160208266
+ANKRD37	0.644400268061014
+NCKAP1L	-0.38869429192758
+CAPN5	-0.568639095894228
+SERINC3	-0.473478678274642
+CEBPB	0.386715054596765
+PRDM10	-0.575525391963737
+HCN1	-0.384931312491389
+CAMTA1	-0.435666315274373
+KLHDC1	0.27598504319864
+DUSP1	0.576414053338242
+QRICH1	-0.533552393948272
+SH3KBP1	-0.391446975914019
+EBF1	-0.379385913897609
+PPP1R16B	-0.356903880861572
+BTBD3	-0.327196312551472
+NRXN2	-0.509283550099326
+KAZ	-0.541421535478964
+KIAA0317	-0.636085461640037
+NDST3	-0.426753877235142
+GMCL1	0.45632888308336
+P2RX5	-0.283914132520413
+IGFL3	0.297606727720448
+LOC286161	-0.366837279825892
+PLEKHM1	-0.408702703852517
+RIMS1	-0.372721943202267
+UBE2Q2P1	0.327173892822723
+TTYH2	-0.407525904378876
+DES	0.06209856553185
+DBNDD2	-0.30225683329951
+ENPP2	-0.409429156664166
+NTN4	0.494337823155339
+SUN2	-0.276353435973038
+ACTG2	-0.210220455726459
+CA2	-0.0242596436213912
+THBS1	-0.221580234422776
+LDLRAD3	-0.360622764104025
+SNX1	-0.0377961368749078
+ERBB3	-0.405973590470433
+TTN	0.391623015044573
+ATRN	-0.52540142288716
+NPC1	-0.267674240960311
+GNS	-0.181466206971045
+KLK6	-0.378431280290618
+FOS	0.360516377902882
+CD69	0.377148542537053
+LYVE1	0.138789282779698
+FTL	0.237591315022414
+JUNB	0.394473562572383
+GSTM5	0.217560993654354
+NR4A1	0.24427289755837
+PGAM2	0.551801840506397
+TMEM176A	0.537931366670412
+EGR1	-0.157019974633097
+GPR183	0.107180842069747
+CXCL11	0.395003724312407
+PLA2G12A	-0.18246216314499
+HLA-DMB	0.229795197318716
+CPNE8	0.0508489313725271
+ZFP36	0.42538436064968
+AGPAT4	-0.467855141787709
+HLA-DPA1	0.408536378107808
+PIK3C2B	-0.591780318571167
+CPNE6	-0.271576531727541
+PLD3	-0.200022062788495
+PVRL1	-0.555155906198138
+GGCT	-0.279243242312552
+P2RY13	-0.360442360434042
+CNTN5	0.00258913839174191
+MCM7	0.195233154899312
+GPR120	-0.199692500084005
+GABRE	0.0682190440098052
+LRRC39	0.498683033772744
+TLR7	-0.164697853025215
+RFC3	-0.486755240432686
+CD33	0.00184280522373291
+CA8	0.363290764959567
+MAS1	-0.492009752548035
+FBLN5	-0.511286958021381
+TMTC1	-0.332133706392934
+C1orf51	0.45497717618641
+RPL35	-0.0899084146126614
+DKK2	-0.38611669080376
+USP53	0.412868805138869
+CD177	-0.217675402988493
+ELAVL1	-0.579547221944692
+AIFM3	0.577935690502709
+ASCL1	0.37568323074867
+EXPH5	-0.575008199569129
+CBWD3	0.283287779368243
+PEPD	-0.0553830875558683
+GPNMB	0.364500938005497
+NEDD4L	-0.508710397589902
+CALB2	-0.425755713683833
+FAM49A	-0.447197463197697
+NT5DC3	-0.265234061560778
+HES6	0.347000889525298
+GDA	-0.336613721691585
+RASAL1	-0.344295261121664
+ANO3	-0.518790055621458
+C14orf145	0.508493948450919
+MSRB3	0.374050410076754
+CC2D2B	0.438851338613457
+FAM65B	-0.254284575986291
+KIRREL3	-0.539616579176257
+CKLF	0.222793814048359
+DNAJA4	-0.486836211576555
+BCOR	-0.579019889055718
+CBLL1	-0.642779519205918
+CACNG3	-0.428582206819538
+GRIN2B	-0.577739683994275
+LRRC67	0.341366642004448
+RELL2	0.405916058000189
+NUDT3	-0.340375787654433
+MAST2	-0.541618527665053
+S100A10	-0.105037624066791
+OR13C2	0.379430219617317
+HSPC157	0.570528832119166
+NOP10	0.322245514370384
+C6orf174	-0.338629613564291
+LRRC61	0.0251744454575518
+FOLR2	0.131043427693804
+DYRK2	-0.522163896119695
+CALHM2	0.169628414381558
+CST7	0.313658960797421
+DUSP7	-0.523627393294567
+MTMR10	-0.415446285885383
+PPM1G	-0.464776264617981
+ADCY1	-0.454137407761092
+RPL13	0.506459486318965
+RRN3P1	0.525814578931781
+CXCL2	0.3672098081501
+RXRG	0.0402026385616925
+SRGN	0.531671866088554
+HIST1H2AE	0.293542472070096
+CYP2B6	0.275105405791745
+HHIP	-0.466578712584274
+KIAA1324L	-0.40123393199988
+FLJ90757	-0.507490069062372
+MYT1L	-0.584482026813831
+EIF2C2	-0.484852873283777
+NKAIN2	-0.549382635628517
+EIF2AK2	-0.489504988062896
+KIF21A	-0.359563932905791
+CCT6A	-0.177223944265096
+CDV3	-0.391589063759768
+HIVEP2	-0.600071683037855
+SPATA1	0.543060390879784
+FKBP11	-0.615494036116273
+NDST1	-0.475889745275566
+ARHGEF10	-0.250541551205642
+ZHX1	0.482981433720838
+SLC10A7	-0.337979122832437
+JAKMIP2	-0.415964197082499
+NAV1	-0.510622036406541
+NDUFB2	0.377202661234421
+ZNF507	-0.468104205569414
+MGAT2	0.222876912868186
+TTR	0.346175361449992
+EPB41L3	-0.411485674977879
+CNTNAP2	-0.327376463196595
+HNRNPU	-0.346139332150707
+ZNRD1	0.194397447066282
+PMF1	0.232524370350156
+TNFRSF21	-0.387936336469165
+KCNB1	-0.405472129261546
+FOXG1	-0.471157786135538
+S100A13	0.557308910766736
+BRD4	-0.517114201471415
+TIGD6	0.442112009917649
+RSPH9	0.182331610189591
+RGS20	0.417845235693366
+ASAP1	-0.536170937682141
+SLC7A14	-0.280031937135622
+MGAT3	-0.448766981367882
+IFITM4P	0.485622606827836
+SFRS15	-0.542060168583627
+PITPNM3	-0.42639997101521
+PTPRE	-0.530218005259195
+ZEB1	-0.477757026844139
+KCNQ3	-0.429926385373833
+CRB1	0.536038063001376
+MAPT	-0.50877997133818
+ABCA3	-0.360772553926051
+NPAS2	-0.419863325483148
+CLIC2	0.498878325957547
+LARP1	-0.49884819681315
+NLGN2	-0.429454573027551
+ALS2CR11	0.294226279272528
+NAP1L2	-0.313096105976879
+SLIT1	-0.434411983489453
+PHB	0.00979800238909777
+ZNF587	-0.0136127665384343
+STRN4	-0.576565248356412
+DSCAML1	-0.596992679910324
+MBD2	-0.20298332637123
+CENPQ	0.422898511661338
+PHF10	0.395502631449537
+MAP3K9	-0.405184359146696
+XRCC1	-0.370898065524857
+AKR1C3	0.453192387807177
+TTC29	0.290819126414233
+ISG20L2	-0.428905666986556
+TMEM165	0.492824884935657
+C2CD3	-0.514182826428327
+DPP4	0.23910770529895
+CCDC92	-0.53622071697372
+EXT1	-0.382555479091514
+C1QL2	-0.201706565681442
+ABHD2	-0.301021168563018
+SMURF1	-0.635507196661467
+CSNK1G2	-0.414657842955022
+TSPO	0.312759943492922
+EFEMP1	0.418307207101287
+HIST1H2BC	0.155466056856681
+CACNA1G	-0.603776648047605
+FCGRT	0.35186075288181
+OR6N2	0.19188744379883
+LILRA4	0.402116115371683
+GRIA1	-0.509922904695054
+HOXD8	0.311094779788594
+UPP1	0.48025126950744
+C17orf88	0.245494799347336
+MKL2	-0.495926848441475
+TAB3	-0.397855481558619
+KRTAP19-5	0.333726211690568
+PCDHB3	-0.42089893790206
+KLRF1	0.238176912312437
+TLR4	0.293561440425403
+SEPT14	0.268206811480962
+BSN	-0.301460000103249
+GRLF1	-0.466342462809911
+C1orf61	0.409705166908955
+GSTM1	0.580671376408388
+SDCCAG3	0.339086319326061
+NHLH2	0.264436125619991
+CRTC1	-0.364358124950179
+ZNF701	0.262422484025346
+FTO	-0.484606564596535
+KIAA0430	-0.323429860829196
+HPSE2	0.444523469491999
+AAK1	-0.336960928171931
+ZNF592	-0.459711729876906
+INF2	-0.368727716463355
+UNC80	-0.203435560684691
+KCNJ9	-0.385326074668389
+CREBBP	-0.48479916887186
+TMEM187	0.353577074222219
+GIMAP6	0.196334054611495
+MSH4	0.495021650163618
+CYP2F1	-0.202379731783218
+WARS	-0.36956071999387
+EIF4H	-0.324258084689287
+LMF1	-0.465196534142832
+SLC9A11	0.380530864151023
+RPLP0	0.401187575431913
+SORCS3	-0.524716179920174
+SMPD1	-0.371378049257817
+MLL2	-0.382849048834827
+ACTA2	-0.351473562308814
+CD84	0.0440334284755635
+LRRC57	-0.0868790230732024
+ADAM28	-0.234050278113392
+FLJ37543	0.329929076805089
+NR4A2	-0.525703760298336
+METT11D1	0.315411883405057
+MEX3C	-0.570394569556345
+ST8SIA5	-0.525318796364569
+HRH1	-0.276472654345764
+RAB3IP	-0.23897971786832
+ETV6	-0.448657117826825
+LUZP2	-0.409590511647277
+TRIM44	-0.386063986999447
+MYH11	-0.280352372336459
+TPK1	0.485143439818794
+C1QC	-0.0250872517448672
+A2ML1	0.356485052871728
+ZNF365	0.476040462817264
+CCL2	0.160044975309114
+ADRA2A	-0.511689669158592
+TMPRSS5	0.299973105357606
+C5orf53	0.490994640268981
+MORC2	-0.41225212616417
diff --git a/converter-CellDesigner/src/test/resources/log4j.properties b/converter-CellDesigner/src/test/resources/log4j.properties
index c749802b0e..28f78fc187 100644
--- a/converter-CellDesigner/src/test/resources/log4j.properties
+++ b/converter-CellDesigner/src/test/resources/log4j.properties
@@ -1,21 +1,21 @@
-#Set root logger 's level and its appender to an appender called CONSOLE which is defined below.
-log4j.rootLogger=info, CONSOLE, R
-
-#Set the behavior of the CONSOLE appender 
-log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
-log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
-log4j.appender.CONSOLE.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
-#log4j.appender.CONSOLE.layout.ConversionPattern=%m%n
-
-
-#Set the behavior of the FILE appender 
-log4j.appender.R=org.apache.log4j.FileAppender
-log4j.appender.R.File=${catalina.home}/logs/MapViewer.log
-log4j.appender.R.layout=org.apache.log4j.PatternLayout
-log4j.appender.R.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
-
-
-log4j.logger.org.springframework=warn
-log4j.logger.org.hibernate=warn
-log4j.logger.lcsb=debug
-log4j.logger.lcsb.mapviewer.common.comparator=info
+#Set root logger 's level and its appender to an appender called CONSOLE which is defined below.
+log4j.rootLogger=info, CONSOLE, R
+
+#Set the behavior of the CONSOLE appender 
+log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
+log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
+log4j.appender.CONSOLE.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
+#log4j.appender.CONSOLE.layout.ConversionPattern=%m%n
+
+
+#Set the behavior of the FILE appender 
+log4j.appender.R=org.apache.log4j.FileAppender
+log4j.appender.R.File=${catalina.home}/logs/MapViewer.log
+log4j.appender.R.layout=org.apache.log4j.PatternLayout
+log4j.appender.R.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
+
+
+log4j.logger.org.springframework=warn
+log4j.logger.org.hibernate=warn
+log4j.logger.lcsb=debug
+log4j.logger.lcsb.mapviewer.common.comparator=info
diff --git a/converter-CellDesigner/testFiles/annotation/invalid_rdf.xml b/converter-CellDesigner/testFiles/annotation/invalid_rdf.xml
index 11bcfac129..b2e5fb5e7d 100644
--- a/converter-CellDesigner/testFiles/annotation/invalid_rdf.xml
+++ b/converter-CellDesigner/testFiles/annotation/invalid_rdf.xml
@@ -1,2 +1,2 @@
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
 </rdf:RDF>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/annotation/invalid_rdf2.xml b/converter-CellDesigner/testFiles/annotation/invalid_rdf2.xml
index df2d68b495..5e21af6c7d 100644
--- a/converter-CellDesigner/testFiles/annotation/invalid_rdf2.xml
+++ b/converter-CellDesigner/testFiles/annotation/invalid_rdf2.xml
@@ -1,10 +1,10 @@
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#re836">
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li/>
-<rdf:li rdf:resource="urn:miriam:pubmed:15639314"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-</rdf:Description>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#re836">
+<bqbiol:isVersionOf>
+<rdf:Bag>
+<rdf:li/>
+<rdf:li rdf:resource="urn:miriam:pubmed:15639314"/>
+</rdf:Bag>
+</bqbiol:isVersionOf>
+</rdf:Description>
 </rdf:RDF>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/annotation/invalid_rdf3.xml b/converter-CellDesigner/testFiles/annotation/invalid_rdf3.xml
index 6e67e05da3..225ad4bb56 100644
--- a/converter-CellDesigner/testFiles/annotation/invalid_rdf3.xml
+++ b/converter-CellDesigner/testFiles/annotation/invalid_rdf3.xml
@@ -1,10 +1,10 @@
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#re836">
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn"/>
-<rdf:li rdf:resource="urn:miriam:pubmed:15639314"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-</rdf:Description>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#re836">
+<bqbiol:isVersionOf>
+<rdf:Bag>
+<rdf:li rdf:resource="urn"/>
+<rdf:li rdf:resource="urn:miriam:pubmed:15639314"/>
+</rdf:Bag>
+</bqbiol:isVersionOf>
+</rdf:Description>
 </rdf:RDF>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/annotation/invalid_rdf4.xml b/converter-CellDesigner/testFiles/annotation/invalid_rdf4.xml
index cbdc94e696..b94751fdf0 100644
--- a/converter-CellDesigner/testFiles/annotation/invalid_rdf4.xml
+++ b/converter-CellDesigner/testFiles/annotation/invalid_rdf4.xml
@@ -1,9 +1,9 @@
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#re836">
-<bqbiol:unk>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A28870"/>
-</rdf:Bag>
-</bqbiol:unk>
-</rdf:Description>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#re836">
+<bqbiol:unk>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A28870"/>
+</rdf:Bag>
+</bqbiol:unk>
+</rdf:Description>
 </rdf:RDF>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/antisense_rna.xml b/converter-CellDesigner/testFiles/invalid/antisense_rna.xml
index a8bbcd098c..16ee1973b9 100644
--- a/converter-CellDesigner/testFiles/invalid/antisense_rna.xml
+++ b/converter-CellDesigner/testFiles/invalid/antisense_rna.xml
@@ -1,16 +1,16 @@
-<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-some notes
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfRegions>
-<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="CodingRegion"/>
-<unk/>
-</celldesigner:listOfRegions>
+<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+some notes
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="CodingRegion"/>
+<unk/>
+</celldesigner:listOfRegions>
 </celldesigner:AntisenseRNA>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/antisense_rna2.xml b/converter-CellDesigner/testFiles/invalid/antisense_rna2.xml
index 5bed846e3d..8911982737 100644
--- a/converter-CellDesigner/testFiles/invalid/antisense_rna2.xml
+++ b/converter-CellDesigner/testFiles/invalid/antisense_rna2.xml
@@ -1,16 +1,16 @@
-<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
-<unk/>
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-some notes
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfRegions>
-<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="CodingRegion"/>
-</celldesigner:listOfRegions>
+<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
+<unk/>
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+some notes
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="CodingRegion"/>
+</celldesigner:listOfRegions>
 </celldesigner:AntisenseRNA>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/antisense_rna3.xml b/converter-CellDesigner/testFiles/invalid/antisense_rna3.xml
index 75a9bab434..6bf281a7fb 100644
--- a/converter-CellDesigner/testFiles/invalid/antisense_rna3.xml
+++ b/converter-CellDesigner/testFiles/invalid/antisense_rna3.xml
@@ -1,15 +1,15 @@
-<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-some notes
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfRegions>
-<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="unkBlaType"/>
-</celldesigner:listOfRegions>
+<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+some notes
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="unkBlaType"/>
+</celldesigner:listOfRegions>
 </celldesigner:AntisenseRNA>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/antisense_rna4.xml b/converter-CellDesigner/testFiles/invalid/antisense_rna4.xml
index 310a5b13d5..81c4083034 100644
--- a/converter-CellDesigner/testFiles/invalid/antisense_rna4.xml
+++ b/converter-CellDesigner/testFiles/invalid/antisense_rna4.xml
@@ -1,17 +1,17 @@
-<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-some notes
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfRegions>
-<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="CodingRegion">
-<unk/>
-</celldesigner:region>
-</celldesigner:listOfRegions>
+<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+some notes
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="CodingRegion">
+<unk/>
+</celldesigner:region>
+</celldesigner:listOfRegions>
 </celldesigner:AntisenseRNA>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/antisense_rna_collection.xml b/converter-CellDesigner/testFiles/invalid/antisense_rna_collection.xml
index fe47951f26..ad061bc48c 100644
--- a/converter-CellDesigner/testFiles/invalid/antisense_rna_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/antisense_rna_collection.xml
@@ -1,3 +1,3 @@
-<celldesigner:listOfAntisenseRNAs>
-<unknoen/>
+<celldesigner:listOfAntisenseRNAs>
+<unknoen/>
 </celldesigner:listOfAntisenseRNAs>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/block_diagrams.xml b/converter-CellDesigner/testFiles/invalid/block_diagrams.xml
index 8cbe9778ab..53f93e7b14 100644
--- a/converter-CellDesigner/testFiles/invalid/block_diagrams.xml
+++ b/converter-CellDesigner/testFiles/invalid/block_diagrams.xml
@@ -1,3 +1,3 @@
-<celldesigner:listOfBlockDiagrams>
-<unk_block/>
-</celldesigner:listOfBlockDiagrams>
+<celldesigner:listOfBlockDiagrams>
+<unk_block/>
+</celldesigner:listOfBlockDiagrams>
diff --git a/converter-CellDesigner/testFiles/invalid/compartment.xml b/converter-CellDesigner/testFiles/invalid/compartment.xml
index da48b5c4e5..d132817999 100644
--- a/converter-CellDesigner/testFiles/invalid/compartment.xml
+++ b/converter-CellDesigner/testFiles/invalid/compartment.xml
@@ -1,4 +1,4 @@
-<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
-<annotation_inv>
-</annotation_inv>
-</compartment>
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<annotation_inv>
+</annotation_inv>
+</compartment>
diff --git a/converter-CellDesigner/testFiles/invalid/compartment2.xml b/converter-CellDesigner/testFiles/invalid/compartment2.xml
index 81ee8645d5..b161a3d10c 100644
--- a/converter-CellDesigner/testFiles/invalid/compartment2.xml
+++ b/converter-CellDesigner/testFiles/invalid/compartment2.xml
@@ -1,8 +1,8 @@
-<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
-<annotation>
-<celldesigner:extension>
-<celldesigner:name>c1</celldesigner:name>
-</celldesigner:extension>
-<ins_inv/>
-</annotation>
-</compartment>
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c1</celldesigner:name>
+</celldesigner:extension>
+<ins_inv/>
+</annotation>
+</compartment>
diff --git a/converter-CellDesigner/testFiles/invalid/compartment3.xml b/converter-CellDesigner/testFiles/invalid/compartment3.xml
index 8b5b409563..438e87b6bd 100644
--- a/converter-CellDesigner/testFiles/invalid/compartment3.xml
+++ b/converter-CellDesigner/testFiles/invalid/compartment3.xml
@@ -1,8 +1,8 @@
-<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
-<annotation>
-<celldesigner:extension>
-<celldesigner:name>c1</celldesigner:name>
-<ext_inv/>
-</celldesigner:extension>
-</annotation>
-</compartment>
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c1</celldesigner:name>
+<ext_inv/>
+</celldesigner:extension>
+</annotation>
+</compartment>
diff --git a/converter-CellDesigner/testFiles/invalid/compartment_alias.xml b/converter-CellDesigner/testFiles/invalid/compartment_alias.xml
index e65eee095a..1d050e6d79 100644
--- a/converter-CellDesigner/testFiles/invalid/compartment_alias.xml
+++ b/converter-CellDesigner/testFiles/invalid/compartment_alias.xml
@@ -1,8 +1,8 @@
-<celldesigner:compartmentAlias id="ca1" compartment="c1">
-<celldesigner:class>UNKNOWN_TYPE_BLA</celldesigner:class>
-<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
-<celldesigner:namePoint x="392.5" y="196.5"/>
-<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
-<celldesigner:paint color="ffcccc00" scheme="Color"/>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>UNKNOWN_TYPE_BLA</celldesigner:class>
+<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
+<celldesigner:namePoint x="392.5" y="196.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
 </celldesigner:compartmentAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/compartment_alias2.xml b/converter-CellDesigner/testFiles/invalid/compartment_alias2.xml
index 24ad80ce5f..ee09c1e2e0 100644
--- a/converter-CellDesigner/testFiles/invalid/compartment_alias2.xml
+++ b/converter-CellDesigner/testFiles/invalid/compartment_alias2.xml
@@ -1,9 +1,9 @@
-<celldesigner:compartmentAlias id="ca1" compartment="c1">
-<celldesigner:class>SQUARE</celldesigner:class>
-<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
-<celldesigner:namePoint x="392.5" y="196.5"/>
-<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
-<celldesigner:paint color="ffcccc00" scheme="Color"/>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-<celldesigner:point/>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
+<celldesigner:namePoint x="392.5" y="196.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:point/>
 </celldesigner:compartmentAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/compartment_alias3.xml b/converter-CellDesigner/testFiles/invalid/compartment_alias3.xml
index 3a9634e094..3d56061e24 100644
--- a/converter-CellDesigner/testFiles/invalid/compartment_alias3.xml
+++ b/converter-CellDesigner/testFiles/invalid/compartment_alias3.xml
@@ -1,9 +1,9 @@
-<celldesigner:compartmentAlias id="ca1" compartment="c1">
-<unk_tag/>
-<celldesigner:class>SQUARE</celldesigner:class>
-<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
-<celldesigner:namePoint x="392.5" y="196.5"/>
-<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
-<celldesigner:paint color="ffcccc00" scheme="Color"/>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<unk_tag/>
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
+<celldesigner:namePoint x="392.5" y="196.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
 </celldesigner:compartmentAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/compartment_alias_collection.xml b/converter-CellDesigner/testFiles/invalid/compartment_alias_collection.xml
index 9d475028ce..09ceb78c35 100644
--- a/converter-CellDesigner/testFiles/invalid/compartment_alias_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/compartment_alias_collection.xml
@@ -1,27 +1,27 @@
-<celldesigner:listOfCompartmentAliases>
-<unk/>
-<celldesigner:compartmentAlias id="ca1" compartment="c1">
-<celldesigner:class>SQUARE</celldesigner:class>
-<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
-<celldesigner:namePoint x="392.5" y="196.5"/>
-<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
-<celldesigner:paint color="ffcccc00" scheme="Color"/>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:compartmentAlias>
-<celldesigner:compartmentAlias id="ca2" compartment="c2">
-<celldesigner:class>SQUARE</celldesigner:class>
-<celldesigner:bounds x="707.0" y="187.0" w="118.0" h="73.0"/>
-<celldesigner:namePoint x="758.5" y="223.5"/>
-<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
-<celldesigner:paint color="ffcccc00" scheme="Color"/>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:compartmentAlias>
-<celldesigner:compartmentAlias id="ca3" compartment="c3">
-<celldesigner:class>OVAL</celldesigner:class>
-<celldesigner:bounds x="185.0" y="143.0" w="86.0" h="50.0"/>
-<celldesigner:namePoint x="220.5" y="156.11618483532334"/>
-<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
-<celldesigner:paint color="ffcccc00" scheme="Color"/>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:compartmentAlias>
-</celldesigner:listOfCompartmentAliases>
+<celldesigner:listOfCompartmentAliases>
+<unk/>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
+<celldesigner:namePoint x="392.5" y="196.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+<celldesigner:compartmentAlias id="ca2" compartment="c2">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="707.0" y="187.0" w="118.0" h="73.0"/>
+<celldesigner:namePoint x="758.5" y="223.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+<celldesigner:compartmentAlias id="ca3" compartment="c3">
+<celldesigner:class>OVAL</celldesigner:class>
+<celldesigner:bounds x="185.0" y="143.0" w="86.0" h="50.0"/>
+<celldesigner:namePoint x="220.5" y="156.11618483532334"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+</celldesigner:listOfCompartmentAliases>
diff --git a/converter-CellDesigner/testFiles/invalid/complex_alias_collection.xml b/converter-CellDesigner/testFiles/invalid/complex_alias_collection.xml
index 9ee6cee1ef..4fbc36c284 100644
--- a/converter-CellDesigner/testFiles/invalid/complex_alias_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/complex_alias_collection.xml
@@ -1,66 +1,66 @@
-<celldesigner:listOfComplexSpeciesAliases>
-<unk/>
-<celldesigner:complexSpeciesAlias id="csa1" species="s2597">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="744.0" y="0.0" w="100.0" h="120.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="100.0" height="120.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
-<celldesigner:complexSpeciesAlias id="csa2" species="s2598">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="863.0" y="35.0" w="100.0" h="120.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="100.0" height="120.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
-<celldesigner:complexSpeciesAlias id="csa3" species="s2599" complexSpeciesAlias="csa1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="767.0" y="15.0" w="61.0" h="87.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="23.0" y="15.0"/>
-<celldesigner:boxSize width="61.0" height="87.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
-</celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:listOfComplexSpeciesAliases>
+<unk/>
+<celldesigner:complexSpeciesAlias id="csa1" species="s2597">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="744.0" y="0.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa2" species="s2598">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="863.0" y="35.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa3" species="s2599" complexSpeciesAlias="csa1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="767.0" y="15.0" w="61.0" h="87.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="23.0" y="15.0"/>
+<celldesigner:boxSize width="61.0" height="87.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+</celldesigner:listOfComplexSpeciesAliases>
diff --git a/converter-CellDesigner/testFiles/invalid/gene_collection.xml b/converter-CellDesigner/testFiles/invalid/gene_collection.xml
index 4633a9e50e..bc790db2e5 100644
--- a/converter-CellDesigner/testFiles/invalid/gene_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/gene_collection.xml
@@ -1,3 +1,3 @@
-<celldesigner:listOfGenes>
-<unkgenenode/>
+<celldesigner:listOfGenes>
+<unkgenenode/>
 </celldesigner:listOfGenes>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/group_collection.xml b/converter-CellDesigner/testFiles/invalid/group_collection.xml
index e9107f1b2f..27ec8b138a 100644
--- a/converter-CellDesigner/testFiles/invalid/group_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/group_collection.xml
@@ -1,4 +1,4 @@
-<celldesigner:listOfGroups>
-<invalid/>
-<celldesigner:group id="g1" members="sa1,sa2,sa3"/>
-</celldesigner:listOfGroups>
+<celldesigner:listOfGroups>
+<invalid/>
+<celldesigner:group id="g1" members="sa1,sa2,sa3"/>
+</celldesigner:listOfGroups>
diff --git a/converter-CellDesigner/testFiles/invalid/group_collection2.xml b/converter-CellDesigner/testFiles/invalid/group_collection2.xml
index 38bc03af63..85276ccffb 100644
--- a/converter-CellDesigner/testFiles/invalid/group_collection2.xml
+++ b/converter-CellDesigner/testFiles/invalid/group_collection2.xml
@@ -1,3 +1,3 @@
-<celldesigner:listOfGroups>
-<celldesigner:group id="g1" members="sa1,sa2,sa3"/>
-</celldesigner:listOfGroups>
+<celldesigner:listOfGroups>
+<celldesigner:group id="g1" members="sa1,sa2,sa3"/>
+</celldesigner:listOfGroups>
diff --git a/converter-CellDesigner/testFiles/invalid/group_collection3.xml b/converter-CellDesigner/testFiles/invalid/group_collection3.xml
index 26d55307dd..ccbce7c5e7 100644
--- a/converter-CellDesigner/testFiles/invalid/group_collection3.xml
+++ b/converter-CellDesigner/testFiles/invalid/group_collection3.xml
@@ -1,5 +1,5 @@
-<celldesigner:listOfGroups>
-<celldesigner:group id="g1" members="sa1">
-<x/>
-</celldesigner:group>
-</celldesigner:listOfGroups>
+<celldesigner:listOfGroups>
+<celldesigner:group id="g1" members="sa1">
+<x/>
+</celldesigner:group>
+</celldesigner:listOfGroups>
diff --git a/converter-CellDesigner/testFiles/invalid/included_species_collection.xml b/converter-CellDesigner/testFiles/invalid/included_species_collection.xml
index d070c64ad5..341460a27e 100644
--- a/converter-CellDesigner/testFiles/invalid/included_species_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/included_species_collection.xml
@@ -1,53 +1,53 @@
-<celldesigner:listOfIncludedSpecies>
-<celldesigner:species name="s10">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>COMPLEX</celldesigner:class>
-<celldesigner:name>s10</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
-<celldesigner:species id="s11" name="s11">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
-<celldesigner:species id="s12" name="s12">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s10</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species name="s10">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s10</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s11" name="s11">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s12" name="s12">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s10</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
 </celldesigner:listOfIncludedSpecies>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/included_species_collection2.xml b/converter-CellDesigner/testFiles/invalid/included_species_collection2.xml
index 046af22cb2..8c53aac2aa 100644
--- a/converter-CellDesigner/testFiles/invalid/included_species_collection2.xml
+++ b/converter-CellDesigner/testFiles/invalid/included_species_collection2.xml
@@ -1,46 +1,46 @@
-<celldesigner:listOfIncludedSpecies>
-<celldesigner:species id="s10" name="s10">
-<unk/>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>COMPLEX</celldesigner:class>
-<celldesigner:name>s10</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
-<celldesigner:species id="s11" name="s11">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
-<celldesigner:species id="s12" name="s12">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s10</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species id="s10" name="s10">
+<unk/>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s10</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s11" name="s11">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s12" name="s12">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s10</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
 </celldesigner:listOfIncludedSpecies>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/included_species_collection3.xml b/converter-CellDesigner/testFiles/invalid/included_species_collection3.xml
index 05595cc967..02212bf749 100644
--- a/converter-CellDesigner/testFiles/invalid/included_species_collection3.xml
+++ b/converter-CellDesigner/testFiles/invalid/included_species_collection3.xml
@@ -1,46 +1,46 @@
-<celldesigner:listOfIncludedSpecies>
-<celldesigner:species id="s10" name="s10">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-</celldesigner:species>
-<celldesigner:species id="s11" name="s11">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
-<celldesigner:species id="s12" name="s12">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s10</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species id="s10" name="s10">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+</celldesigner:species>
+<celldesigner:species id="s11" name="s11">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s12" name="s12">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s10</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
 </celldesigner:listOfIncludedSpecies>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/included_species_collection4.xml b/converter-CellDesigner/testFiles/invalid/included_species_collection4.xml
index d84317a77e..e737a6a6d6 100644
--- a/converter-CellDesigner/testFiles/invalid/included_species_collection4.xml
+++ b/converter-CellDesigner/testFiles/invalid/included_species_collection4.xml
@@ -1,15 +1,15 @@
-<celldesigner:listOfIncludedSpecies>
-<celldesigner:species id="s10" name="s10">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
-</celldesigner:annotation>
-</celldesigner:species>
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species id="s10" name="s10">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+</celldesigner:annotation>
+</celldesigner:species>
 </celldesigner:listOfIncludedSpecies>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/included_species_collection5.xml b/converter-CellDesigner/testFiles/invalid/included_species_collection5.xml
index 888aed4ed2..8a7a04567a 100644
--- a/converter-CellDesigner/testFiles/invalid/included_species_collection5.xml
+++ b/converter-CellDesigner/testFiles/invalid/included_species_collection5.xml
@@ -1,3 +1,3 @@
-<celldesigner:listOfIncludedSpecies>
-<unkTag/>
+<celldesigner:listOfIncludedSpecies>
+<unkTag/>
 </celldesigner:listOfIncludedSpecies>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/included_species_collection6.xml b/converter-CellDesigner/testFiles/invalid/included_species_collection6.xml
index f40ba39830..157626af26 100644
--- a/converter-CellDesigner/testFiles/invalid/included_species_collection6.xml
+++ b/converter-CellDesigner/testFiles/invalid/included_species_collection6.xml
@@ -1,14 +1,14 @@
-<celldesigner:listOfIncludedSpecies>
-<celldesigner:species id="s10" name="s10">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-</celldesigner:annotation>
-</celldesigner:species>
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species id="s10" name="s10">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+</celldesigner:annotation>
+</celldesigner:species>
 </celldesigner:listOfIncludedSpecies>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias.xml b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias.xml
index c14c5db903..ea5cb8370e 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias.xml
@@ -1,21 +1,21 @@
-<celldesigner:complexSpeciesAlias id="csa2" species="s3">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="151.0" height="221.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa2" species="s3">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="151.0" height="221.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias2.xml b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias2.xml
index a3464b72e9..da8f004bb3 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias2.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias2.xml
@@ -1,3 +1,3 @@
-<celldesigner:complexSpeciesAlias id="csa2" species="s3">
-<celldesigner:bla>inactive</celldesigner:bla>
-</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa2" species="s3">
+<celldesigner:bla>inactive</celldesigner:bla>
+</celldesigner:complexSpeciesAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias3.xml b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias3.xml
index 04c8b010b2..6f14d52022 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias3.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias3.xml
@@ -1,21 +1,21 @@
-<celldesigner:complexSpeciesAlias id="csa2" species="s3">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="unusual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="151.0" height="221.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa2" species="s3">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="unusual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="151.0" height="221.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias4.xml b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias4.xml
index 8350cc3625..721599b232 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias4.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias4.xml
@@ -1,21 +1,21 @@
-<celldesigner:complexSpeciesAlias id="csa2" species="s3">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="151.0" height="221.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="unkown state" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa2" species="s3">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="151.0" height="221.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="unkown state" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias5.xml b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias5.xml
index 292bba6e3d..8606089f47 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_complex_alias5.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_complex_alias5.xml
@@ -1,21 +1,21 @@
-<celldesigner:complexSpeciesAlias id="csa2" species="s3" compartmentAlias="ca">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="151.0" height="221.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa2" species="s3" compartmentAlias="ca">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="202.0" y="12.0" w="151.0" h="221.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="151.0" height="221.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_gene_1.xml b/converter-CellDesigner/testFiles/invalid/invalid_gene_1.xml
index 0bb0451dde..3a68590eaf 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_gene_1.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_gene_1.xml
@@ -1,3 +1,3 @@
-<celldesigner:gene id="gn3" name="BCL6" type="GENE">
-<celldesigner:bla/>
+<celldesigner:gene id="gn3" name="BCL6" type="GENE">
+<celldesigner:bla/>
 </celldesigner:gene>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_gene_2.xml b/converter-CellDesigner/testFiles/invalid/invalid_gene_2.xml
index 00244cc2b8..61ac67a16d 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_gene_2.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_gene_2.xml
@@ -1,6 +1,6 @@
-<celldesigner:gene id="gn3" name="BCL6" type="GENE">
-<celldesigner:listOfRegions>
-<html xmlns="http://www.w3.org/1999/xhtml">
-</html>
-</celldesigner:listOfRegions>
+<celldesigner:gene id="gn3" name="BCL6" type="GENE">
+<celldesigner:listOfRegions>
+<html xmlns="http://www.w3.org/1999/xhtml">
+</html>
+</celldesigner:listOfRegions>
 </celldesigner:gene>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_modification_residue.xml b/converter-CellDesigner/testFiles/invalid/invalid_modification_residue.xml
index b32104cee7..84fb68e6d0 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_modification_residue.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_modification_residue.xml
@@ -1,3 +1,3 @@
-<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla"  id="rs1" side="none">
-<bla/>
-</celldesigner:modificationResidue>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla"  id="rs1" side="none">
+<bla/>
+</celldesigner:modificationResidue>
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein.xml
index 586e73748d..e39cee0ea7 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein.xml
@@ -1,2 +1,2 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein10.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein10.xml
index 252648ee0b..786bd74c6d 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein10.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein10.xml
@@ -1,11 +1,11 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:class>GENE</celldesigner:class>
-<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein11.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein11.xml
index b40e452964..12881f9195 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein11.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein11.xml
@@ -1,11 +1,11 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:geneReference>pr1116</celldesigner:geneReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:geneReference>pr1116</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein12.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein12.xml
index b4c7076289..7ee1cdad8a 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein12.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein12.xml
@@ -1,11 +1,11 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:class>GENE</celldesigner:class>
-<celldesigner:rnaReference>pr1116</celldesigner:rnaReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:rnaReference>pr1116</celldesigner:rnaReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein13.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein13.xml
index 8da810b0fc..0fecf616ae 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein13.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein13.xml
@@ -1,12 +1,12 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:class>GENE</celldesigner:class>
-<celldesigner:hypothetical>true</celldesigner:hypothetical>
-<celldesigner:antisensernaReference>pr1116</celldesigner:antisensernaReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+<celldesigner:antisensernaReference>pr1116</celldesigner:antisensernaReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein14.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein14.xml
index 21ba7ba1aa..3239790cd5 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein14.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein14.xml
@@ -1,13 +1,13 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:class>GENE</celldesigner:class>
-<uknNode>GENE</uknNode>
-<celldesigner:hypothetical>true</celldesigner:hypothetical>
-<celldesigner:antisensernaReference>pr1116</celldesigner:antisensernaReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<uknNode>GENE</uknNode>
+<celldesigner:hypothetical>true</celldesigner:hypothetical>
+<celldesigner:antisensernaReference>pr1116</celldesigner:antisensernaReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein2.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein2.xml
index c2cf173e62..f8b124466d 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein2.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein2.xml
@@ -1,3 +1,3 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<bla/>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<bla/>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein3.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein3.xml
index 59b9da4168..effc0711a6 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein3.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein3.xml
@@ -1,5 +1,5 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<unk_bla/>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<unk_bla/>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein4.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein4.xml
index 4c00c684f8..a18cf28fd9 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein4.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein4.xml
@@ -1,4 +1,4 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein5.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein5.xml
index 833df09379..f991e46f1c 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein5.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein5.xml
@@ -1,7 +1,7 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<ann_unk/>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<ann_unk/>
+</celldesigner:extension>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein6.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein6.xml
index 9910d3a610..9d731baa24 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein6.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein6.xml
@@ -1,6 +1,6 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+</celldesigner:extension>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein7.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein7.xml
index 1ff2733782..a2acae126e 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein7.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein7.xml
@@ -1,11 +1,11 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein8.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein8.xml
index 132c8ff439..d42a079021 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein8.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein8.xml
@@ -1,10 +1,10 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein9.xml b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein9.xml
index fa5e0be439..0efef2fb1c 100644
--- a/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein9.xml
+++ b/converter-CellDesigner/testFiles/invalid/invalid_sbml_protein9.xml
@@ -1,11 +1,11 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:speciesIdentity>
-<celldesigner:class>unknown_protein_class</celldesigner:class>
-<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
-</celldesigner:extension>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:speciesIdentity>
+<celldesigner:class>unknown_protein_class</celldesigner:class>
+<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+<celldesigner:positionToCompartment>unkPos</celldesigner:positionToCompartment>
+</celldesigner:extension>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/layer.xml b/converter-CellDesigner/testFiles/invalid/layer.xml
index 8c6691cb42..d01e773294 100644
--- a/converter-CellDesigner/testFiles/invalid/layer.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer.xml
@@ -1,35 +1,35 @@
-<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
-<celldesigner:listOfTexts>
-<celldesigner:unkLayerSpeciesAlias2 />
-<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
-<celldesigner:layerNotes>
-text node
-</celldesigner:layerNotes>
-<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
-<celldesigner:paint color="ff000000"/>
-<celldesigner:font size="11"/>
-</celldesigner:layerSpeciesAlias>
-</celldesigner:listOfTexts>
-<celldesigner:listOfSquares>
-<celldesigner:layerCompartmentAlias type="Oval">
-<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-<celldesigner:layerCompartmentAlias type="Square">
-<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-</celldesigner:listOfSquares>
-<celldesigner:listOfFreeLines>
-<celldesigner:layerFreeLine isArrow="false" isDotted="false">
-<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-<celldesigner:layerFreeLine isArrow="true" isDotted="false">
-<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-</celldesigner:listOfFreeLines>
-</celldesigner:layer>
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:listOfTexts>
+<celldesigner:unkLayerSpeciesAlias2 />
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+<celldesigner:listOfSquares>
+<celldesigner:layerCompartmentAlias type="Oval">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+</celldesigner:listOfSquares>
+<celldesigner:listOfFreeLines>
+<celldesigner:layerFreeLine isArrow="false" isDotted="false">
+<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+</celldesigner:listOfFreeLines>
+</celldesigner:layer>
diff --git a/converter-CellDesigner/testFiles/invalid/layer2.xml b/converter-CellDesigner/testFiles/invalid/layer2.xml
index 88661cd0e0..34308d7f17 100644
--- a/converter-CellDesigner/testFiles/invalid/layer2.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer2.xml
@@ -1,34 +1,34 @@
-<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
-<celldesigner:listOfTexts>
-<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
-<celldesigner:layerNotes>
-text node
-</celldesigner:layerNotes>
-<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
-<celldesigner:paint color="ff000000"/>
-<celldesigner:font size="11"/>
-</celldesigner:layerSpeciesAlias>
-</celldesigner:listOfTexts>
-<celldesigner:listOfSquares>
-<celldesigner:layerCompartmentAlias type="Custom_Triangle">
-<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-<celldesigner:layerCompartmentAlias type="Square">
-<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-</celldesigner:listOfSquares>
-<celldesigner:listOfFreeLines>
-<celldesigner:layerFreeLine isArrow="false" isDotted="false">
-<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-<celldesigner:layerFreeLine isArrow="true" isDotted="false">
-<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-</celldesigner:listOfFreeLines>
-</celldesigner:layer>
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:listOfTexts>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+<celldesigner:listOfSquares>
+<celldesigner:layerCompartmentAlias type="Custom_Triangle">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+</celldesigner:listOfSquares>
+<celldesigner:listOfFreeLines>
+<celldesigner:layerFreeLine isArrow="false" isDotted="false">
+<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+</celldesigner:listOfFreeLines>
+</celldesigner:layer>
diff --git a/converter-CellDesigner/testFiles/invalid/layer3.xml b/converter-CellDesigner/testFiles/invalid/layer3.xml
index d2b37a8acb..37dd3a4f5a 100644
--- a/converter-CellDesigner/testFiles/invalid/layer3.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer3.xml
@@ -1,35 +1,35 @@
-<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
-<celldesigner:listOfTexts>
-<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
-<celldesigner:layerNotes>
-text node
-</celldesigner:layerNotes>
-<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
-<celldesigner:paint color="ff000000"/>
-<celldesigner:font size="11"/>
-</celldesigner:layerSpeciesAlias>
-</celldesigner:listOfTexts>
-<celldesigner:listOfSquares>
-<celldesigner:customLayerCompartmentAliasTag/>
-<celldesigner:layerCompartmentAlias type="Oval">
-<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-<celldesigner:layerCompartmentAlias type="Square">
-<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-</celldesigner:listOfSquares>
-<celldesigner:listOfFreeLines>
-<celldesigner:layerFreeLine isArrow="false" isDotted="false">
-<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-<celldesigner:layerFreeLine isArrow="true" isDotted="false">
-<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-</celldesigner:listOfFreeLines>
-</celldesigner:layer>
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:listOfTexts>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+<celldesigner:listOfSquares>
+<celldesigner:customLayerCompartmentAliasTag/>
+<celldesigner:layerCompartmentAlias type="Oval">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+</celldesigner:listOfSquares>
+<celldesigner:listOfFreeLines>
+<celldesigner:layerFreeLine isArrow="false" isDotted="false">
+<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+</celldesigner:listOfFreeLines>
+</celldesigner:layer>
diff --git a/converter-CellDesigner/testFiles/invalid/layer4.xml b/converter-CellDesigner/testFiles/invalid/layer4.xml
index 596a08d267..d02105499e 100644
--- a/converter-CellDesigner/testFiles/invalid/layer4.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer4.xml
@@ -1,35 +1,35 @@
-<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
-<celldesigner:listOfTexts>
-<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
-<celldesigner:layerNotes>
-text node
-</celldesigner:layerNotes>
-<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
-<celldesigner:paint color="ff000000"/>
-<celldesigner:font size="11"/>
-</celldesigner:layerSpeciesAlias>
-</celldesigner:listOfTexts>
-<celldesigner:listOfSquares>
-<celldesigner:layerCompartmentAlias type="Oval">
-<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-<celldesigner:layerCompartmentAlias type="Square">
-<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-</celldesigner:listOfSquares>
-<celldesigner:listOfFreeLines>
-<celldesigner:customLayerFreeLine isArrow="false" isDotted="false"/>
-<celldesigner:layerFreeLine isArrow="false" isDotted="false">
-<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-<celldesigner:layerFreeLine isArrow="true" isDotted="false">
-<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-</celldesigner:listOfFreeLines>
-</celldesigner:layer>
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:listOfTexts>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+<celldesigner:listOfSquares>
+<celldesigner:layerCompartmentAlias type="Oval">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+</celldesigner:listOfSquares>
+<celldesigner:listOfFreeLines>
+<celldesigner:customLayerFreeLine isArrow="false" isDotted="false"/>
+<celldesigner:layerFreeLine isArrow="false" isDotted="false">
+<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+</celldesigner:listOfFreeLines>
+</celldesigner:layer>
diff --git a/converter-CellDesigner/testFiles/invalid/layer5.xml b/converter-CellDesigner/testFiles/invalid/layer5.xml
index 215c1789b6..24fac76547 100644
--- a/converter-CellDesigner/testFiles/invalid/layer5.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer5.xml
@@ -1,35 +1,35 @@
-<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
-<customLayerTag/>
-<celldesigner:listOfTexts>
-<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
-<celldesigner:layerNotes>
-text node
-</celldesigner:layerNotes>
-<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
-<celldesigner:paint color="ff000000"/>
-<celldesigner:font size="11"/>
-</celldesigner:layerSpeciesAlias>
-</celldesigner:listOfTexts>
-<celldesigner:listOfSquares>
-<celldesigner:layerCompartmentAlias type="Oval">
-<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-<celldesigner:layerCompartmentAlias type="Square">
-<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-</celldesigner:listOfSquares>
-<celldesigner:listOfFreeLines>
-<celldesigner:layerFreeLine isArrow="false" isDotted="false">
-<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-<celldesigner:layerFreeLine isArrow="true" isDotted="false">
-<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-</celldesigner:listOfFreeLines>
-</celldesigner:layer>
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<customLayerTag/>
+<celldesigner:listOfTexts>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+<celldesigner:listOfSquares>
+<celldesigner:layerCompartmentAlias type="Oval">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+</celldesigner:listOfSquares>
+<celldesigner:listOfFreeLines>
+<celldesigner:layerFreeLine isArrow="false" isDotted="false">
+<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+</celldesigner:listOfFreeLines>
+</celldesigner:layer>
diff --git a/converter-CellDesigner/testFiles/invalid/layer_collection.xml b/converter-CellDesigner/testFiles/invalid/layer_collection.xml
index 654f981181..d454896309 100644
--- a/converter-CellDesigner/testFiles/invalid/layer_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer_collection.xml
@@ -1,37 +1,37 @@
-<celldesigner:listOfLayers>
-<invalid_node/>
-<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
-<celldesigner:listOfTexts>
-<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
-<celldesigner:layerNotes>
-text node
-</celldesigner:layerNotes>
-<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
-<celldesigner:paint color="ff000000"/>
-<celldesigner:font size="11"/>
-</celldesigner:layerSpeciesAlias>
-</celldesigner:listOfTexts>
-<celldesigner:listOfSquares>
-<celldesigner:layerCompartmentAlias type="Oval">
-<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-<celldesigner:layerCompartmentAlias type="Square">
-<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
-</celldesigner:listOfSquares>
-<celldesigner:listOfFreeLines>
-<celldesigner:layerFreeLine isArrow="false" isDotted="false">
-<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-<celldesigner:layerFreeLine isArrow="true" isDotted="false">
-<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
-</celldesigner:listOfFreeLines>
-</celldesigner:layer>
+<celldesigner:listOfLayers>
+<invalid_node/>
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:listOfTexts>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+<celldesigner:listOfSquares>
+<celldesigner:layerCompartmentAlias type="Oval">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+</celldesigner:listOfSquares>
+<celldesigner:listOfFreeLines>
+<celldesigner:layerFreeLine isArrow="false" isDotted="false">
+<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+</celldesigner:listOfFreeLines>
+</celldesigner:layer>
 </celldesigner:listOfLayers>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/layer_line.xml b/converter-CellDesigner/testFiles/invalid/layer_line.xml
index 504007efcf..bdfb767316 100644
--- a/converter-CellDesigner/testFiles/invalid/layer_line.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer_line.xml
@@ -1,5 +1,5 @@
-<celldesigner:layerFreeLine isArrow="true" isDotted="true">
-<inv_content/>
-<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
-<celldesigner:line width="5.0" color="ff000000"/>
-</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="true">
+<inv_content/>
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
diff --git a/converter-CellDesigner/testFiles/invalid/layer_oval.xml b/converter-CellDesigner/testFiles/invalid/layer_oval.xml
index a1543f5376..836be26362 100644
--- a/converter-CellDesigner/testFiles/invalid/layer_oval.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer_oval.xml
@@ -1,6 +1,6 @@
-<celldesigner:layerCompartmentAlias type="Oval">
-<inv_tag/>
-<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Oval">
+<inv_tag/>
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/layer_square.xml b/converter-CellDesigner/testFiles/invalid/layer_square.xml
index 64bdda46f6..ec6a623786 100644
--- a/converter-CellDesigner/testFiles/invalid/layer_square.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer_square.xml
@@ -1,6 +1,6 @@
-<celldesigner:layerCompartmentAlias type="Square">
-<inv_element/>
-<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
-<celldesigner:paint color="ff000000" scheme="Gradation"/>
-<celldesigner:ispaint inner="false"/>
-</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<inv_element/>
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/layer_text.xml b/converter-CellDesigner/testFiles/invalid/layer_text.xml
index d860055a35..40d6f92c1e 100644
--- a/converter-CellDesigner/testFiles/invalid/layer_text.xml
+++ b/converter-CellDesigner/testFiles/invalid/layer_text.xml
@@ -1,9 +1,9 @@
-<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
-<inv_tabg/>
-<celldesigner:layerNotes>
-text node
-</celldesigner:layerNotes>
-<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
-<celldesigner:paint color="ff000000"/>
-<celldesigner:font size="11"/>
-</celldesigner:layerSpeciesAlias>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<inv_tabg/>
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
diff --git a/converter-CellDesigner/testFiles/invalid/listOfCompartments.xml b/converter-CellDesigner/testFiles/invalid/listOfCompartments.xml
index 1fb3bacf9c..e902591a73 100644
--- a/converter-CellDesigner/testFiles/invalid/listOfCompartments.xml
+++ b/converter-CellDesigner/testFiles/invalid/listOfCompartments.xml
@@ -1,11 +1,11 @@
-<listOfCompartments>
-<compartment metaid="default" id="default" size="1" units="volume"/>
-<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
-<annotation>
-<celldesigner:extension>
-<celldesigner:name>c1</celldesigner:name>
-</celldesigner:extension>
-</annotation>
-</compartment>
-<compartment2/>
-</listOfCompartments>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c1</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+<compartment2/>
+</listOfCompartments>
diff --git a/converter-CellDesigner/testFiles/invalid/list_of_species_alias.xml b/converter-CellDesigner/testFiles/invalid/list_of_species_alias.xml
index 0d760a7628..e22c3d53af 100644
--- a/converter-CellDesigner/testFiles/invalid/list_of_species_alias.xml
+++ b/converter-CellDesigner/testFiles/invalid/list_of_species_alias.xml
@@ -1,553 +1,553 @@
-<celldesigner:listOfSpeciesAliases>
-<celldesigner:speciesAlias id="sa1" species="s1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="12.0" y="6.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffffff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa2" species="s2">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="165.0" y="43.0" w="80.0" h="50.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="50.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa3" species="s3">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="289.0" y="39.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa4" species="s4">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="419.0" y="45.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffcccc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa5" species="s5">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="0.0" y="118.5" w="90.0" h="25.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="90.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ff66ff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa6" species="s6">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="101.0" y="129.5" w="90.0" h="25.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
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+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa29" species="s25">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="819.0" y="134.0" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa30" species="s2612">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1022.7317629179333" y="209.5" w="140.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2114.4635258358667" y="3282.5"/>
+<celldesigner:boxSize width="140.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa31" species="s841">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1197.2682370820667" y="287.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2281.0" y="3282.5"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa32" species="s2611">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1225.7682370820667" y="66.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2360.5" y="3189.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffffffff" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa33" species="s817">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1243.7682370820667" y="12.50000000000091" w="25.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2364.5" y="3112.500000000001"/>
+<celldesigner:boxSize width="25.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ff9999ff" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa34" species="s815">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1214.2682370820667" y="128.5000000000009" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2267.0" y="3112.500000000001"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa35" species="s4532">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="1044.7317629179333" y="27.50000000000091" w="140.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="2114.4635258358667" y="3112.500000000001"/>
+<celldesigner:boxSize width="140.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
diff --git a/converter-CellDesigner/testFiles/invalid/list_of_species_alias2.xml b/converter-CellDesigner/testFiles/invalid/list_of_species_alias2.xml
index 1c27ebdd26..ac07e81a9f 100644
--- a/converter-CellDesigner/testFiles/invalid/list_of_species_alias2.xml
+++ b/converter-CellDesigner/testFiles/invalid/list_of_species_alias2.xml
@@ -1,554 +1,554 @@
-<celldesigner:listOfSpeciesAliases>
-<unk/>
-<celldesigner:speciesAlias id="sa1" species="s1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="12.0" y="6.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffffff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa2" species="s2">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="165.0" y="43.0" w="80.0" h="50.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="50.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa3" species="s3">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="289.0" y="39.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa4" species="s4">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="419.0" y="45.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffcccc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa5" species="s5">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="0.0" y="118.5" w="90.0" h="25.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="90.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ff66ff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa6" species="s6">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="101.0" y="129.5" w="90.0" h="25.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="90.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffff6666" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa7" species="s7">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="213.0" y="128.0" w="80.0" h="30.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="30.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffcc99ff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa8" species="s8">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="358.5" y="125.5" w="25.0" h="25.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="25.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ff9999ff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa9" species="s9">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="455.0" y="169.5" w="70.0" h="25.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="70.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa10" species="s10">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="0.0" y="186.0" w="80.0" h="30.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="30.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffff00ff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa11" species="s11">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="105.0" y="203.5" w="70.0" h="25.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="70.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="7fcccccc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa12" species="s13">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="401.0" y="235.0" w="30.0" h="30.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="30.0" height="30.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffcccc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa13" species="s14" complexSpeciesAlias="csa1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="279.0" y="233.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="8.0" y="26.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa14" species="s15">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11.0" y="236.0" w="118.0" h="66.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="118.0" height="66.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
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-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa15" species="s16">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="160.0" y="332.0" w="119.0" h="63.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
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-</celldesigner:usualView>
-<celldesigner:briefView>
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diff --git a/converter-CellDesigner/testFiles/invalid/protein.xml b/converter-CellDesigner/testFiles/invalid/protein.xml
index 8eb55f9abd..d5e33d960c 100644
--- a/converter-CellDesigner/testFiles/invalid/protein.xml
+++ b/converter-CellDesigner/testFiles/invalid/protein.xml
@@ -1,16 +1,16 @@
-<celldesigner:protein id="pr23" name="SDHA" type="UNK_TYPE_BLA">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-UniProtKB	P31040	SDHA		GO:0005749	GO_REF:0000024|UniProtKB:Q0QF01	ISS	UniProtKB:Q0QF01	C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20100125	UniProtKB
-UniProtKB	P31040	SDHA		GO:0005749	PMID:7550341	TAS		C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20060419	UniProtKB
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfModificationResidues>
-<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla"  id="rs1" side="none"/>
-</celldesigner:listOfModificationResidues>
+<celldesigner:protein id="pr23" name="SDHA" type="UNK_TYPE_BLA">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+UniProtKB	P31040	SDHA		GO:0005749	GO_REF:0000024|UniProtKB:Q0QF01	ISS	UniProtKB:Q0QF01	C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20100125	UniProtKB
+UniProtKB	P31040	SDHA		GO:0005749	PMID:7550341	TAS		C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20060419	UniProtKB
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla"  id="rs1" side="none"/>
+</celldesigner:listOfModificationResidues>
 </celldesigner:protein>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/protein2.xml b/converter-CellDesigner/testFiles/invalid/protein2.xml
index 8b19845e6e..2ecfe74847 100644
--- a/converter-CellDesigner/testFiles/invalid/protein2.xml
+++ b/converter-CellDesigner/testFiles/invalid/protein2.xml
@@ -1,17 +1,17 @@
-<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-UniProtKB	P31040	SDHA		GO:0005749	GO_REF:0000024|UniProtKB:Q0QF01	ISS	UniProtKB:Q0QF01	C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20100125	UniProtKB
-UniProtKB	P31040	SDHA		GO:0005749	PMID:7550341	TAS		C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20060419	UniProtKB
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfModificationResidues>
-<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla"  id="rs1" side="none"/>
-<unkNode/>
-</celldesigner:listOfModificationResidues>
+<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+UniProtKB	P31040	SDHA		GO:0005749	GO_REF:0000024|UniProtKB:Q0QF01	ISS	UniProtKB:Q0QF01	C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20100125	UniProtKB
+UniProtKB	P31040	SDHA		GO:0005749	PMID:7550341	TAS		C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20060419	UniProtKB
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla"  id="rs1" side="none"/>
+<unkNode/>
+</celldesigner:listOfModificationResidues>
 </celldesigner:protein>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/protein3.xml b/converter-CellDesigner/testFiles/invalid/protein3.xml
index 0ca56fd5be..674b6a9e85 100644
--- a/converter-CellDesigner/testFiles/invalid/protein3.xml
+++ b/converter-CellDesigner/testFiles/invalid/protein3.xml
@@ -1,17 +1,17 @@
-<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-UniProtKB	P31040	SDHA		GO:0005749	GO_REF:0000024|UniProtKB:Q0QF01	ISS	UniProtKB:Q0QF01	C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20100125	UniProtKB
-UniProtKB	P31040	SDHA		GO:0005749	PMID:7550341	TAS		C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20060419	UniProtKB
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfModificationResidues>
-<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla"  id="rs1" side="none"/>
-</celldesigner:listOfModificationResidues>
-<xxx/>
+<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+UniProtKB	P31040	SDHA		GO:0005749	GO_REF:0000024|UniProtKB:Q0QF01	ISS	UniProtKB:Q0QF01	C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20100125	UniProtKB
+UniProtKB	P31040	SDHA		GO:0005749	PMID:7550341	TAS		C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20060419	UniProtKB
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla"  id="rs1" side="none"/>
+</celldesigner:listOfModificationResidues>
+<xxx/>
 </celldesigner:protein>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/protein4.xml b/converter-CellDesigner/testFiles/invalid/protein4.xml
index cfd7e5b23c..f84c2a325f 100644
--- a/converter-CellDesigner/testFiles/invalid/protein4.xml
+++ b/converter-CellDesigner/testFiles/invalid/protein4.xml
@@ -1,18 +1,18 @@
-<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-UniProtKB	P31040	SDHA		GO:0005749	GO_REF:0000024|UniProtKB:Q0QF01	ISS	UniProtKB:Q0QF01	C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20100125	UniProtKB
-UniProtKB	P31040	SDHA		GO:0005749	PMID:7550341	TAS		C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20060419	UniProtKB
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfModificationResidues>
-<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla"  id="rs1" side="none">
-<xxx/>
-</celldesigner:modificationResidue>
-</celldesigner:listOfModificationResidues>
+<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+UniProtKB	P31040	SDHA		GO:0005749	GO_REF:0000024|UniProtKB:Q0QF01	ISS	UniProtKB:Q0QF01	C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20100125	UniProtKB
+UniProtKB	P31040	SDHA		GO:0005749	PMID:7550341	TAS		C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20060419	UniProtKB
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla"  id="rs1" side="none">
+<xxx/>
+</celldesigner:modificationResidue>
+</celldesigner:listOfModificationResidues>
 </celldesigner:protein>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/protein5.xml b/converter-CellDesigner/testFiles/invalid/protein5.xml
index cfd7e5b23c..f84c2a325f 100644
--- a/converter-CellDesigner/testFiles/invalid/protein5.xml
+++ b/converter-CellDesigner/testFiles/invalid/protein5.xml
@@ -1,18 +1,18 @@
-<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-UniProtKB	P31040	SDHA		GO:0005749	GO_REF:0000024|UniProtKB:Q0QF01	ISS	UniProtKB:Q0QF01	C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20100125	UniProtKB
-UniProtKB	P31040	SDHA		GO:0005749	PMID:7550341	TAS		C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20060419	UniProtKB
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfModificationResidues>
-<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla"  id="rs1" side="none">
-<xxx/>
-</celldesigner:modificationResidue>
-</celldesigner:listOfModificationResidues>
+<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+UniProtKB	P31040	SDHA		GO:0005749	GO_REF:0000024|UniProtKB:Q0QF01	ISS	UniProtKB:Q0QF01	C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20100125	UniProtKB
+UniProtKB	P31040	SDHA		GO:0005749	PMID:7550341	TAS		C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20060419	UniProtKB
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla"  id="rs1" side="none">
+<xxx/>
+</celldesigner:modificationResidue>
+</celldesigner:listOfModificationResidues>
 </celldesigner:protein>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/protein6.xml b/converter-CellDesigner/testFiles/invalid/protein6.xml
index cfd7e5b23c..f84c2a325f 100644
--- a/converter-CellDesigner/testFiles/invalid/protein6.xml
+++ b/converter-CellDesigner/testFiles/invalid/protein6.xml
@@ -1,18 +1,18 @@
-<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-UniProtKB	P31040	SDHA		GO:0005749	GO_REF:0000024|UniProtKB:Q0QF01	ISS	UniProtKB:Q0QF01	C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20100125	UniProtKB
-UniProtKB	P31040	SDHA		GO:0005749	PMID:7550341	TAS		C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20060419	UniProtKB
-</body>
-</html>
-</celldesigner:notes>
-<celldesigner:listOfModificationResidues>
-<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla"  id="rs1" side="none">
-<xxx/>
-</celldesigner:modificationResidue>
-</celldesigner:listOfModificationResidues>
+<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+UniProtKB	P31040	SDHA		GO:0005749	GO_REF:0000024|UniProtKB:Q0QF01	ISS	UniProtKB:Q0QF01	C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20100125	UniProtKB
+UniProtKB	P31040	SDHA		GO:0005749	PMID:7550341	TAS		C	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial	A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF	protein	taxon:9606	20060419	UniProtKB
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla"  id="rs1" side="none">
+<xxx/>
+</celldesigner:modificationResidue>
+</celldesigner:listOfModificationResidues>
 </celldesigner:protein>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/protein_collection.xml b/converter-CellDesigner/testFiles/invalid/protein_collection.xml
index 653c678b4e..b64c6eb849 100644
--- a/converter-CellDesigner/testFiles/invalid/protein_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/protein_collection.xml
@@ -1,3 +1,3 @@
-<celldesigner:listOfProteins>
-<unkproteinnode/>
+<celldesigner:listOfProteins>
+<unkproteinnode/>
 </celldesigner:listOfProteins>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/rna.xml b/converter-CellDesigner/testFiles/invalid/rna.xml
index 62e29d7ee2..15e15b96b1 100644
--- a/converter-CellDesigner/testFiles/invalid/rna.xml
+++ b/converter-CellDesigner/testFiles/invalid/rna.xml
@@ -1,6 +1,6 @@
-<celldesigner:RNA id="rn49" name="TRNAU1" type="RNA">
-<celldesigner:listOfRegions>
-<celldesigner:region id="tr1" size="0.0" pos="0.10569105691056911" type="Modification Site"/>
-<unknode/>
-</celldesigner:listOfRegions>
+<celldesigner:RNA id="rn49" name="TRNAU1" type="RNA">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" size="0.0" pos="0.10569105691056911" type="Modification Site"/>
+<unknode/>
+</celldesigner:listOfRegions>
 </celldesigner:RNA>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/rna2.xml b/converter-CellDesigner/testFiles/invalid/rna2.xml
index 84be995a07..1217e85424 100644
--- a/converter-CellDesigner/testFiles/invalid/rna2.xml
+++ b/converter-CellDesigner/testFiles/invalid/rna2.xml
@@ -1,6 +1,6 @@
-<celldesigner:RNA id="rn49" name="TRNAU1" type="RNA">
-<celldesigner:listOfRegions>
-<celldesigner:region id="tr1" size="0.0" pos="0.10569105691056911" type="Modification Site"/>
-</celldesigner:listOfRegions>
-<unknode/>
+<celldesigner:RNA id="rn49" name="TRNAU1" type="RNA">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" size="0.0" pos="0.10569105691056911" type="Modification Site"/>
+</celldesigner:listOfRegions>
+<unknode/>
 </celldesigner:RNA>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/rna3.xml b/converter-CellDesigner/testFiles/invalid/rna3.xml
index 4a5d2d45f1..8ff8c125aa 100644
--- a/converter-CellDesigner/testFiles/invalid/rna3.xml
+++ b/converter-CellDesigner/testFiles/invalid/rna3.xml
@@ -1,7 +1,7 @@
-<celldesigner:RNA id="rn49" name="TRNAU1" type="RNA">
-<celldesigner:listOfRegions>
-<celldesigner:region id="tr1" size="0.0" pos="0.10569105691056911" type="Modification Site">
-<unknode/>
-</celldesigner:region >
-</celldesigner:listOfRegions>
+<celldesigner:RNA id="rn49" name="TRNAU1" type="RNA">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" size="0.0" pos="0.10569105691056911" type="Modification Site">
+<unknode/>
+</celldesigner:region >
+</celldesigner:listOfRegions>
 </celldesigner:RNA>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/rna_collection.xml b/converter-CellDesigner/testFiles/invalid/rna_collection.xml
index 04081ecf74..d3ffb5f3e8 100644
--- a/converter-CellDesigner/testFiles/invalid/rna_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/rna_collection.xml
@@ -1,5 +1,5 @@
-<celldesigner:listOfRNAs>
-<unknown_node/>
-<celldesigner:RNA id="rn1" name="s5" type="RNA"/>
-<celldesigner:RNA id="rn2" name="s7" type="RNA"/>
+<celldesigner:listOfRNAs>
+<unknown_node/>
+<celldesigner:RNA id="rn1" name="s5" type="RNA"/>
+<celldesigner:RNA id="rn2" name="s7" type="RNA"/>
 </celldesigner:listOfRNAs>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/sbml_collection.xml b/converter-CellDesigner/testFiles/invalid/sbml_collection.xml
index 64fb5055e7..9dc20a3fd8 100644
--- a/converter-CellDesigner/testFiles/invalid/sbml_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/sbml_collection.xml
@@ -1,102 +1,102 @@
-<listOfSpecies>
-<unknode/>
-<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>GENE</celldesigner:class>
-<celldesigner:geneReference>gn1</celldesigner:geneReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>GENE</celldesigner:class>
-<celldesigner:geneReference>gn2</celldesigner:geneReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s5" id="s5" name="s5" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>RNA</celldesigner:class>
-<celldesigner:rnaReference>rn1</celldesigner:rnaReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s6" id="s6" name="s6" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
-<celldesigner:antisensernaReference>arn1</celldesigner:antisensernaReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s7" id="s7" name="s7" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>RNA</celldesigner:class>
-<celldesigner:rnaReference>rn2</celldesigner:rnaReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s8" id="s8" name="s8" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
-<celldesigner:antisensernaReference>arn2</celldesigner:antisensernaReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s9" id="s9" name="s9" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>COMPLEX</celldesigner:class>
-<celldesigner:name>s9</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
+<listOfSpecies>
+<unknode/>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn1</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn2</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s5" id="s5" name="s5" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>rn1</celldesigner:rnaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s6" id="s6" name="s6" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
+<celldesigner:antisensernaReference>arn1</celldesigner:antisensernaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s7" id="s7" name="s7" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>rn2</celldesigner:rnaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s8" id="s8" name="s8" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
+<celldesigner:antisensernaReference>arn2</celldesigner:antisensernaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s9" id="s9" name="s9" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s9</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
 </listOfSpecies>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/species_alias.xml b/converter-CellDesigner/testFiles/invalid/species_alias.xml
index 49e4039690..beec5151a7 100644
--- a/converter-CellDesigner/testFiles/invalid/species_alias.xml
+++ b/converter-CellDesigner/testFiles/invalid/species_alias.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa36" species="ss78" compartmentAlias="ca1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="ss78" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
 </celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/species_alias2.xml b/converter-CellDesigner/testFiles/invalid/species_alias2.xml
index 9ae72330ea..45c1c2f61a 100644
--- a/converter-CellDesigner/testFiles/invalid/species_alias2.xml
+++ b/converter-CellDesigner/testFiles/invalid/species_alias2.xml
@@ -1,20 +1,20 @@
-<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
-<unk/>
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
+<unk/>
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
 </celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/species_alias3.xml b/converter-CellDesigner/testFiles/invalid/species_alias3.xml
index c082780aa1..a9e14fad3e 100644
--- a/converter-CellDesigner/testFiles/invalid/species_alias3.xml
+++ b/converter-CellDesigner/testFiles/invalid/species_alias3.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="unusual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="unusual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
 </celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/species_alias4.xml b/converter-CellDesigner/testFiles/invalid/species_alias4.xml
index ec93873ff7..0a65186bf8 100644
--- a/converter-CellDesigner/testFiles/invalid/species_alias4.xml
+++ b/converter-CellDesigner/testFiles/invalid/species_alias4.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ccca1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ccca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
 </celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/species_alias5.xml b/converter-CellDesigner/testFiles/invalid/species_alias5.xml
index fe54056792..f8c77a3503 100644
--- a/converter-CellDesigner/testFiles/invalid/species_alias5.xml
+++ b/converter-CellDesigner/testFiles/invalid/species_alias5.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa36" species="s78" complexSpeciesAlias="ccca1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="s78" complexSpeciesAlias="ccca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
 </celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/species_alias6.xml b/converter-CellDesigner/testFiles/invalid/species_alias6.xml
index 6dfcf60c59..9f5bd07fde 100644
--- a/converter-CellDesigner/testFiles/invalid/species_alias6.xml
+++ b/converter-CellDesigner/testFiles/invalid/species_alias6.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa36" species="s78" >
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="unknown" angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="s78" >
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="unknown" angle="-1.5707963267948966"/>
 </celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/invalid/species_alias_collection.xml b/converter-CellDesigner/testFiles/invalid/species_alias_collection.xml
index fd531560a8..9d3b3607e2 100644
--- a/converter-CellDesigner/testFiles/invalid/species_alias_collection.xml
+++ b/converter-CellDesigner/testFiles/invalid/species_alias_collection.xml
@@ -1,79 +1,79 @@
-<celldesigner:listOfSpeciesAliases>
-<unk/>
-<celldesigner:speciesAlias id="sa8" species="s2594">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="510.83547998986796" y="449.34999999999997" w="261.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="1459.6161980749753" y="5346.0"/>
-<celldesigner:boxSize width="261.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa9" species="s2506">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="506.33547998986796" y="613.8499999999999" w="262.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="1459.1161980749753" y="5539.5"/>
-<celldesigner:boxSize width="262.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa10" species="s2595">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="282.0" y="75.0" w="134.0" h="94.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="134.0" height="94.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa11" species="s2596">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="483.0" y="76.0" w="82.0" h="96.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="82.0" height="96.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfSpeciesAliases>
+<unk/>
+<celldesigner:speciesAlias id="sa8" species="s2594">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="510.83547998986796" y="449.34999999999997" w="261.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="1459.6161980749753" y="5346.0"/>
+<celldesigner:boxSize width="261.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa9" species="s2506">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="506.33547998986796" y="613.8499999999999" w="262.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="1459.1161980749753" y="5539.5"/>
+<celldesigner:boxSize width="262.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa10" species="s2595">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="282.0" y="75.0" w="134.0" h="94.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="134.0" height="94.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa11" species="s2596">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="483.0" y="76.0" w="82.0" h="96.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="82.0" height="96.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/block_diagrams.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/block_diagrams.xml
index 9d55f16950..15d462cb5d 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/block_diagrams.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/block_diagrams.xml
@@ -1,15 +1,15 @@
-<celldesigner:listOfBlockDiagrams>
-<celldesigner:blockDiagram protein="pr1">
-<celldesigner:canvas height="312" width="476"/>
-<celldesigner:block height="90" nameOffsetX="-8.0" nameOffsetY="-8.0" width="140" x="100" y="50"/>
-<celldesigner:halo height="150" width="200" x="70" y="20"/>
-<celldesigner:listOfResiduesInBlockDiagram>
-<celldesigner:residueInBlockDiagram id="0" offsetX="-27.0" type="dontcare"/>
-</celldesigner:listOfResiduesInBlockDiagram>
-<celldesigner:listOfExternalNamesForResidue/>
-<celldesigner:listOfBindingSitesInBlockDiagram/>
-<celldesigner:listOfEffectSitesInBlockDiagram/>
-<celldesigner:listOfInternalOperatorsInBlockDiagram/>
-<celldesigner:listOfInternalLinksInBlockDiagram/>
-</celldesigner:blockDiagram>
-</celldesigner:listOfBlockDiagrams>
+<celldesigner:listOfBlockDiagrams>
+<celldesigner:blockDiagram protein="pr1">
+<celldesigner:canvas height="312" width="476"/>
+<celldesigner:block height="90" nameOffsetX="-8.0" nameOffsetY="-8.0" width="140" x="100" y="50"/>
+<celldesigner:halo height="150" width="200" x="70" y="20"/>
+<celldesigner:listOfResiduesInBlockDiagram>
+<celldesigner:residueInBlockDiagram id="0" offsetX="-27.0" type="dontcare"/>
+</celldesigner:listOfResiduesInBlockDiagram>
+<celldesigner:listOfExternalNamesForResidue/>
+<celldesigner:listOfBindingSitesInBlockDiagram/>
+<celldesigner:listOfEffectSitesInBlockDiagram/>
+<celldesigner:listOfInternalOperatorsInBlockDiagram/>
+<celldesigner:listOfInternalLinksInBlockDiagram/>
+</celldesigner:blockDiagram>
+</celldesigner:listOfBlockDiagrams>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml
index d9f1852510..bf37613db8 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml
@@ -1,21 +1,21 @@
-<celldesigner:complexSpeciesAlias id="csa1" species="s2597">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="744.0" y="0.0" w="100.0" h="120.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="100.0" height="120.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa1" species="s2597">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="744.0" y="0.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes.xml
index 11d122e7e9..07e958faee 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes.xml
@@ -1,10 +1,10 @@
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Description: some notes
-</body>
-</html>
-</celldesigner:notes>
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Description: some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes2.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes2.xml
index c16aea799b..fe5db406a2 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes2.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes2.xml
@@ -1,23 +1,23 @@
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Symbol: SNCA
-Previous Symbols: X1, X2, X3
-Synonyms: Y1, Y2, Y3
-Name: Synuclein alpha (or something)
-Abbreviation: SN
-Formula: form
-MechanicalConfidenceScore: 2
-LowerBound: 2
-UpperBound: 2
-Subsystem: 2
-GeneProteinReaction: 1
-ChargedFormula: 1
-Charge:15
-some notes
-</body>
-</html>
-</celldesigner:notes>
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Symbol: SNCA
+Previous Symbols: X1, X2, X3
+Synonyms: Y1, Y2, Y3
+Name: Synuclein alpha (or something)
+Abbreviation: SN
+Formula: form
+MechanicalConfidenceScore: 2
+LowerBound: 2
+UpperBound: 2
+Subsystem: 2
+GeneProteinReaction: 1
+ChargedFormula: 1
+Charge:15
+some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes3.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes3.xml
index 8a9da0796e..68f0aadbf7 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes3.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes3.xml
@@ -1,11 +1,11 @@
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Description: some notes
-some notes
-</body>
-</html>
-</celldesigner:notes>
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Description: some notes
+some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes4.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes4.xml
index aae1b31a33..444dade224 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes4.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes4.xml
@@ -1,11 +1,11 @@
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Description: some notes some notes Symbol: strange2
-some notes some notes Symbol: strange3
-</body>
-</html>
-</celldesigner:notes>
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Description: some notes some notes Symbol: strange2
+some notes some notes Symbol: strange3
+</body>
+</html>
+</celldesigner:notes>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes5.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes5.xml
index f416ace968..b4d6531235 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes5.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes5.xml
@@ -1,43 +1,43 @@
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdfa:Description rdf:about="#s6095">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:18429"/></rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family:PTHR11695"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_036344.2"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001139580.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family:ADH_Sf_Zn"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:22949"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001139581.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:22949"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdfa:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:18429"/></rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family:PTHR11695"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_036344.2"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139580.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family:ADH_Sf_Zn"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139581.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
 </rdf:RDF>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml
index 1df09c4a02..8e2a9d5f76 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml
@@ -1,11 +1,11 @@
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Charge:a15
-some notes
-</body>
-</html>
-</celldesigner:notes>
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Charge:a15
+some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_gene.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_gene.xml
index 0c05a8d203..3d176259f8 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_gene.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_gene.xml
@@ -1,73 +1,73 @@
-<species metaid="s5916" id="s5916" name="Ptgr1" compartment="c20" initialAmount="0" charge="0">
-<notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Symbol: PTGR1
-Name: prostaglandin reductase 1
-Description: RecName: Full=Prostaglandin reductase 1; Short=PRG-1; EC=1.3.1.-; AltName: Full=15-oxoprostaglandin 13-reductase; EC=1.3.1.48; AltName: Full=NADP-dependent leukotriene B4 12-hydroxydehydrogenase; EC=1.3.1.74;
-Previous Symbols: LTB4DH
-Synonyms: LTB4DH
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s6095">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:22949"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</body>
-</html>
-</notes>
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>GENE</celldesigner:class>
-<celldesigner:geneReference>gn95</celldesigner:geneReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s5916">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:18429"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR11695"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_036344.2"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001139580.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3AADH_Sf_Zn"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A22949"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001139581.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
+<species metaid="s5916" id="s5916" name="Ptgr1" compartment="c20" initialAmount="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Symbol: PTGR1
+Name: prostaglandin reductase 1
+Description: RecName: Full=Prostaglandin reductase 1; Short=PRG-1; EC=1.3.1.-; AltName: Full=15-oxoprostaglandin 13-reductase; EC=1.3.1.48; AltName: Full=NADP-dependent leukotriene B4 12-hydroxydehydrogenase; EC=1.3.1.74;
+Previous Symbols: LTB4DH
+Synonyms: LTB4DH
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn95</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5916">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:18429"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR11695"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_036344.2"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139580.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3AADH_Sf_Zn"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139581.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_ion.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_ion.xml
index 0562f1e849..5c2222a435 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_ion.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_ion.xml
@@ -1,124 +1,124 @@
-<species metaid="s6029" id="s6029" name="Pi" compartment="c1" initialConcentration="0" charge="0">
-<notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Long Name:  PiSynonym:  Synonym not specifiedAccession:  U02720
-Symbol: SERPINA1
-Name: serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1
-Description: RecName: Full=Alpha-1-antitrypsin; AltName: Full=Alpha-1 protease inhibitor; AltName: Full=Alpha-1-antiproteinase; AltName: Full=Serpin A1; Contains: RecName: Full=Short peptide from AAT; Short=SPAAT; Flags: Precursor;
-Previous Symbols: PI
-Synonyms: AAT, PI
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s6095">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:5265"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</body>
-</html>
-</notes>
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>ION</celldesigner:class>
-<celldesigner:name>Pi</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s6029">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121172.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3AProt_inh_serpin"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA35509"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR11461"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121174.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:8941"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001002235.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121175.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121176.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121179.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121173.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121177.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:reactome:REACT_3705"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001121178.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001002236.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_000286.3"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A5265"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
+<species metaid="s6029" id="s6029" name="Pi" compartment="c1" initialConcentration="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Long Name:  PiSynonym:  Synonym not specifiedAccession:  U02720
+Symbol: SERPINA1
+Name: serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1
+Description: RecName: Full=Alpha-1-antitrypsin; AltName: Full=Alpha-1 protease inhibitor; AltName: Full=Alpha-1-antiproteinase; AltName: Full=Serpin A1; Contains: RecName: Full=Short peptide from AAT; Short=SPAAT; Flags: Precursor;
+Previous Symbols: PI
+Synonyms: AAT, PI
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:5265"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ION</celldesigner:class>
+<celldesigner:name>Pi</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6029">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121172.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3AProt_inh_serpin"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA35509"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR11461"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121174.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:8941"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001002235.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121175.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121176.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121179.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121173.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121177.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_3705"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121178.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001002236.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_000286.3"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A5265"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_protein.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_protein.xml
index 586c93a1cb..0f8d55a9f6 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_protein.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_protein.xml
@@ -1,63 +1,63 @@
-<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
-<notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>protein tyrosine phosphatase, receptor type, C
-also known as CED45
-Symbol: PTPRC
-Name: protein tyrosine phosphatase, receptor type, C
-Description: RecName: Full=Receptor-type tyrosine-protein phosphatase C; EC=3.1.3.48; AltName: Full=Leukocyte common antigen; Short=L-CA; AltName: Full=T200; AltName: CD_antigen=CD45; Flags: Precursor;
-Previous Symbols: CD45
-Synonyms: CD45
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s5456">
-<bqbiol:is>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:entrez.gene:5788"/></rdf:Bag>
-</bqbiol:is>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_002829.2"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:reactome:REACT_13296"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</body>
-</html>
-</notes>
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s5456">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_563578.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA34011"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:9666"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>protein tyrosine phosphatase, receptor type, C
+also known as CED45
+Symbol: PTPRC
+Name: protein tyrosine phosphatase, receptor type, C
+Description: RecName: Full=Receptor-type tyrosine-protein phosphatase C; EC=3.1.3.48; AltName: Full=Leukocyte common antigen; Short=L-CA; AltName: Full=T200; AltName: CD_antigen=CD45; Flags: Precursor;
+Previous Symbols: CD45
+Synonyms: CD45
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5456">
+<bqbiol:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:entrez.gene:5788"/></rdf:Bag>
+</bqbiol:is>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_002829.2"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_13296"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5456">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_563578.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA34011"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:9666"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_rna.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_rna.xml
index 2531787c25..a848f327dc 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_rna.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/sbml_rna.xml
@@ -1,78 +1,78 @@
-<species metaid="s5914" id="s5914" name="Fmo3" compartment="c20" initialAmount="0" charge="0">
-<notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>
-Symbol: FMO3
-Name: flavin containing monooxygenase 3
-Description: RecName: Full=Dimethylaniline monooxygenase [N-oxide-forming] 3; EC=1.14.13.8; AltName: Full=Dimethylaniline oxidase 3; AltName: Full=FMO II; AltName: Full=FMO form 2; AltName: Full=Hepatic flavin-containing monooxygenase 3; Short=FMO 3;
-Previous Symbols:
-Synonyms:
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s6095">
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:ncbigene:2328"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-</rdf:Description>
-</rdf:RDF>
-</body>
-</html>
-</notes>
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>RNA</celldesigner:class>
-<celldesigner:rnaReference>rn101</celldesigner:rnaReference>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s5914">
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:8486388"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_001002294.1"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:reactome:REACT_5740"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA166"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A2328"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:refseq:NP_008825.4"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:hasVersion>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:hgnc:3771"/>
-</rdf:Bag>
-</bqbiol:hasVersion>
-<bqbiol:isVersionOf>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:9417913"/>
-</rdf:Bag>
-</bqbiol:isVersionOf>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
+<species metaid="s5914" id="s5914" name="Fmo3" compartment="c20" initialAmount="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Symbol: FMO3
+Name: flavin containing monooxygenase 3
+Description: RecName: Full=Dimethylaniline monooxygenase [N-oxide-forming] 3; EC=1.14.13.8; AltName: Full=Dimethylaniline oxidase 3; AltName: Full=FMO II; AltName: Full=FMO form 2; AltName: Full=Hepatic flavin-containing monooxygenase 3; Short=FMO 3;
+Previous Symbols:
+Synonyms:
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:2328"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>rn101</celldesigner:rnaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5914">
+<bqbiol:isVersionOf>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pubmed:8486388"/>
+</rdf:Bag>
+</bqbiol:isVersionOf>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001002294.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_5740"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA166"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A2328"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_008825.4"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:3771"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:isVersionOf>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pubmed:9417913"/>
+</rdf:Bag>
+</bqbiol:isVersionOf>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
 </species>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias.xml
index fa35a946eb..f3e98a7910 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info angle="-1.5707963267948966"/>
 </celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_with_font.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_with_font.xml
index b689e984c9..893947c964 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_with_font.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_with_font.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa1" species="s78">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="78.0" y="207.0" w="307.0" h="110.0"/>
-<celldesigner:font size="30"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="307.0" height="110.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa1" species="s78">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="78.0" y="207.0" w="307.0" h="110.0"/>
+<celldesigner:font size="30"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="307.0" height="110.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_without_state.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_without_state.xml
index 0c4992aaf3..267d16430a 100644
--- a/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_without_state.xml
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/species_alias_without_state.xml
@@ -1,19 +1,19 @@
-<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
-<celldesigner:font size="16"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10416.0" y="2424.5"/>
-<celldesigner:boxSize width="80.0" height="25.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccff66" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
 </celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index 6e3adb813d..c6ec75fd87 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -1,421 +1,421 @@
-package lcsb.mapviewer.converter;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.lang.reflect.Modifier;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipFile;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.zip.DataMiningZipEntryFile;
-import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
-import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
-import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.graph.DataMiningSet;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class allows to create complex {@link Model} that contains submaps. It's
- * written in generic way and use {@link IConverter} as a class to parse single
- * submap.
- * 
- * @author Piotr Gawron
- * 
- * @param <T>
- *          class used to create single submap from a file
- */
-public class ComplexZipConverter<T extends IConverter> {
-
-	/**
-	 * Size of the buffer used for accessing single chunk of data from input
-	 * stream.
-	 */
-	private static final int BUFFER_SIZE = 1024;
-	/**
-	 * Default class logger.
-	 */
-	@SuppressWarnings("unused")
-	private static Logger		 logger			 = Logger.getLogger(ComplexZipConverter.class);
-	/**
-	 * Class used to create single submap from a file.
-	 */
-	private Class<T>				 converterClazz;
-
-	/**
-	 * Default constructor. Checks if the class given in the parameter is proper
-	 * {@link IConverter} implementation.
-	 * 
-	 * @param clazz
-	 *          {@link IConverter} class used for creation of the single submap
-	 */
-	public ComplexZipConverter(Class<T> clazz) {
-		if (Modifier.isAbstract(clazz.getModifiers())) {
-			throw new InvalidClassException("Param class cannot be abstract");
-		}
-
-		if (Modifier.isInterface(clazz.getModifiers())) {
-			throw new InvalidClassException("Param class cannot be an interface");
-		}
-
-		converterClazz = clazz;
-	}
-
-	/**
-	 * Creates complex {@link Model} that contains submaps.
-	 * 
-	 * @param params
-	 *          {@link ComplexZipConverterParams object} with information about
-	 *          data from which result is going to be created
-	 * @return complex {@link Model} created from input data
-	 * @throws InvalidInputDataExecption
-	 *           thrown when there is a problem with accessing input data
-	 */
-	public Model createModel(ComplexZipConverterParams params) throws InvalidInputDataExecption {
-		try {
-			ZipFile zipFile = params.getZipFile();
-			Enumeration<? extends ZipEntry> entries;
-			String mapping = validateSubmodelInformation(params, zipFile);
-
-			IConverter converter = createConverterInstance();
-			Map<String, Model> filenameModelMap = new HashMap<String, Model>();
-			Map<String, Model> nameModelMap = new HashMap<String, Model>();
-
-			entries = zipFile.entries();
-			Model result = null;
-			List<Layout> layouts = new ArrayList<Layout>();
-			List<ImageZipEntryFile> imageEntries = new ArrayList<ImageZipEntryFile>();
-			List<DataMiningSet> dataMiningSets = new ArrayList<DataMiningSet>();
-			while (entries.hasMoreElements()) {
-				ZipEntry entry = entries.nextElement();
-				if (!entry.isDirectory()) {
-					ZipEntryFile zef = params.getEntry(entry.getName());
-					if (zef instanceof ModelZipEntryFile) {
-						ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
-						InputStream is = zipFile.getInputStream(entry);
-						ConverterParams cParams = new ConverterParams();
-						cParams.inputStream(is);
-						Model model = converter.createModel(cParams);
-						model.setName(modelEntryFile.getName());
-						filenameModelMap.put(entry.getName(), model);
-						nameModelMap.put(FilenameUtils.getBaseName(modelEntryFile.getFilename()), model);
-						if (modelEntryFile.isRoot()) {
-							result = model;
-						}
-					} else if (zef instanceof LayoutZipEntryFile) {
-						layouts.add(layoutZipEntryFileToLayout(params, zipFile, entry, (LayoutZipEntryFile) zef));
-					} else if (zef instanceof ImageZipEntryFile) {
-						imageEntries.add((ImageZipEntryFile) zef);
-					} else if (zef instanceof DataMiningZipEntryFile) {
-						dataMiningSets.add(dataMiningZipEntryToDataMiningSet(zipFile, entry, (DataMiningZipEntryFile) zef));
-					} else {
-						throw new NotImplementedException("Unknwon entry type: " + zef.getClass());
-					}
-				}
-			}
-
-			if (imageEntries.size() > 0) {
-				OverviewParser parser = new OverviewParser();
-				result.setOverviewImages(parser.parseOverviewLinks(filenameModelMap, imageEntries, params.getVisualizationDir()));
-			}
-			result.addDataMiningSets(dataMiningSets);
-
-			for (Entry<String, Model> entry : filenameModelMap.entrySet()) {
-				String filename = entry.getKey();
-				Model model = entry.getValue();
-				ZipEntryFile zef = params.getEntry(filename);
-				if (zef instanceof ModelZipEntryFile) {
-					ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
-					if (!modelEntryFile.isRoot() && !modelEntryFile.isMappingFile()) {
-						ModelSubmodelConnection submodel = new ModelSubmodelConnection(model, modelEntryFile.getType());
-						submodel.setName(modelEntryFile.getName());
-						result.addSubmodelConnection(submodel);
-					}
-				}
-			}
-			for (Layout layout : layouts) {
-				Layout topLayout = new Layout(layout);
-				result.addLayout(topLayout);
-				int modelId = 0;
-				topLayout.setDirectory(topLayout.getDirectory() + modelId);
-				modelId++;
-				for (ModelSubmodelConnection connection : result.getSubmodelConnections()) {
-					Layout childLayout = new Layout(layout);
-					// we need to set separate directory names for different submodels
-					childLayout.setDirectory(childLayout.getDirectory() + modelId);
-					modelId++;
-					childLayout.setParentLayout(topLayout);
-					connection.getSubmodel().addLayout(childLayout);
-				}
-			}
-			Model mappingModel = filenameModelMap.get(mapping);
-			if (mappingModel != null) {
-				for (Reaction reaction : mappingModel.getReactions()) {
-					processReaction(mapping, nameModelMap, result, reaction);
-				}
-			}
-			return result;
-		} catch (IOException e) {
-			throw new InvalidArgumentException(e);
-		}
-	}
-
-	/**
-	 * Process a single reaction in mapping file (transfomring reaction into
-	 * connection between submodels).
-	 * 
-	 * @param mapping
-	 *          name of the mapping file
-	 * @param nameModelMap
-	 *          mapping between file names and models
-	 * @param topModel
-	 *          top model
-	 * @param reaction
-	 *          reaction to transform into connection
-	 */
-	public void processReaction(String mapping, Map<String, Model> nameModelMap, Model topModel, Reaction reaction) {
-		if (reaction.getReactants().size() > 1) {
-			topModel.addCreationWarning(
-					"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains too many reactants. Skipped");
-		} else if (reaction.getProducts().size() > 1) {
-			topModel.addCreationWarning(
-					"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains too many products. Skipped");
-		} else if (reaction.getModifiers().size() > 0) {
-			topModel
-					.addCreationWarning("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains modifiers. Skipped");
-		} else {
-			Alias fromAlias = reaction.getReactants().get(0).getAlias();
-			Element fromElement = fromAlias.getElement();
-			Alias toAlias = reaction.getProducts().get(0).getAlias();
-			Element toElement = toAlias.getElement();
-			if (!(fromAlias instanceof SpeciesAlias)) {
-				topModel.addCreationWarning(
-						"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start in species. Skipped");
-			} else if (!(toAlias instanceof SpeciesAlias)) {
-				topModel.addCreationWarning(
-						"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end in species. Skipped");
-			} else {
-				Species from = (Species) fromElement;
-				ComplexAlias complexFrom = ((SpeciesAlias) fromAlias).getComplexAlias();
-				Species to = (Species) toElement;
-				ComplexAlias complexTo = ((SpeciesAlias) toAlias).getComplexAlias();
-				if (complexFrom == null) {
-					topModel.addCreationWarning(
-							"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start inside complex. Skipped");
-				} else if (complexTo == null && (!(toAlias instanceof ComplexAlias))) {
-					topModel.addCreationWarning(
-							"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end inside complex. Skipped");
-				} else {
-					if (complexTo == null) {
-						complexTo = (ComplexAlias) toAlias;
-					}
-					String fromName = complexFrom.getElement().getName();
-					String toName = complexTo.getElement().getName();
-					Model fromModel = nameModelMap.get(fromName);
-					Model toModel = nameModelMap.get(toName);
-					if (fromModel == null) {
-						throw new InvalidArgumentException("Mapping file references to " + fromName + " submodel. But such model doesn't exist");
-					} else if (toModel == null) {
-						throw new InvalidArgumentException("Mapping file references to " + toName + " submodel. But such model doesn't exist");
-					}
-					Alias source = fromModel.getAliasByAliasId(from.getName());
-					if (source == null) {
-						throw new InvalidArgumentException("Mapping file references to element with alias: " + from.getName() + ". But such element doesn't exist");
-					}
-					Alias dest = null;
-					if (!(toAlias instanceof ComplexAlias)) {
-						dest = fromModel.getAliasByAliasId(to.getName());
-					}
-					SubmodelType type = SubmodelType.UNKNOWN;
-					if (from instanceof Protein) {
-						type = SubmodelType.DOWNSTREAM_TARGETS;
-					} else if (from instanceof Phenotype) {
-						type = SubmodelType.PATHWAY;
-					}
-					AliasSubmodelConnection connection = new AliasSubmodelConnection(toModel, type);
-					connection.setFromAlias(source);
-					connection.setToAlias(dest);
-					connection.setName(toModel.getName());
-					source.setSubmodel(connection);
-				}
-			}
-		}
-	}
-
-	/**
-	 * This method validates if information about model and submodels in the
-	 * params are sufficient. If not then apropriate exception will be thrown.
-	 * 
-	 * @param params
-	 *          parameters to validate
-	 * @param zipFile
-	 *          original {@link ZipFile}
-	 * @return name of the file containg mapping between submodels
-	 */
-	protected String validateSubmodelInformation(ComplexZipConverterParams params, ZipFile zipFile) {
-		Enumeration<? extends ZipEntry> entries = zipFile.entries();
-		Set<String> processed = new HashSet<String>();
-
-		String root = null;
-		String mapping = null;
-		while (entries.hasMoreElements()) {
-			ZipEntry entry = entries.nextElement();
-			if (!entry.isDirectory()) {
-				String name = entry.getName();
-				ZipEntryFile zef = params.getEntry(name);
-				if (zef == null) {
-					throw new InvalidArgumentException("No information found in params about file: " + name);
-				}
-				if (zef instanceof ModelZipEntryFile) {
-					ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
-					if (modelEntryFile.isRoot()) {
-						if (root != null) {
-							throw new InvalidArgumentException("Two roots found: " + name + ", " + root + ". There can be only one.");
-						}
-						root = name;
-					}
-					if (modelEntryFile.isMappingFile()) {
-						if (mapping != null) {
-							throw new InvalidArgumentException("Two mapping files found: " + name + ", " + mapping + ". There can be only one.");
-						}
-						mapping = name;
-					}
-				}
-				processed.add(name);
-			}
-		}
-		if (root == null) {
-			throw new InvalidArgumentException("No root map found.");
-		}
-		for (String entryName : params.getFilenames()) {
-			if (!processed.contains(entryName)) {
-				throw new InvalidArgumentException("Entry " + entryName + " doesn't exists in the zip file.");
-			}
-		}
-		return mapping;
-	}
-
-	/**
-	 * Transforms {@link DataMiningZipEntryFile} into {@link DataMiningSet}.
-	 * 
-	 * @param zipFile
-	 *          original {@link ZipFile}
-	 * @param entry
-	 *          entry in a zip file
-	 * @param dmEntry
-	 *          {@link DataMiningZipEntryFile} to transform
-	 * @return {@link DataMiningSet} for a given {@link DataMiningZipEntryFile}
-	 * @throws IOException
-	 *           thrown when there is a problem with accessing {@link ZipFile}
-	 */
-	protected DataMiningSet dataMiningZipEntryToDataMiningSet(ZipFile zipFile, ZipEntry entry, DataMiningZipEntryFile dmEntry) throws IOException {
-		DataMiningSet dmSet = new DataMiningSet();
-		dmSet.setName(dmEntry.getName());
-		dmSet.setInputData(IOUtils.toByteArray(zipFile.getInputStream(entry)));
-		dmSet.setDescription(dmEntry.getDescription());
-		dmSet.setSource(dmEntry.getSource());
-		dmSet.setType(dmEntry.getType());
-		return dmSet;
-	}
-
-	/**
-	 * Transforms {@link LayoutZipEntryFile} into {@link Layout}.
-	 * 
-	 * @param zipFile
-	 *          original {@link ZipFile}
-	 * @param entry
-	 *          entry in a zip file
-	 * @param params
-	 *          parameters used to make general conversion (we use directory where
-	 *          layout should be stored)
-	 * @param layoutEntry
-	 *          {@link LayoutZipEntryFile} to transform
-	 * @return {@link LAyout} for a given {@link LayoutZipEntryFile}
-	 * @throws IOException
-	 *           thrown when there is a problem with accessing {@link ZipFile}
-	 */
-	protected Layout layoutZipEntryFileToLayout(ComplexZipConverterParams params, ZipFile zipFile, ZipEntry entry, LayoutZipEntryFile layoutEntry)
-			throws IOException {
-		Layout layout = new Layout();
-		layout.setDescription(layoutEntry.getDescription());
-		layout.setDirectory(params.getVisualizationDir() + "/" + layoutEntry.getName().replaceAll(" ", "_"));
-		UploadedFileEntry fileEntry = new UploadedFileEntry();
-		fileEntry.setFileContent(IOUtils.toByteArray(zipFile.getInputStream(entry)));
-		fileEntry.setOriginalFileName(entry.getName());
-		layout.setInputData(fileEntry);
-		layout.setPublicLayout(true);
-		layout.setTitle(layoutEntry.getName());
-		return layout;
-	}
-
-	/**
-	 * Copy file from zip entry into temporary file.
-	 * 
-	 * @param zipFile
-	 *          input zip file
-	 * @param entry
-	 *          entry in the zip file
-	 * @return {@link File} with a copy of data from zip entry
-	 * @throws IOException
-	 *           thrown when there is a problem with input or output file
-	 */
-	protected File saveFileFromZipFile(ZipFile zipFile, ZipEntry entry) throws IOException {
-		InputStream is = zipFile.getInputStream(entry);
-		File result = File.createTempFile("temp-file-name", ".png");
-		FileOutputStream fos = new FileOutputStream(result);
-		byte[] bytes = new byte[BUFFER_SIZE];
-		int length;
-		while ((length = is.read(bytes)) >= 0) {
-			fos.write(bytes, 0, length);
-		}
-		fos.close();
-		return result;
-	}
-
-	/**
-	 * Creates inctance of {@link IConverter} used as a template parameter for
-	 * this class instatiation.
-	 * 
-	 * @return inctance of {@link IConverter}
-	 */
-	protected IConverter createConverterInstance() {
-		IConverter converter;
-		try {
-			converter = converterClazz.newInstance();
-		} catch (InstantiationException e) {
-			throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
-		} catch (IllegalAccessException e) {
-			throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
-		}
-		return converter;
-	}
-}
+package lcsb.mapviewer.converter;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.lang.reflect.Modifier;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidClassException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.zip.DataMiningZipEntryFile;
+import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
+import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
+import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class allows to create complex {@link Model} that contains submaps. It's
+ * written in generic way and use {@link IConverter} as a class to parse single
+ * submap.
+ * 
+ * @author Piotr Gawron
+ * 
+ * @param <T>
+ *          class used to create single submap from a file
+ */
+public class ComplexZipConverter<T extends IConverter> {
+
+	/**
+	 * Size of the buffer used for accessing single chunk of data from input
+	 * stream.
+	 */
+	private static final int BUFFER_SIZE = 1024;
+	/**
+	 * Default class logger.
+	 */
+	@SuppressWarnings("unused")
+	private static Logger		 logger			 = Logger.getLogger(ComplexZipConverter.class);
+	/**
+	 * Class used to create single submap from a file.
+	 */
+	private Class<T>				 converterClazz;
+
+	/**
+	 * Default constructor. Checks if the class given in the parameter is proper
+	 * {@link IConverter} implementation.
+	 * 
+	 * @param clazz
+	 *          {@link IConverter} class used for creation of the single submap
+	 */
+	public ComplexZipConverter(Class<T> clazz) {
+		if (Modifier.isAbstract(clazz.getModifiers())) {
+			throw new InvalidClassException("Param class cannot be abstract");
+		}
+
+		if (Modifier.isInterface(clazz.getModifiers())) {
+			throw new InvalidClassException("Param class cannot be an interface");
+		}
+
+		converterClazz = clazz;
+	}
+
+	/**
+	 * Creates complex {@link Model} that contains submaps.
+	 * 
+	 * @param params
+	 *          {@link ComplexZipConverterParams object} with information about
+	 *          data from which result is going to be created
+	 * @return complex {@link Model} created from input data
+	 * @throws InvalidInputDataExecption
+	 *           thrown when there is a problem with accessing input data
+	 */
+	public Model createModel(ComplexZipConverterParams params) throws InvalidInputDataExecption {
+		try {
+			ZipFile zipFile = params.getZipFile();
+			Enumeration<? extends ZipEntry> entries;
+			String mapping = validateSubmodelInformation(params, zipFile);
+
+			IConverter converter = createConverterInstance();
+			Map<String, Model> filenameModelMap = new HashMap<String, Model>();
+			Map<String, Model> nameModelMap = new HashMap<String, Model>();
+
+			entries = zipFile.entries();
+			Model result = null;
+			List<Layout> layouts = new ArrayList<Layout>();
+			List<ImageZipEntryFile> imageEntries = new ArrayList<ImageZipEntryFile>();
+			List<DataMiningSet> dataMiningSets = new ArrayList<DataMiningSet>();
+			while (entries.hasMoreElements()) {
+				ZipEntry entry = entries.nextElement();
+				if (!entry.isDirectory()) {
+					ZipEntryFile zef = params.getEntry(entry.getName());
+					if (zef instanceof ModelZipEntryFile) {
+						ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
+						InputStream is = zipFile.getInputStream(entry);
+						ConverterParams cParams = new ConverterParams();
+						cParams.inputStream(is);
+						Model model = converter.createModel(cParams);
+						model.setName(modelEntryFile.getName());
+						filenameModelMap.put(entry.getName(), model);
+						nameModelMap.put(FilenameUtils.getBaseName(modelEntryFile.getFilename()), model);
+						if (modelEntryFile.isRoot()) {
+							result = model;
+						}
+					} else if (zef instanceof LayoutZipEntryFile) {
+						layouts.add(layoutZipEntryFileToLayout(params, zipFile, entry, (LayoutZipEntryFile) zef));
+					} else if (zef instanceof ImageZipEntryFile) {
+						imageEntries.add((ImageZipEntryFile) zef);
+					} else if (zef instanceof DataMiningZipEntryFile) {
+						dataMiningSets.add(dataMiningZipEntryToDataMiningSet(zipFile, entry, (DataMiningZipEntryFile) zef));
+					} else {
+						throw new NotImplementedException("Unknwon entry type: " + zef.getClass());
+					}
+				}
+			}
+
+			if (imageEntries.size() > 0) {
+				OverviewParser parser = new OverviewParser();
+				result.setOverviewImages(parser.parseOverviewLinks(filenameModelMap, imageEntries, params.getVisualizationDir()));
+			}
+			result.addDataMiningSets(dataMiningSets);
+
+			for (Entry<String, Model> entry : filenameModelMap.entrySet()) {
+				String filename = entry.getKey();
+				Model model = entry.getValue();
+				ZipEntryFile zef = params.getEntry(filename);
+				if (zef instanceof ModelZipEntryFile) {
+					ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
+					if (!modelEntryFile.isRoot() && !modelEntryFile.isMappingFile()) {
+						ModelSubmodelConnection submodel = new ModelSubmodelConnection(model, modelEntryFile.getType());
+						submodel.setName(modelEntryFile.getName());
+						result.addSubmodelConnection(submodel);
+					}
+				}
+			}
+			for (Layout layout : layouts) {
+				Layout topLayout = new Layout(layout);
+				result.addLayout(topLayout);
+				int modelId = 0;
+				topLayout.setDirectory(topLayout.getDirectory() + modelId);
+				modelId++;
+				for (ModelSubmodelConnection connection : result.getSubmodelConnections()) {
+					Layout childLayout = new Layout(layout);
+					// we need to set separate directory names for different submodels
+					childLayout.setDirectory(childLayout.getDirectory() + modelId);
+					modelId++;
+					childLayout.setParentLayout(topLayout);
+					connection.getSubmodel().addLayout(childLayout);
+				}
+			}
+			Model mappingModel = filenameModelMap.get(mapping);
+			if (mappingModel != null) {
+				for (Reaction reaction : mappingModel.getReactions()) {
+					processReaction(mapping, nameModelMap, result, reaction);
+				}
+			}
+			return result;
+		} catch (IOException e) {
+			throw new InvalidArgumentException(e);
+		}
+	}
+
+	/**
+	 * Process a single reaction in mapping file (transfomring reaction into
+	 * connection between submodels).
+	 * 
+	 * @param mapping
+	 *          name of the mapping file
+	 * @param nameModelMap
+	 *          mapping between file names and models
+	 * @param topModel
+	 *          top model
+	 * @param reaction
+	 *          reaction to transform into connection
+	 */
+	public void processReaction(String mapping, Map<String, Model> nameModelMap, Model topModel, Reaction reaction) {
+		if (reaction.getReactants().size() > 1) {
+			topModel.addCreationWarning(
+					"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains too many reactants. Skipped");
+		} else if (reaction.getProducts().size() > 1) {
+			topModel.addCreationWarning(
+					"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains too many products. Skipped");
+		} else if (reaction.getModifiers().size() > 0) {
+			topModel
+					.addCreationWarning("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains modifiers. Skipped");
+		} else {
+			Alias fromAlias = reaction.getReactants().get(0).getAlias();
+			Element fromElement = fromAlias.getElement();
+			Alias toAlias = reaction.getProducts().get(0).getAlias();
+			Element toElement = toAlias.getElement();
+			if (!(fromAlias instanceof SpeciesAlias)) {
+				topModel.addCreationWarning(
+						"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start in species. Skipped");
+			} else if (!(toAlias instanceof SpeciesAlias)) {
+				topModel.addCreationWarning(
+						"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end in species. Skipped");
+			} else {
+				Species from = (Species) fromElement;
+				ComplexAlias complexFrom = ((SpeciesAlias) fromAlias).getComplexAlias();
+				Species to = (Species) toElement;
+				ComplexAlias complexTo = ((SpeciesAlias) toAlias).getComplexAlias();
+				if (complexFrom == null) {
+					topModel.addCreationWarning(
+							"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start inside complex. Skipped");
+				} else if (complexTo == null && (!(toAlias instanceof ComplexAlias))) {
+					topModel.addCreationWarning(
+							"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end inside complex. Skipped");
+				} else {
+					if (complexTo == null) {
+						complexTo = (ComplexAlias) toAlias;
+					}
+					String fromName = complexFrom.getElement().getName();
+					String toName = complexTo.getElement().getName();
+					Model fromModel = nameModelMap.get(fromName);
+					Model toModel = nameModelMap.get(toName);
+					if (fromModel == null) {
+						throw new InvalidArgumentException("Mapping file references to " + fromName + " submodel. But such model doesn't exist");
+					} else if (toModel == null) {
+						throw new InvalidArgumentException("Mapping file references to " + toName + " submodel. But such model doesn't exist");
+					}
+					Alias source = fromModel.getAliasByAliasId(from.getName());
+					if (source == null) {
+						throw new InvalidArgumentException("Mapping file references to element with alias: " + from.getName() + ". But such element doesn't exist");
+					}
+					Alias dest = null;
+					if (!(toAlias instanceof ComplexAlias)) {
+						dest = fromModel.getAliasByAliasId(to.getName());
+					}
+					SubmodelType type = SubmodelType.UNKNOWN;
+					if (from instanceof Protein) {
+						type = SubmodelType.DOWNSTREAM_TARGETS;
+					} else if (from instanceof Phenotype) {
+						type = SubmodelType.PATHWAY;
+					}
+					AliasSubmodelConnection connection = new AliasSubmodelConnection(toModel, type);
+					connection.setFromAlias(source);
+					connection.setToAlias(dest);
+					connection.setName(toModel.getName());
+					source.setSubmodel(connection);
+				}
+			}
+		}
+	}
+
+	/**
+	 * This method validates if information about model and submodels in the
+	 * params are sufficient. If not then apropriate exception will be thrown.
+	 * 
+	 * @param params
+	 *          parameters to validate
+	 * @param zipFile
+	 *          original {@link ZipFile}
+	 * @return name of the file containg mapping between submodels
+	 */
+	protected String validateSubmodelInformation(ComplexZipConverterParams params, ZipFile zipFile) {
+		Enumeration<? extends ZipEntry> entries = zipFile.entries();
+		Set<String> processed = new HashSet<String>();
+
+		String root = null;
+		String mapping = null;
+		while (entries.hasMoreElements()) {
+			ZipEntry entry = entries.nextElement();
+			if (!entry.isDirectory()) {
+				String name = entry.getName();
+				ZipEntryFile zef = params.getEntry(name);
+				if (zef == null) {
+					throw new InvalidArgumentException("No information found in params about file: " + name);
+				}
+				if (zef instanceof ModelZipEntryFile) {
+					ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
+					if (modelEntryFile.isRoot()) {
+						if (root != null) {
+							throw new InvalidArgumentException("Two roots found: " + name + ", " + root + ". There can be only one.");
+						}
+						root = name;
+					}
+					if (modelEntryFile.isMappingFile()) {
+						if (mapping != null) {
+							throw new InvalidArgumentException("Two mapping files found: " + name + ", " + mapping + ". There can be only one.");
+						}
+						mapping = name;
+					}
+				}
+				processed.add(name);
+			}
+		}
+		if (root == null) {
+			throw new InvalidArgumentException("No root map found.");
+		}
+		for (String entryName : params.getFilenames()) {
+			if (!processed.contains(entryName)) {
+				throw new InvalidArgumentException("Entry " + entryName + " doesn't exists in the zip file.");
+			}
+		}
+		return mapping;
+	}
+
+	/**
+	 * Transforms {@link DataMiningZipEntryFile} into {@link DataMiningSet}.
+	 * 
+	 * @param zipFile
+	 *          original {@link ZipFile}
+	 * @param entry
+	 *          entry in a zip file
+	 * @param dmEntry
+	 *          {@link DataMiningZipEntryFile} to transform
+	 * @return {@link DataMiningSet} for a given {@link DataMiningZipEntryFile}
+	 * @throws IOException
+	 *           thrown when there is a problem with accessing {@link ZipFile}
+	 */
+	protected DataMiningSet dataMiningZipEntryToDataMiningSet(ZipFile zipFile, ZipEntry entry, DataMiningZipEntryFile dmEntry) throws IOException {
+		DataMiningSet dmSet = new DataMiningSet();
+		dmSet.setName(dmEntry.getName());
+		dmSet.setInputData(IOUtils.toByteArray(zipFile.getInputStream(entry)));
+		dmSet.setDescription(dmEntry.getDescription());
+		dmSet.setSource(dmEntry.getSource());
+		dmSet.setType(dmEntry.getType());
+		return dmSet;
+	}
+
+	/**
+	 * Transforms {@link LayoutZipEntryFile} into {@link Layout}.
+	 * 
+	 * @param zipFile
+	 *          original {@link ZipFile}
+	 * @param entry
+	 *          entry in a zip file
+	 * @param params
+	 *          parameters used to make general conversion (we use directory where
+	 *          layout should be stored)
+	 * @param layoutEntry
+	 *          {@link LayoutZipEntryFile} to transform
+	 * @return {@link LAyout} for a given {@link LayoutZipEntryFile}
+	 * @throws IOException
+	 *           thrown when there is a problem with accessing {@link ZipFile}
+	 */
+	protected Layout layoutZipEntryFileToLayout(ComplexZipConverterParams params, ZipFile zipFile, ZipEntry entry, LayoutZipEntryFile layoutEntry)
+			throws IOException {
+		Layout layout = new Layout();
+		layout.setDescription(layoutEntry.getDescription());
+		layout.setDirectory(params.getVisualizationDir() + "/" + layoutEntry.getName().replaceAll(" ", "_"));
+		UploadedFileEntry fileEntry = new UploadedFileEntry();
+		fileEntry.setFileContent(IOUtils.toByteArray(zipFile.getInputStream(entry)));
+		fileEntry.setOriginalFileName(entry.getName());
+		layout.setInputData(fileEntry);
+		layout.setPublicLayout(true);
+		layout.setTitle(layoutEntry.getName());
+		return layout;
+	}
+
+	/**
+	 * Copy file from zip entry into temporary file.
+	 * 
+	 * @param zipFile
+	 *          input zip file
+	 * @param entry
+	 *          entry in the zip file
+	 * @return {@link File} with a copy of data from zip entry
+	 * @throws IOException
+	 *           thrown when there is a problem with input or output file
+	 */
+	protected File saveFileFromZipFile(ZipFile zipFile, ZipEntry entry) throws IOException {
+		InputStream is = zipFile.getInputStream(entry);
+		File result = File.createTempFile("temp-file-name", ".png");
+		FileOutputStream fos = new FileOutputStream(result);
+		byte[] bytes = new byte[BUFFER_SIZE];
+		int length;
+		while ((length = is.read(bytes)) >= 0) {
+			fos.write(bytes, 0, length);
+		}
+		fos.close();
+		return result;
+	}
+
+	/**
+	 * Creates inctance of {@link IConverter} used as a template parameter for
+	 * this class instatiation.
+	 * 
+	 * @return inctance of {@link IConverter}
+	 */
+	protected IConverter createConverterInstance() {
+		IConverter converter;
+		try {
+			converter = converterClazz.newInstance();
+		} catch (InstantiationException e) {
+			throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
+		} catch (IllegalAccessException e) {
+			throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
+		}
+		return converter;
+	}
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java
index f1e0095ad6..bcc0546a33 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java
@@ -1,82 +1,82 @@
-package lcsb.mapviewer.converter;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Interface used for reading data from file and putting it into {@link Model}
- * object.
- * 
- * @author Piotr Gawron
- * 
- */
-public interface IConverter {
-
-	/**
-	 * Parse input source and transformes it into a model object.
-	 * 
-	 * @param params
-	 *          input params used for reading data
-	 * @return model obtained from inut source
-	 * @throws InvalidInputDataExecption
-	 *           thrown when input parameters are invalid
-	 */
-
-	Model createModel(ConverterParams params) throws InvalidInputDataExecption;
-
-	/**
-	 * Export model to {@link InputStream}.
-	 * 
-	 * @param model
-	 *          model to be exported
-	 * @return {@link InputStream} with exported data
-	 * @throws InconsistentModelException
-	 *           thrown when given model is inconsistent and unable to be exported
-	 * @throws ConverterException
-	 *           thrown when there is unknown problem in a converter
-	 */
-	InputStream exportModelToInputStream(Model model) throws ConverterException, InconsistentModelException;
-
-	/**
-	 * Export model to {@link File}.
-	 * 
-	 * @param model
-	 *          model to be exported
-	 * @param filePath
-	 *          exported file path
-	 * @return {@link File} with exported data
-	 * @throws InconsistentModelException
-	 *           thrown when given model is inconsistent and unable to be exported
-	 * @throws ConverterException
-	 *           thrown when there is unknown problem in a converter
-	 * @throws IOException thrown when there is a problem with writing to file
-	 */
-	File exportModelToFile(Model model, String filePath) throws ConverterException, InconsistentModelException, IOException;
-
-	/**
-	 * Returns a common name of data format used in the converter.
-	 * 
-	 * @return common name of data format used in the converter
-	 */
-	String getCommonName();
-
-	/**
-	 * Returns {@link MimeType} of the exported data.
-	 * 
-	 * @return {@link MimeType} of the exported data
-	 */
-	MimeType getMimeType();
-
-	/**
-	 * Returns extension of the exported file.
-	 * 
-	 * @return extension of the exported file
-	 */
-	String getFileExtension();
-
-}
+package lcsb.mapviewer.converter;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * Interface used for reading data from file and putting it into {@link Model}
+ * object.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public interface IConverter {
+
+	/**
+	 * Parse input source and transformes it into a model object.
+	 * 
+	 * @param params
+	 *          input params used for reading data
+	 * @return model obtained from inut source
+	 * @throws InvalidInputDataExecption
+	 *           thrown when input parameters are invalid
+	 */
+
+	Model createModel(ConverterParams params) throws InvalidInputDataExecption;
+
+	/**
+	 * Export model to {@link InputStream}.
+	 * 
+	 * @param model
+	 *          model to be exported
+	 * @return {@link InputStream} with exported data
+	 * @throws InconsistentModelException
+	 *           thrown when given model is inconsistent and unable to be exported
+	 * @throws ConverterException
+	 *           thrown when there is unknown problem in a converter
+	 */
+	InputStream exportModelToInputStream(Model model) throws ConverterException, InconsistentModelException;
+
+	/**
+	 * Export model to {@link File}.
+	 * 
+	 * @param model
+	 *          model to be exported
+	 * @param filePath
+	 *          exported file path
+	 * @return {@link File} with exported data
+	 * @throws InconsistentModelException
+	 *           thrown when given model is inconsistent and unable to be exported
+	 * @throws ConverterException
+	 *           thrown when there is unknown problem in a converter
+	 * @throws IOException thrown when there is a problem with writing to file
+	 */
+	File exportModelToFile(Model model, String filePath) throws ConverterException, InconsistentModelException, IOException;
+
+	/**
+	 * Returns a common name of data format used in the converter.
+	 * 
+	 * @return common name of data format used in the converter
+	 */
+	String getCommonName();
+
+	/**
+	 * Returns {@link MimeType} of the exported data.
+	 * 
+	 * @return {@link MimeType} of the exported data
+	 */
+	MimeType getMimeType();
+
+	/**
+	 * Returns extension of the exported file.
+	 * 
+	 * @return extension of the exported file
+	 */
+	String getFileExtension();
+
+}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java b/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
index ceed4f3913..19a555096a 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
@@ -1,13 +1,13 @@
-package lcsb.mapviewer.converter;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ ComplexZipConverterTest.class, //
-		OverviewParserTest.class,//
-})
-public class AllTests {
-
-}
+package lcsb.mapviewer.converter;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ ComplexZipConverterTest.class, //
+		OverviewParserTest.class,//
+})
+public class AllTests {
+
+}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
index f6a8929e55..9d328c20fb 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
@@ -1,610 +1,610 @@
-package lcsb.mapviewer.converter;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Point2D;
-import java.io.File;
-import java.io.InputStream;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipFile;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewLink;
-import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ComplexZipConverterTest {
-	private static Logger	logger	= Logger.getLogger(ComplexZipConverterTest.class);
-
-	private abstract class AbstractConverter implements IConverter {
-
-	}
-
-	private interface InterfaceConverter extends IConverter {
-
-	}
-
-	public static class MockConverter implements IConverter {
-
-		@Override
-		public Model createModel(ConverterParams params) {
-			Model result = new ModelFullIndexed(null);
-
-			Protein s1 = new GenericProtein();
-			s1.setElementId("s1");
-			SpeciesAlias sa1 = new SpeciesAlias(s1);
-			sa1.setAliasId("sa1");
-			result.addAlias(sa1);
-			result.addElement(s1);
-
-			Protein s2 = new GenericProtein();
-			s2.setElementId("s2");
-			SpeciesAlias sa2 = new SpeciesAlias(s2);
-			sa2.setAliasId("sa2");
-			result.addAlias(sa2);
-			result.addElement(s2);
-
-			Protein s3 = new GenericProtein();
-			s3.setElementId("s3");
-			SpeciesAlias sa3 = new SpeciesAlias(s3);
-			sa3.setAliasId("sa3");
-			result.addAlias(sa3);
-			result.addElement(s3);
-
-			Phenotype s4 = new Phenotype();
-			s4.setElementId("s4");
-			SpeciesAlias sa4 = new SpeciesAlias(s4);
-			sa4.setAliasId("sa4");
-			result.addAlias(sa4);
-			result.addElement(s4);
-
-			ComplexSpecies cs1 = new ComplexSpecies();
-			ComplexAlias ca1 = new ComplexAlias(cs1);
-			ca1.setAliasId("ca1");
-			cs1.setElementId("cs1");
-			cs1.setName("main");
-			result.addAlias(ca1);
-			result.addElement(cs1);
-			Protein s5 = new GenericProtein();
-			s5.setElementId("s5");
-			s5.setName("sa1");
-			SpeciesAlias sa5 = new SpeciesAlias(s5);
-			sa5.setAliasId("sa5");
-			result.addAlias(sa5);
-			result.addElement(s5);
-			ca1.addAlias(sa5);
-			cs1.addElement(s5);
-			Phenotype s6 = new Phenotype();
-			s6.setElementId("s6");
-			s6.setName("sa4");
-			SpeciesAlias sa6 = new SpeciesAlias(s6);
-			sa6.setAliasId("sa6");
-			result.addAlias(sa6);
-			result.addElement(s6);
-			ca1.addAlias(sa6);
-			cs1.addElement(s6);
-
-			ComplexSpecies cs2 = new ComplexSpecies();
-			ComplexAlias ca2 = new ComplexAlias(cs2);
-			ca2.setAliasId("ca2");
-			cs2.setElementId("cs2");
-			cs2.setName("s1");
-			result.addAlias(ca2);
-			result.addElement(cs2);
-			Protein s7 = new GenericProtein();
-			s7.setElementId("s7");
-			s7.setName("sa1");
-			SpeciesAlias sa7 = new SpeciesAlias(s7);
-			sa7.setAliasId("sa7");
-			result.addAlias(sa7);
-			result.addElement(s7);
-			ca2.addAlias(sa7);
-			cs2.addElement(s7);
-
-			ComplexSpecies cs3 = new ComplexSpecies();
-			ComplexAlias ca3 = new ComplexAlias(cs3);
-			ca3.setAliasId("ca3");
-			cs3.setElementId("cs3");
-			cs3.setName("s2");
-			result.addAlias(ca3);
-			result.addElement(cs3);
-
-			ComplexSpecies cs4 = new ComplexSpecies();
-			ComplexAlias ca4 = new ComplexAlias(cs4);
-			ca4.setAliasId("ca4");
-			cs4.setElementId("cs4");
-			cs4.setName("s3");
-			result.addAlias(ca4);
-			result.addElement(cs4);
-
-			Reaction r1 = new TransportReaction();
-			r1.addReactant(new Reactant(sa5, s5));
-			r1.addProduct(new Product(sa7, s7));
-			result.addReaction(r1);
-
-			Reaction r2 = new TransportReaction();
-			r2.addReactant(new Reactant(sa6, s6));
-			r2.addProduct(new Product(ca3, cs3));
-			result.addReaction(r2);
-
-			Reaction r3 = new TransportReaction();
-			r3.addReactant(new Reactant(sa7, s7));
-			r3.addProduct(new Product(ca4, cs4));
-			result.addReaction(r3);
-			return result;
-		}
-
-		@Override
-		public InputStream exportModelToInputStream(Model model) throws InconsistentModelException {
-			// TODO Auto-generated method stub
-			return null;
-		}
-
-		@Override
-		public File exportModelToFile(Model model, String filePath) throws InconsistentModelException {
-			// TODO Auto-generated method stub
-			return null;
-		}
-
-		@Override
-		public String getCommonName() {
-			// TODO Auto-generated method stub
-			return null;
-	}
-
-		@Override
-		public MimeType getMimeType() {
-			// TODO Auto-generated method stub
-			return null;
-		}
-
-		@Override
-		public String getFileExtension() {
-			// TODO Auto-generated method stub
-			return null;
-		}
-
-	}
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testConstructor() throws Exception {
-		try {
-			try {
-				new ComplexZipConverter<AbstractConverter>(AbstractConverter.class);
-				fail("Exception expected");
-			} catch (InvalidClassException e) {
-
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testConstructor2() throws Exception {
-		try {
-			try {
-				new ComplexZipConverter<InterfaceConverter>(InterfaceConverter.class);
-				fail("Exception expected");
-			} catch (InvalidClassException e) {
-
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testConstructor3() throws Exception {
-		try {
-			new ComplexZipConverter<MockConverter>(MockConverter.class);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testParamsOk() throws Exception {
-		try {
-			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
-			ComplexZipConverterParams params = new ComplexZipConverterParams();
-			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
-			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
-			params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
-			params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
-			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
-			params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
-			Model model = converter.createModel(params);
-			assertNotNull(model);
-			assertEquals("main", model.getName());
-			assertEquals(3, model.getSubmodelConnections().size());
-
-			Model s1Model = null;
-			Model s2Model = null;
-			Model s3Model = null;
-
-			for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
-				if (submodel.getName().equals("s1")) {
-					s1Model = submodel.getSubmodel().getModel();
-				}
-				if (submodel.getName().equals("s2")) {
-					s2Model = submodel.getSubmodel().getModel();
-				}
-				if (submodel.getName().equals("s3")) {
-					s3Model = submodel.getSubmodel().getModel();
-				}
-			}
-			assertNotNull(s1Model);
-			assertNotNull(s2Model);
-			assertNotNull(s3Model);
-
-			Alias al1 = model.getAliasByAliasId("sa1");
-			assertNotNull(al1.getSubmodel());
-			assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
-			assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
-
-			Alias al2 = model.getAliasByAliasId("sa2");
-			assertNull(al2.getSubmodel());
-
-			Alias al4 = model.getAliasByAliasId("sa4");
-			assertNotNull(al4.getSubmodel());
-			assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
-			assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
-
-			Alias s1_al1 = s1Model.getAliasByAliasId("sa1");
-			assertNotNull(s1_al1.getSubmodel());
-			assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
-			assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testChangeModelZipEntry() throws Exception {
-		try {
-			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
-			ComplexZipConverterParams params = new ComplexZipConverterParams();
-			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
-			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
-			params.entry(new ModelZipEntryFile("s1.xml", "s12", false, false, SubmodelType.DOWNSTREAM_TARGETS));
-			params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
-			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
-			params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
-			Model model = converter.createModel(params);
-			assertNotNull(model);
-			assertEquals("main", model.getName());
-			assertEquals(3, model.getSubmodelConnections().size());
-
-			Model s1Model = null;
-			Model s2Model = null;
-			Model s3Model = null;
-
-			for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
-				if (submodel.getName().equals("s12")) {
-					s1Model = submodel.getSubmodel().getModel();
-				}
-				if (submodel.getName().equals("s2")) {
-					s2Model = submodel.getSubmodel().getModel();
-				}
-				if (submodel.getName().equals("s3")) {
-					s3Model = submodel.getSubmodel().getModel();
-				}
-			}
-			assertNotNull(s1Model);
-			assertNotNull(s2Model);
-			assertNotNull(s3Model);
-
-			Alias al1 = model.getAliasByAliasId("sa1");
-			assertNotNull(al1.getSubmodel());
-			assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
-			assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
-
-			Alias al2 = model.getAliasByAliasId("sa2");
-			assertNull(al2.getSubmodel());
-
-			Alias al4 = model.getAliasByAliasId("sa4");
-			assertNotNull(al4.getSubmodel());
-			assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
-			assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
-
-			Alias s1_al1 = s1Model.getAliasByAliasId("sa1");
-			assertNotNull(s1_al1.getSubmodel());
-			assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
-			assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testParamsMissing() throws Exception {
-		try {
-			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
-			ComplexZipConverterParams params = new ComplexZipConverterParams();
-			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
-			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
-			params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
-			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
-			params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
-			try {
-				converter.createModel(params);
-				fail("Exception expected");
-			} catch (InvalidArgumentException e) {
-
-			}
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testParamsInvalid1() throws Exception {
-		try {
-			// two mains
-			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
-			ComplexZipConverterParams params = new ComplexZipConverterParams();
-			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
-			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
-			params.entry(new ModelZipEntryFile("s1.xml", "s1", true, false, SubmodelType.DOWNSTREAM_TARGETS));
-			params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
-			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
-			params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
-			try {
-				converter.createModel(params);
-				fail("Exception expected");
-			} catch (InvalidArgumentException e) {
-
-			}
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testParamsInvalid2() throws Exception {
-		try {
-			// zero mains
-			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
-			ComplexZipConverterParams params = new ComplexZipConverterParams();
-			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
-			params.entry(new ModelZipEntryFile("main.xml", "main", false, false, null));
-			params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
-			params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
-			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
-			params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
-			try {
-				converter.createModel(params);
-				fail("Exception expected");
-			} catch (InvalidArgumentException e) {
-
-			}
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testParamsInvalid3() throws Exception {
-		try {
-			// two mappings
-			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
-			ComplexZipConverterParams params = new ComplexZipConverterParams();
-			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
-			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
-			params.entry(new ModelZipEntryFile("s1.xml", "s1", false, true, SubmodelType.DOWNSTREAM_TARGETS));
-			params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
-			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
-			params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
-			try {
-				converter.createModel(params);
-				fail("Exception expected");
-			} catch (InvalidArgumentException e) {
-
-			}
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testParamsMissingMapping() throws Exception {
-		try {
-			// zero mappings (should be ok)
-			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
-			ComplexZipConverterParams params = new ComplexZipConverterParams();
-			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
-			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
-			params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
-			params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
-			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
-			params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
-			Model model = converter.createModel(params);
-
-			assertNotNull(model);
-
-			assertEquals(4, model.getSubmodelConnections().size());
-
-			for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
-				if (submodel.getName().equals("s1")) {
-					assertEquals(SubmodelType.DOWNSTREAM_TARGETS, submodel.getType());
-				} else if (submodel.getName().equals("s2")) {
-					assertEquals(SubmodelType.PATHWAY, submodel.getType());
-				} else if (submodel.getName().equals("s3")) {
-					assertEquals(SubmodelType.UNKNOWN, submodel.getType());
-				} else if (submodel.getName().equals("mapping")) {
-					assertEquals(SubmodelType.UNKNOWN, submodel.getType());
-				}
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-	@Test
-	public void testTooManyParams() throws Exception {
-		try {
-			// zero mappings (should be ok)
-			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
-			ComplexZipConverterParams params = new ComplexZipConverterParams();
-			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
-			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
-			params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
-			params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
-			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
-			params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
-			params.entry(new ModelZipEntryFile("blabla.xml", "s3", false, false, SubmodelType.UNKNOWN));
-			try {
-				converter.createModel(params);
-				fail("Exception expected");
-			} catch (InvalidArgumentException e) {
-
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testInvalidMappingFile() throws Exception {
-		try {
-			// zero mappings (should be ok)
-			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
-			ComplexZipConverterParams params = new ComplexZipConverterParams();
-			params.zipFile(new ZipFile("testFiles/invalid_mapping.zip"));
-			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
-			params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
-			try {
-				Model model = converter.createModel(params);
-				for (String string : model.getCreationWarnings()) {
-					logger.debug(string);
-				}
-				fail("Exception expected");
-			} catch (InvalidArgumentException e) {
-
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testOverviewImageLink() throws Exception {
-		try {
-			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
-			ZipFile zipFile = new ZipFile("testFiles/complex_model_with_img.zip");
-			ComplexZipConverterParams params = new ComplexZipConverterParams();
-			params.zipFile(zipFile);
-
-			ZipEntryFileFactory factory = new ZipEntryFileFactory();
-			Enumeration<? extends ZipEntry> entries = zipFile.entries();
-			while (entries.hasMoreElements()) {
-				ZipEntry entry = entries.nextElement();
-				if (!entry.isDirectory()) {
-					params.entry(factory.createZipEntryFile(entry, zipFile));
-				}
-			}
-
-			Model model = converter.createModel(params);
-			assertNotNull(model);
-			assertEquals("main", model.getName());
-
-			List<OverviewImage> result = model.getOverviewImages();
-
-			assertNotNull(result);
-			assertEquals(1, result.size());
-
-			OverviewImage img = result.get(0);
-
-			assertEquals("test.png", img.getFilename());
-			assertEquals((Integer) 639, img.getHeight());
-			assertEquals((Integer) 963, img.getWidth());
-			assertEquals(2, img.getLinks().size());
-
-			OverviewLink link = img.getLinks().get(0);
-			List<Point2D> polygon = link.getPolygonCoordinates();
-			assertEquals(4, polygon.size());
-
-			assertTrue(link instanceof OverviewModelLink);
-
-			OverviewModelLink mLink = (OverviewModelLink) link;
-			assertEquals((Integer) 10, mLink.getxCoord());
-			assertEquals((Integer) 10, mLink.getyCoord());
-			assertEquals((Integer) 3, mLink.getZoomLevel());
-			assertEquals(model, mLink.getLinkedModel());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-
-	}
-
-}
+package lcsb.mapviewer.converter;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+import java.io.File;
+import java.io.InputStream;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidClassException;
+import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.OverviewLink;
+import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.ComplexSpecies;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ComplexZipConverterTest {
+	private static Logger	logger	= Logger.getLogger(ComplexZipConverterTest.class);
+
+	private abstract class AbstractConverter implements IConverter {
+
+	}
+
+	private interface InterfaceConverter extends IConverter {
+
+	}
+
+	public static class MockConverter implements IConverter {
+
+		@Override
+		public Model createModel(ConverterParams params) {
+			Model result = new ModelFullIndexed(null);
+
+			Protein s1 = new GenericProtein();
+			s1.setElementId("s1");
+			SpeciesAlias sa1 = new SpeciesAlias(s1);
+			sa1.setAliasId("sa1");
+			result.addAlias(sa1);
+			result.addElement(s1);
+
+			Protein s2 = new GenericProtein();
+			s2.setElementId("s2");
+			SpeciesAlias sa2 = new SpeciesAlias(s2);
+			sa2.setAliasId("sa2");
+			result.addAlias(sa2);
+			result.addElement(s2);
+
+			Protein s3 = new GenericProtein();
+			s3.setElementId("s3");
+			SpeciesAlias sa3 = new SpeciesAlias(s3);
+			sa3.setAliasId("sa3");
+			result.addAlias(sa3);
+			result.addElement(s3);
+
+			Phenotype s4 = new Phenotype();
+			s4.setElementId("s4");
+			SpeciesAlias sa4 = new SpeciesAlias(s4);
+			sa4.setAliasId("sa4");
+			result.addAlias(sa4);
+			result.addElement(s4);
+
+			ComplexSpecies cs1 = new ComplexSpecies();
+			ComplexAlias ca1 = new ComplexAlias(cs1);
+			ca1.setAliasId("ca1");
+			cs1.setElementId("cs1");
+			cs1.setName("main");
+			result.addAlias(ca1);
+			result.addElement(cs1);
+			Protein s5 = new GenericProtein();
+			s5.setElementId("s5");
+			s5.setName("sa1");
+			SpeciesAlias sa5 = new SpeciesAlias(s5);
+			sa5.setAliasId("sa5");
+			result.addAlias(sa5);
+			result.addElement(s5);
+			ca1.addAlias(sa5);
+			cs1.addElement(s5);
+			Phenotype s6 = new Phenotype();
+			s6.setElementId("s6");
+			s6.setName("sa4");
+			SpeciesAlias sa6 = new SpeciesAlias(s6);
+			sa6.setAliasId("sa6");
+			result.addAlias(sa6);
+			result.addElement(s6);
+			ca1.addAlias(sa6);
+			cs1.addElement(s6);
+
+			ComplexSpecies cs2 = new ComplexSpecies();
+			ComplexAlias ca2 = new ComplexAlias(cs2);
+			ca2.setAliasId("ca2");
+			cs2.setElementId("cs2");
+			cs2.setName("s1");
+			result.addAlias(ca2);
+			result.addElement(cs2);
+			Protein s7 = new GenericProtein();
+			s7.setElementId("s7");
+			s7.setName("sa1");
+			SpeciesAlias sa7 = new SpeciesAlias(s7);
+			sa7.setAliasId("sa7");
+			result.addAlias(sa7);
+			result.addElement(s7);
+			ca2.addAlias(sa7);
+			cs2.addElement(s7);
+
+			ComplexSpecies cs3 = new ComplexSpecies();
+			ComplexAlias ca3 = new ComplexAlias(cs3);
+			ca3.setAliasId("ca3");
+			cs3.setElementId("cs3");
+			cs3.setName("s2");
+			result.addAlias(ca3);
+			result.addElement(cs3);
+
+			ComplexSpecies cs4 = new ComplexSpecies();
+			ComplexAlias ca4 = new ComplexAlias(cs4);
+			ca4.setAliasId("ca4");
+			cs4.setElementId("cs4");
+			cs4.setName("s3");
+			result.addAlias(ca4);
+			result.addElement(cs4);
+
+			Reaction r1 = new TransportReaction();
+			r1.addReactant(new Reactant(sa5, s5));
+			r1.addProduct(new Product(sa7, s7));
+			result.addReaction(r1);
+
+			Reaction r2 = new TransportReaction();
+			r2.addReactant(new Reactant(sa6, s6));
+			r2.addProduct(new Product(ca3, cs3));
+			result.addReaction(r2);
+
+			Reaction r3 = new TransportReaction();
+			r3.addReactant(new Reactant(sa7, s7));
+			r3.addProduct(new Product(ca4, cs4));
+			result.addReaction(r3);
+			return result;
+		}
+
+		@Override
+		public InputStream exportModelToInputStream(Model model) throws InconsistentModelException {
+			// TODO Auto-generated method stub
+			return null;
+		}
+
+		@Override
+		public File exportModelToFile(Model model, String filePath) throws InconsistentModelException {
+			// TODO Auto-generated method stub
+			return null;
+		}
+
+		@Override
+		public String getCommonName() {
+			// TODO Auto-generated method stub
+			return null;
+	}
+
+		@Override
+		public MimeType getMimeType() {
+			// TODO Auto-generated method stub
+			return null;
+		}
+
+		@Override
+		public String getFileExtension() {
+			// TODO Auto-generated method stub
+			return null;
+		}
+
+	}
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testConstructor() throws Exception {
+		try {
+			try {
+				new ComplexZipConverter<AbstractConverter>(AbstractConverter.class);
+				fail("Exception expected");
+			} catch (InvalidClassException e) {
+
+			}
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testConstructor2() throws Exception {
+		try {
+			try {
+				new ComplexZipConverter<InterfaceConverter>(InterfaceConverter.class);
+				fail("Exception expected");
+			} catch (InvalidClassException e) {
+
+			}
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testConstructor3() throws Exception {
+		try {
+			new ComplexZipConverter<MockConverter>(MockConverter.class);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testParamsOk() throws Exception {
+		try {
+			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+			ComplexZipConverterParams params = new ComplexZipConverterParams();
+			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+			params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+			params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+			params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+			Model model = converter.createModel(params);
+			assertNotNull(model);
+			assertEquals("main", model.getName());
+			assertEquals(3, model.getSubmodelConnections().size());
+
+			Model s1Model = null;
+			Model s2Model = null;
+			Model s3Model = null;
+
+			for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
+				if (submodel.getName().equals("s1")) {
+					s1Model = submodel.getSubmodel().getModel();
+				}
+				if (submodel.getName().equals("s2")) {
+					s2Model = submodel.getSubmodel().getModel();
+				}
+				if (submodel.getName().equals("s3")) {
+					s3Model = submodel.getSubmodel().getModel();
+				}
+			}
+			assertNotNull(s1Model);
+			assertNotNull(s2Model);
+			assertNotNull(s3Model);
+
+			Alias al1 = model.getAliasByAliasId("sa1");
+			assertNotNull(al1.getSubmodel());
+			assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
+			assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
+
+			Alias al2 = model.getAliasByAliasId("sa2");
+			assertNull(al2.getSubmodel());
+
+			Alias al4 = model.getAliasByAliasId("sa4");
+			assertNotNull(al4.getSubmodel());
+			assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
+			assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
+
+			Alias s1_al1 = s1Model.getAliasByAliasId("sa1");
+			assertNotNull(s1_al1.getSubmodel());
+			assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
+			assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testChangeModelZipEntry() throws Exception {
+		try {
+			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+			ComplexZipConverterParams params = new ComplexZipConverterParams();
+			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+			params.entry(new ModelZipEntryFile("s1.xml", "s12", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+			params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+			params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+			Model model = converter.createModel(params);
+			assertNotNull(model);
+			assertEquals("main", model.getName());
+			assertEquals(3, model.getSubmodelConnections().size());
+
+			Model s1Model = null;
+			Model s2Model = null;
+			Model s3Model = null;
+
+			for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
+				if (submodel.getName().equals("s12")) {
+					s1Model = submodel.getSubmodel().getModel();
+				}
+				if (submodel.getName().equals("s2")) {
+					s2Model = submodel.getSubmodel().getModel();
+				}
+				if (submodel.getName().equals("s3")) {
+					s3Model = submodel.getSubmodel().getModel();
+				}
+			}
+			assertNotNull(s1Model);
+			assertNotNull(s2Model);
+			assertNotNull(s3Model);
+
+			Alias al1 = model.getAliasByAliasId("sa1");
+			assertNotNull(al1.getSubmodel());
+			assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
+			assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
+
+			Alias al2 = model.getAliasByAliasId("sa2");
+			assertNull(al2.getSubmodel());
+
+			Alias al4 = model.getAliasByAliasId("sa4");
+			assertNotNull(al4.getSubmodel());
+			assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
+			assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
+
+			Alias s1_al1 = s1Model.getAliasByAliasId("sa1");
+			assertNotNull(s1_al1.getSubmodel());
+			assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
+			assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testParamsMissing() throws Exception {
+		try {
+			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+			ComplexZipConverterParams params = new ComplexZipConverterParams();
+			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+			params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+			params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+			try {
+				converter.createModel(params);
+				fail("Exception expected");
+			} catch (InvalidArgumentException e) {
+
+			}
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testParamsInvalid1() throws Exception {
+		try {
+			// two mains
+			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+			ComplexZipConverterParams params = new ComplexZipConverterParams();
+			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+			params.entry(new ModelZipEntryFile("s1.xml", "s1", true, false, SubmodelType.DOWNSTREAM_TARGETS));
+			params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+			params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+			try {
+				converter.createModel(params);
+				fail("Exception expected");
+			} catch (InvalidArgumentException e) {
+
+			}
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testParamsInvalid2() throws Exception {
+		try {
+			// zero mains
+			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+			ComplexZipConverterParams params = new ComplexZipConverterParams();
+			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+			params.entry(new ModelZipEntryFile("main.xml", "main", false, false, null));
+			params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+			params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+			params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+			try {
+				converter.createModel(params);
+				fail("Exception expected");
+			} catch (InvalidArgumentException e) {
+
+			}
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testParamsInvalid3() throws Exception {
+		try {
+			// two mappings
+			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+			ComplexZipConverterParams params = new ComplexZipConverterParams();
+			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+			params.entry(new ModelZipEntryFile("s1.xml", "s1", false, true, SubmodelType.DOWNSTREAM_TARGETS));
+			params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+			params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+			try {
+				converter.createModel(params);
+				fail("Exception expected");
+			} catch (InvalidArgumentException e) {
+
+			}
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testParamsMissingMapping() throws Exception {
+		try {
+			// zero mappings (should be ok)
+			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+			ComplexZipConverterParams params = new ComplexZipConverterParams();
+			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+			params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+			params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+			params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
+			Model model = converter.createModel(params);
+
+			assertNotNull(model);
+
+			assertEquals(4, model.getSubmodelConnections().size());
+
+			for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
+				if (submodel.getName().equals("s1")) {
+					assertEquals(SubmodelType.DOWNSTREAM_TARGETS, submodel.getType());
+				} else if (submodel.getName().equals("s2")) {
+					assertEquals(SubmodelType.PATHWAY, submodel.getType());
+				} else if (submodel.getName().equals("s3")) {
+					assertEquals(SubmodelType.UNKNOWN, submodel.getType());
+				} else if (submodel.getName().equals("mapping")) {
+					assertEquals(SubmodelType.UNKNOWN, submodel.getType());
+				}
+			}
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+	@Test
+	public void testTooManyParams() throws Exception {
+		try {
+			// zero mappings (should be ok)
+			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+			ComplexZipConverterParams params = new ComplexZipConverterParams();
+			params.zipFile(new ZipFile("testFiles/complex_model.zip"));
+			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+			params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
+			params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
+			params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
+			params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
+			params.entry(new ModelZipEntryFile("blabla.xml", "s3", false, false, SubmodelType.UNKNOWN));
+			try {
+				converter.createModel(params);
+				fail("Exception expected");
+			} catch (InvalidArgumentException e) {
+
+			}
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testInvalidMappingFile() throws Exception {
+		try {
+			// zero mappings (should be ok)
+			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+			ComplexZipConverterParams params = new ComplexZipConverterParams();
+			params.zipFile(new ZipFile("testFiles/invalid_mapping.zip"));
+			params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
+			params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
+			try {
+				Model model = converter.createModel(params);
+				for (String string : model.getCreationWarnings()) {
+					logger.debug(string);
+				}
+				fail("Exception expected");
+			} catch (InvalidArgumentException e) {
+
+			}
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testOverviewImageLink() throws Exception {
+		try {
+			ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+			ZipFile zipFile = new ZipFile("testFiles/complex_model_with_img.zip");
+			ComplexZipConverterParams params = new ComplexZipConverterParams();
+			params.zipFile(zipFile);
+
+			ZipEntryFileFactory factory = new ZipEntryFileFactory();
+			Enumeration<? extends ZipEntry> entries = zipFile.entries();
+			while (entries.hasMoreElements()) {
+				ZipEntry entry = entries.nextElement();
+				if (!entry.isDirectory()) {
+					params.entry(factory.createZipEntryFile(entry, zipFile));
+				}
+			}
+
+			Model model = converter.createModel(params);
+			assertNotNull(model);
+			assertEquals("main", model.getName());
+
+			List<OverviewImage> result = model.getOverviewImages();
+
+			assertNotNull(result);
+			assertEquals(1, result.size());
+
+			OverviewImage img = result.get(0);
+
+			assertEquals("test.png", img.getFilename());
+			assertEquals((Integer) 639, img.getHeight());
+			assertEquals((Integer) 963, img.getWidth());
+			assertEquals(2, img.getLinks().size());
+
+			OverviewLink link = img.getLinks().get(0);
+			List<Point2D> polygon = link.getPolygonCoordinates();
+			assertEquals(4, polygon.size());
+
+			assertTrue(link instanceof OverviewModelLink);
+
+			OverviewModelLink mLink = (OverviewModelLink) link;
+			assertEquals((Integer) 10, mLink.getxCoord());
+			assertEquals((Integer) 10, mLink.getyCoord());
+			assertEquals((Integer) 3, mLink.getZoomLevel());
+			assertEquals(model, mLink.getLinkedModel());
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+
+	}
+
+}
diff --git a/converter/tmp/test.png b/converter/tmp/test.png
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T6ag1J;R!g}?zEw9^*{Mvpf}H#

literal 0
HcmV?d00001

diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
index adbf07b637..73e2aa0ff7 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -1,356 +1,356 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.ArrowTypeData;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This {@link ModelCommand} colors a model (nodes and reactions) according to
- * set of {@link ColorSchema rules}.
- * 
- * @author Piotr Gawron
- * 
- */
-public class ColorModelCommand extends ModelCommand {
-
-	/**
-	 * Default class logger.
-	 */
-	@SuppressWarnings("unused")
-	private Logger									logger = Logger.getLogger(ColorModelCommand.class);
-
-	/**
-	 * Set of color schemas used in this command to color model.
-	 */
-	private Collection<ColorSchema>	schemas;
-
-	/**
-	 * Default constructor.
-	 * 
-	 * @param model
-	 *          original model
-	 * @param schemas
-	 *          set of color schemas used in this command to color model.
-	 */
-	public ColorModelCommand(Model model, Collection<ColorSchema> schemas) {
-		super(model);
-		this.schemas = schemas;
-	}
-
-	/**
-	 * Applies color schema into the reaction.
-	 * 
-	 * @param reaction
-	 *          object to be colored
-	 * @param schema
-	 *          color schema to be used
-	 * @throws InvalidColorSchemaException
-	 *           thrown when alias was already colored by other schema
-	 */
-	private void applyColor(Reaction reaction, ColorSchema schema) throws InvalidColorSchemaException {
-		if (!reaction.getReactants().get(0).getLine().getColor().equals(Color.BLACK)) {
-			throw new InvalidColorSchemaException("At least two rows try to set color to reaction: " + reaction.getIdReaction());
-		}
-
-		Color color = schema.getNormalizedColor();
-		for (AbstractNode node : reaction.getNodes()) {
-			node.getLine().setColor(color);
-			if (schema.getLineWidth() != null) {
-				node.getLine().setWidth(schema.getLineWidth());
-			}
-		}
-		if (schema.getReverseReaction() != null && schema.getReverseReaction()) {
-			ArrowTypeData atdBegining = reaction.getReactants().get(0).getLine().getBeginAtd();
-			ArrowTypeData atdEnd = reaction.getProducts().get(0).getLine().getEndAtd();
-			for (Reactant reactant : reaction.getReactants()) {
-				reactant.getLine().setBeginAtd(atdEnd);
-			}
-			for (Product product : reaction.getProducts()) {
-				product.getLine().setEndAtd(atdBegining);
-			}
-		}
-	}
-
-	/**
-	 * Checks if the coloring schema should be used for the reaction.
-	 * 
-	 * @param reaction
-	 *          reaction to which coloring schema is checked
-	 * @param schema
-	 *          coloring schema
-	 * @return <code>true</code> if coloring schema should be used for alias,
-	 *         <code>false</code> otherwise
-	 */
-	private boolean match(Reaction reaction, ColorSchema schema) {
-		if (schema.getName() != null) {
-			return false;
-		}
-		
-		if (schema.getReactionIdentifier() != null && schema.getReactionIdentifier().equalsIgnoreCase(reaction.getIdReaction())) {
-			return true;
-		}
-		if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
-			MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
-
-			if (reaction.getMiriamData().contains(md)) {
-				return true;
-			}
-		}
-		for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
-			if (pair.getRight() != null && !pair.getRight().equals("")) {
-
-				MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
-				if (reaction.getMiriamData().contains(md)) {
-					return true;
-				}
-			}
-		}
-
-		return false;
-	}
-
-	/**
-	 * Applies color schema into the alias.
-	 * 
-	 * @param alias
-	 *          object to be colored
-	 * @param schema
-	 *          color schema to be used
-	 * @throws InvalidColorSchemaException
-	 *           thrown when alias was already colored by other schema
-	 */
-	private void applyColor(Alias alias, ColorSchema schema) throws InvalidColorSchemaException {
-		if (alias instanceof SpeciesAlias) {
-			Species species = ((SpeciesAlias) alias).getSpecies();
-
-			if (!alias.getColor().equals(Color.WHITE)) {
-				throw new InvalidColorSchemaException("At least two rows try to set color to element: " + species.getName());
-			}
-
-			alias.setColor(schema.getNormalizedColor());
-		}
-
-	}
-
-	/**
-	 * Checks if the coloring schema should be used for the alias.
-	 * 
-	 * @param alias
-	 *          alias to which coloring schema is checked
-	 * @param schema
-	 *          coloring schema
-	 * @return <code>true</code> if coloring schema should be used for alias,
-	 *         <code>false</code> otherwise
-	 */
-	protected boolean match(Alias alias, ColorSchema schema) {
-		if (alias instanceof SpeciesAlias) {
-			Species species = ((SpeciesAlias) alias).getSpecies();
-			if (schema.getName() != null) {
-				if (!species.getName().equalsIgnoreCase(schema.getName())) {
-					return false;
-				}
-			}
-			if (schema.getTypes().size() > 0) {
-				if (!schema.getTypes().contains(species.getClass())) {
-					return false;
-				}
-			}
-			if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
-				MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
-
-				if (!species.getMiriamData().contains(md)) {
-					return false;
-				}
-			}
-			for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
-				if (pair.getRight() != null && !pair.getRight().equals("")) {
-					MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
-					if (!species.getMiriamData().contains(md)) {
-						return false;
-					}
-				}
-			}
-
-			if (schema.getCompartments().size() > 0) {
-				boolean found = false;
-				for (CompartmentAlias cAlias : alias.getModelData().getModel().getCompartmentsAliases()) {
-					for (String compartmentName : schema.getCompartments()) {
-						if (cAlias.getCompartment() != null) {
-							if (cAlias.getCompartment().getName().equalsIgnoreCase(compartmentName)) {
-								if (cAlias.cross(alias)) {
-									found = true;
-								}
-							}
-						}
-					}
-				}
-				if (!found) {
-					return false;
-				}
-			}
-
-			// if we have reaction id to match then reject
-			if (schema.getReactionIdentifier() != null) {
-				return false;
-			}
-			return true;
-		} else {
-			return false;
-		}
-	}
-
-	/**
-	 * Checks which coloring schemas weren't used in the model coloring process.
-	 * 
-	 * @return list of schemas that weren't used during coloring
-	 */
-	public Collection<ColorSchema> getMissingSchema() {
-		List<ColorSchema> result = new ArrayList<ColorSchema>();
-		for (ColorSchema schema : schemas) {
-			boolean found = false;
-			for (Alias alias : getModel().getAliases()) {
-				if (match(alias, schema)) {
-					found = true;
-				}
-			}
-			for (Reaction reaction : getModel().getReactions()) {
-				if (match(reaction, schema)) {
-					found = true;
-				}
-			}
-			if (!found) {
-				result.add(schema);
-			}
-		}
-		return result;
-	}
-
-	/**
-	 * Returns list of elements ({@link Reaction reactions} and {@link Alias
-	 * aliases}) that are modified by the coloring command.
-	 * 
-	 * @return {@link Map}, where key corresponds to modified {@link Reaction} or
-	 *         {@link Alias} and value is a {@link ColorSchema} that should be
-	 *         used for coloring
-	 * @throws InvalidColorSchemaException
-	 *           thrown when more than one {@link ColorSchema} match an element
-	 */
-	public Map<Object, ColorSchema> getModifiedElements() throws InvalidColorSchemaException {
-		Map<Object, ColorSchema> result = new HashMap<>();
-
-		List<Model> models = new ArrayList<>();
-		models.add(getModel());
-		models.addAll(getModel().getSubmodels());
-		for (Model model2 : models) {
-			for (ColorSchema schema : schemas) {
-				for (Alias alias : model2.getAliases()) {
-					if (match(alias, schema)) {
-						if (result.get(alias) != null && !result.get(alias).getNormalizedColor().equals(Color.WHITE)) {
-							throw new InvalidColorSchemaException("Alias " + alias.getAliasId() + " is colored by more than one rule.");
-						}
-						result.put(alias, schema);
-					}
-				}
-				for (Reaction reaction : model2.getReactions()) {
-					if (match(reaction, schema)) {
-						if (result.get(reaction) != null && !result.get(reaction).getNormalizedColor().equals(Color.WHITE)) {
-							throw new InvalidColorSchemaException("Reaction " + reaction.getIdReaction() + " is colored by more than one rule.");
-						}
-						result.put(reaction, schema);
-					}
-				}
-			}
-		}
-		return result;
-	}
-
-	@Override
-	protected void undoImplementation() throws CommandExecutionException {
-		throw new NotImplementedException();
-
-	}
-
-	@Override
-	protected void redoImplementation() throws CommandExecutionException {
-		throw new NotImplementedException();
-	}
-
-	/**
-	 * Colors parameter model using coloring for this command. This method is used
-	 * internally to color either top {@link Model} or one of it's sumbodels.
-	 * 
-	 * @param result
-	 *          model to color
-	 * @param top
-	 *          is the model a top (parent) model
-	 * @throws InvalidColorSchemaException
-	 *           thrown when set of {@link ColorSchema} is invalid
-	 */
-	private void colorModel(Model result, boolean top) throws InvalidColorSchemaException {
-
-		for (Alias alias : result.getAliases()) {
-			alias.setColor(Color.WHITE);
-		}
-		for (Reaction reaction : result.getReactions()) {
-			for (AbstractNode node : reaction.getNodes()) {
-				node.getLine().setColor(Color.BLACK);
-			}
-		}
-
-		for (ColorSchema schema : schemas) {
-			for (Alias alias : result.getAliases()) {
-				if (match(alias, schema)) {
-					schema.setMatches(schema.getMatches() + 1);
-					applyColor(alias, schema);
-				}
-			}
-			for (Reaction reaction : result.getReactions()) {
-				if (match(reaction, schema)) {
-					schema.setMatches(schema.getMatches() + 1);
-					applyColor(reaction, schema);
-				}
-			}
-		}
-
-		if (top) {
-			for (ModelSubmodelConnection connection : result.getSubmodelConnections()) {
-				colorModel(connection.getSubmodel().getModel(), false);
-			}
-		}
-
-	}
-
-	@Override
-	protected void executeImplementation() throws CommandExecutionException {
-		try {
-			colorModel(getModel(), true);
-		} catch (InvalidColorSchemaException e) {
-			throw new CommandExecutionException(e);
-		}
-	}
-
-}
+package lcsb.mapviewer.commands;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.ArrowTypeData;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This {@link ModelCommand} colors a model (nodes and reactions) according to
+ * set of {@link ColorSchema rules}.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public class ColorModelCommand extends ModelCommand {
+
+	/**
+	 * Default class logger.
+	 */
+	@SuppressWarnings("unused")
+	private Logger									logger = Logger.getLogger(ColorModelCommand.class);
+
+	/**
+	 * Set of color schemas used in this command to color model.
+	 */
+	private Collection<ColorSchema>	schemas;
+
+	/**
+	 * Default constructor.
+	 * 
+	 * @param model
+	 *          original model
+	 * @param schemas
+	 *          set of color schemas used in this command to color model.
+	 */
+	public ColorModelCommand(Model model, Collection<ColorSchema> schemas) {
+		super(model);
+		this.schemas = schemas;
+	}
+
+	/**
+	 * Applies color schema into the reaction.
+	 * 
+	 * @param reaction
+	 *          object to be colored
+	 * @param schema
+	 *          color schema to be used
+	 * @throws InvalidColorSchemaException
+	 *           thrown when alias was already colored by other schema
+	 */
+	private void applyColor(Reaction reaction, ColorSchema schema) throws InvalidColorSchemaException {
+		if (!reaction.getReactants().get(0).getLine().getColor().equals(Color.BLACK)) {
+			throw new InvalidColorSchemaException("At least two rows try to set color to reaction: " + reaction.getIdReaction());
+		}
+
+		Color color = schema.getNormalizedColor();
+		for (AbstractNode node : reaction.getNodes()) {
+			node.getLine().setColor(color);
+			if (schema.getLineWidth() != null) {
+				node.getLine().setWidth(schema.getLineWidth());
+			}
+		}
+		if (schema.getReverseReaction() != null && schema.getReverseReaction()) {
+			ArrowTypeData atdBegining = reaction.getReactants().get(0).getLine().getBeginAtd();
+			ArrowTypeData atdEnd = reaction.getProducts().get(0).getLine().getEndAtd();
+			for (Reactant reactant : reaction.getReactants()) {
+				reactant.getLine().setBeginAtd(atdEnd);
+			}
+			for (Product product : reaction.getProducts()) {
+				product.getLine().setEndAtd(atdBegining);
+			}
+		}
+	}
+
+	/**
+	 * Checks if the coloring schema should be used for the reaction.
+	 * 
+	 * @param reaction
+	 *          reaction to which coloring schema is checked
+	 * @param schema
+	 *          coloring schema
+	 * @return <code>true</code> if coloring schema should be used for alias,
+	 *         <code>false</code> otherwise
+	 */
+	private boolean match(Reaction reaction, ColorSchema schema) {
+		if (schema.getName() != null) {
+			return false;
+		}
+		
+		if (schema.getReactionIdentifier() != null && schema.getReactionIdentifier().equalsIgnoreCase(reaction.getIdReaction())) {
+			return true;
+		}
+		if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
+			MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
+
+			if (reaction.getMiriamData().contains(md)) {
+				return true;
+			}
+		}
+		for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
+			if (pair.getRight() != null && !pair.getRight().equals("")) {
+
+				MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
+				if (reaction.getMiriamData().contains(md)) {
+					return true;
+				}
+			}
+		}
+
+		return false;
+	}
+
+	/**
+	 * Applies color schema into the alias.
+	 * 
+	 * @param alias
+	 *          object to be colored
+	 * @param schema
+	 *          color schema to be used
+	 * @throws InvalidColorSchemaException
+	 *           thrown when alias was already colored by other schema
+	 */
+	private void applyColor(Alias alias, ColorSchema schema) throws InvalidColorSchemaException {
+		if (alias instanceof SpeciesAlias) {
+			Species species = ((SpeciesAlias) alias).getSpecies();
+
+			if (!alias.getColor().equals(Color.WHITE)) {
+				throw new InvalidColorSchemaException("At least two rows try to set color to element: " + species.getName());
+			}
+
+			alias.setColor(schema.getNormalizedColor());
+		}
+
+	}
+
+	/**
+	 * Checks if the coloring schema should be used for the alias.
+	 * 
+	 * @param alias
+	 *          alias to which coloring schema is checked
+	 * @param schema
+	 *          coloring schema
+	 * @return <code>true</code> if coloring schema should be used for alias,
+	 *         <code>false</code> otherwise
+	 */
+	protected boolean match(Alias alias, ColorSchema schema) {
+		if (alias instanceof SpeciesAlias) {
+			Species species = ((SpeciesAlias) alias).getSpecies();
+			if (schema.getName() != null) {
+				if (!species.getName().equalsIgnoreCase(schema.getName())) {
+					return false;
+				}
+			}
+			if (schema.getTypes().size() > 0) {
+				if (!schema.getTypes().contains(species.getClass())) {
+					return false;
+				}
+			}
+			if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
+				MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
+
+				if (!species.getMiriamData().contains(md)) {
+					return false;
+				}
+			}
+			for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
+				if (pair.getRight() != null && !pair.getRight().equals("")) {
+					MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
+					if (!species.getMiriamData().contains(md)) {
+						return false;
+					}
+				}
+			}
+
+			if (schema.getCompartments().size() > 0) {
+				boolean found = false;
+				for (CompartmentAlias cAlias : alias.getModelData().getModel().getCompartmentsAliases()) {
+					for (String compartmentName : schema.getCompartments()) {
+						if (cAlias.getCompartment() != null) {
+							if (cAlias.getCompartment().getName().equalsIgnoreCase(compartmentName)) {
+								if (cAlias.cross(alias)) {
+									found = true;
+								}
+							}
+						}
+					}
+				}
+				if (!found) {
+					return false;
+				}
+			}
+
+			// if we have reaction id to match then reject
+			if (schema.getReactionIdentifier() != null) {
+				return false;
+			}
+			return true;
+		} else {
+			return false;
+		}
+	}
+
+	/**
+	 * Checks which coloring schemas weren't used in the model coloring process.
+	 * 
+	 * @return list of schemas that weren't used during coloring
+	 */
+	public Collection<ColorSchema> getMissingSchema() {
+		List<ColorSchema> result = new ArrayList<ColorSchema>();
+		for (ColorSchema schema : schemas) {
+			boolean found = false;
+			for (Alias alias : getModel().getAliases()) {
+				if (match(alias, schema)) {
+					found = true;
+				}
+			}
+			for (Reaction reaction : getModel().getReactions()) {
+				if (match(reaction, schema)) {
+					found = true;
+				}
+			}
+			if (!found) {
+				result.add(schema);
+			}
+		}
+		return result;
+	}
+
+	/**
+	 * Returns list of elements ({@link Reaction reactions} and {@link Alias
+	 * aliases}) that are modified by the coloring command.
+	 * 
+	 * @return {@link Map}, where key corresponds to modified {@link Reaction} or
+	 *         {@link Alias} and value is a {@link ColorSchema} that should be
+	 *         used for coloring
+	 * @throws InvalidColorSchemaException
+	 *           thrown when more than one {@link ColorSchema} match an element
+	 */
+	public Map<Object, ColorSchema> getModifiedElements() throws InvalidColorSchemaException {
+		Map<Object, ColorSchema> result = new HashMap<>();
+
+		List<Model> models = new ArrayList<>();
+		models.add(getModel());
+		models.addAll(getModel().getSubmodels());
+		for (Model model2 : models) {
+			for (ColorSchema schema : schemas) {
+				for (Alias alias : model2.getAliases()) {
+					if (match(alias, schema)) {
+						if (result.get(alias) != null && !result.get(alias).getNormalizedColor().equals(Color.WHITE)) {
+							throw new InvalidColorSchemaException("Alias " + alias.getAliasId() + " is colored by more than one rule.");
+						}
+						result.put(alias, schema);
+					}
+				}
+				for (Reaction reaction : model2.getReactions()) {
+					if (match(reaction, schema)) {
+						if (result.get(reaction) != null && !result.get(reaction).getNormalizedColor().equals(Color.WHITE)) {
+							throw new InvalidColorSchemaException("Reaction " + reaction.getIdReaction() + " is colored by more than one rule.");
+						}
+						result.put(reaction, schema);
+					}
+				}
+			}
+		}
+		return result;
+	}
+
+	@Override
+	protected void undoImplementation() throws CommandExecutionException {
+		throw new NotImplementedException();
+
+	}
+
+	@Override
+	protected void redoImplementation() throws CommandExecutionException {
+		throw new NotImplementedException();
+	}
+
+	/**
+	 * Colors parameter model using coloring for this command. This method is used
+	 * internally to color either top {@link Model} or one of it's sumbodels.
+	 * 
+	 * @param result
+	 *          model to color
+	 * @param top
+	 *          is the model a top (parent) model
+	 * @throws InvalidColorSchemaException
+	 *           thrown when set of {@link ColorSchema} is invalid
+	 */
+	private void colorModel(Model result, boolean top) throws InvalidColorSchemaException {
+
+		for (Alias alias : result.getAliases()) {
+			alias.setColor(Color.WHITE);
+		}
+		for (Reaction reaction : result.getReactions()) {
+			for (AbstractNode node : reaction.getNodes()) {
+				node.getLine().setColor(Color.BLACK);
+			}
+		}
+
+		for (ColorSchema schema : schemas) {
+			for (Alias alias : result.getAliases()) {
+				if (match(alias, schema)) {
+					schema.setMatches(schema.getMatches() + 1);
+					applyColor(alias, schema);
+				}
+			}
+			for (Reaction reaction : result.getReactions()) {
+				if (match(reaction, schema)) {
+					schema.setMatches(schema.getMatches() + 1);
+					applyColor(reaction, schema);
+				}
+			}
+		}
+
+		if (top) {
+			for (ModelSubmodelConnection connection : result.getSubmodelConnections()) {
+				colorModel(connection.getSubmodel().getModel(), false);
+			}
+		}
+
+	}
+
+	@Override
+	protected void executeImplementation() throws CommandExecutionException {
+		try {
+			colorModel(getModel(), true);
+		} catch (InvalidColorSchemaException e) {
+			throw new CommandExecutionException(e);
+		}
+	}
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CommandExecutionException.java b/model-command/src/main/java/lcsb/mapviewer/commands/CommandExecutionException.java
index ae9195d4b2..ac6585bebd 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CommandExecutionException.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CommandExecutionException.java
@@ -1,55 +1,55 @@
-package lcsb.mapviewer.commands;
-
-/**
- * Exception that is thrown when the data for {@link ModelCommand} is invalid.
- * 
- * @author Piotr Gawron
- *
- */
-public class CommandExecutionException extends Exception {
-
-	/**
-	 * 
-	 */
-	private static final long serialVersionUID = 1L;
-
-	/**
-	 * Default constructor.
-	 */
-	public CommandExecutionException() {
-		super();
-	}
-
-	/**
-	 * Default constructor with message passed in the argument.
-	 * 
-	 * @param string
-	 *          message of this exception
-	 */
-	public CommandExecutionException(String string) {
-		super(string);
-	}
-
-	/**
-	 * Public constructor with parent exception that was catched.
-	 * 
-	 * @param e
-	 *          parent exception
-	 */
-	public CommandExecutionException(Exception e) {
-		super(e.getMessage(), e);
-	}
-
-	/**
-	 * Public constructor with parent exception that was catched.
-	 * 
-	 * @param string
-	 *          message of this exception
-	 * @param e
-	 *          parent exception
-	 */
-	public CommandExecutionException(String string, Exception e) {
-		super(string, e);
-	}
-
-}
+package lcsb.mapviewer.commands;
+
+/**
+ * Exception that is thrown when the data for {@link ModelCommand} is invalid.
+ * 
+ * @author Piotr Gawron
+ *
+ */
+public class CommandExecutionException extends Exception {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * Default constructor.
+	 */
+	public CommandExecutionException() {
+		super();
+	}
+
+	/**
+	 * Default constructor with message passed in the argument.
+	 * 
+	 * @param string
+	 *          message of this exception
+	 */
+	public CommandExecutionException(String string) {
+		super(string);
+	}
+
+	/**
+	 * Public constructor with parent exception that was catched.
+	 * 
+	 * @param e
+	 *          parent exception
+	 */
+	public CommandExecutionException(Exception e) {
+		super(e.getMessage(), e);
+	}
+
+	/**
+	 * Public constructor with parent exception that was catched.
+	 * 
+	 * @param string
+	 *          message of this exception
+	 * @param e
+	 *          parent exception
+	 */
+	public CommandExecutionException(String string, Exception e) {
+		super(string, e);
+	}
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
index 98faf4c786..f2419aed93 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
@@ -1,476 +1,476 @@
-package lcsb.mapviewer.commands;
-
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.graph.DataMiningSet;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelConnection;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Species;
-
-import org.apache.log4j.Logger;
-
-/**
- * Command that creates a new instance of the model with the same data.
- * 
- */
-
-public class CopyCommand extends NewModelCommand {
-	/**
-	 * Defaul class logger.
-	 */
-	private static Logger	logger	= Logger.getLogger(CopyCommand.class);
-
-	/**
-	 * Default constructor.
-	 * 
-	 * @param model
-	 *          {@link #model}
-	 */
-	public CopyCommand(Model model) {
-		super(model);
-	}
-
-	/**
-	 * Executed the operation.
-	 * 
-	 * @return copy of the model
-	 */
-	public Model execute() {
-		Map<Model, Model> copies = new HashMap<Model, Model>();
-
-		Model model = getModel();
-
-		if (model.getModelData().getParentModels().size() > 0) {
-			ModelSubmodelConnection parent = null;
-			for (SubmodelConnection connection : model.getModelData().getParentModels()) {
-				if (connection instanceof ModelSubmodelConnection) {
-					if (parent != null) {
-						throw new InvalidArgumentException("It looks like the model is a submodel, but has more than one parent...");
-					} else {
-						parent = (ModelSubmodelConnection) connection;
-					}
-				}
-			}
-			if (parent != null) {
-				logger.warn("Dirty copying of submodel");
-				CopyCommand copyParentCommand = new CopyCommand(parent.getParentModel().getModel());
-				Model copy = copyParentCommand.execute();
-				for (ModelSubmodelConnection submodel : copy.getSubmodelConnections()) {
-					if (submodel.getName().equals(parent.getName())) {
-						return submodel.getSubmodel().getModel();
-					}
-				}
-				throw new InvalidStateException("Problem with copying submodel of a model");
-			}
-		}
-
-		Model result = createNotNestedCopy(model);
-
-		copies.put(model, result);
-
-		for (ModelSubmodelConnection submodelConnection : model.getSubmodelConnections()) {
-			Model submodel = submodelConnection.getSubmodel().getModel();
-			Model submodelCopy = createNotNestedCopy(submodel);
-			copies.put(submodel, submodelCopy);
-		}
-		for (Model modelCopy : copies.values()) {
-			try {
-				assignModelCopies(modelCopy, copies);
-			} catch (InvalidModelException e) {
-				throw new InvalidArgumentException(e);
-			}
-		}
-		return result;
-
-	}
-
-	/**
-	 * Assign information about submodel to the copied links.
-	 * 
-	 * @param modelCopy
-	 *          copy of a model where substitution should be made
-	 * @param copies
-	 *          map with map copies
-	 * @throws InvalidModelException
-	 *           when there is inconsistency in data
-	 */
-	private void assignModelCopies(Model modelCopy, Map<Model, Model> copies) throws InvalidModelException {
-		for (ModelSubmodelConnection connection : modelCopy.getSubmodelConnections()) {
-			// copy connection reference
-			Model original = connection.getSubmodel().getModel();
-			Model copy = copies.get(original);
-			if (copy == null) {
-				throw new InvalidModelException("Original model contain reference to model that wasn't copied");
-			}
-			connection.setSubmodel(copy);
-
-			// copy connection parent reference
-			if (connection.getParentModel() != null) {
-				original = connection.getParentModel().getModel();
-				if (original != null) {
-					copy = copies.get(original);
-					if (copy == null) {
-						if (!copies.values().contains(original)) {
-							throw new InvalidModelException("Original model contain reference to model that wasn't copied");
-						}
-					} else {
-						connection.setParentModel(copy);
-					}
-				}
-			}
-		}
-		for (Alias alias : modelCopy.getAliases()) {
-			// if alias has connection to submodel
-			if (alias.getSubmodel() != null) {
-				AliasSubmodelConnection connection = alias.getSubmodel();
-				// copy information about submodel
-				Model original = connection.getSubmodel().getModel();
-				Model copy = copies.get(original);
-				if (copy == null) {
-					throw new InvalidModelException("Original model contain reference to model that wasn't copied");
-				}
-				connection.setSubmodel(copy);
-
-				// copy information about original alias
-				if (connection.getFromAlias() != null) {
-					connection.setFromAlias(modelCopy.getAliasByAliasId(connection.getFromAlias().getAliasId()));
-				}
-				// copy information about reference alias
-				if (connection.getToAlias() != null) {
-					connection.setToAlias(modelCopy.getAliasByAliasId(connection.getToAlias().getAliasId()));
-				}
-			}
-		}
-	}
-
-	/**
-	 * Creates copy of the model without modifing information about submodels
-	 * (information about original submodels will be left in the copy).
-	 * 
-	 * @param model
-	 *          original model to copy
-	 * @return copy of the model
-	 */
-	protected Model createNotNestedCopy(Model model) {
-		Model result = new ModelFullIndexed(null);
-		
-		result.setSbgnFormat(model.isSbgnFormat());
-		
-		for (Element element : model.getElements()) {
-			result.addElement(element);
-		}
-		for (Alias alias : model.getAliases()) {
-			if (alias instanceof CompartmentAlias) {
-				CompartmentAlias copy = ((CompartmentAlias) alias).copy();
-				copy.getAliases().clear();
-				result.addAlias(copy);
-			}
-
-		}
-
-		for (Alias alias : model.getAliases()) {
-			if (alias instanceof SpeciesAlias) {
-				SpeciesAlias copy = ((SpeciesAlias) alias).copy();
-				copy.setSpecies(result.getSpeciesBySpeciesId(((SpeciesAlias) alias).getSpecies().getElementId()));
-				CompartmentAlias ca = copy.getCompartmentAlias();
-				Alias parent = copy.getParent();
-				copy.setCompartmentAlias(null);
-				copy.setParent(null);
-
-				// the trick is that in addAlias also some connections are added, so
-				// lets clear info about parents
-
-				result.addAlias(copy);
-
-				if (ca != null) {
-					ca = result.getCompartmentAliasByCompartmentAliasId(ca.getAliasId());
-					copy.setCompartmentAlias(ca);
-				}
-				if (parent instanceof CompartmentAlias) {
-					ca = (CompartmentAlias) parent;
-					ca = result.getCompartmentAliasByCompartmentAliasId(ca.getAliasId());
-					copy.setParent(ca);
-				}
-			} else if (alias instanceof CompartmentAlias) {
-				// we already added compartment alias
-				continue;
-			} else {
-				throw new InvalidClassException("Don't know what to do with: " + alias.getClass());
-			}
-		}
-
-		for (Layer layer : model.getLayers()) {
-			result.addLayer(layer.copy());
-		}
-
-		for (Reaction reaction : model.getReactions()) {
-			result.addReaction(createCopy(reaction));
-		}
-
-		assignSimpleDataToCopy(result, model);
-		for (Layout layout : model.getLayouts()) {
-			result.addLayout(layout.copy());
-		}
-		result.setProject(model.getProject());
-
-		for (Element element : result.getElements()) {
-			updateElementReferences(element, model);
-		}
-		for (Alias alias : result.getAliases()) {
-			updateAliasReferences(alias, result, model);
-		}
-		for (Reaction reaction : result.getReactions()) {
-			updateReactionReferences(reaction, result);
-		}
-		for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
-			result.addSubmodelConnection(connection.copy());
-		}
-		for (OverviewImage oi : model.getOverviewImages()) {
-			result.addOverviewImage(oi.copy());
-		}
-		for (DataMiningSet dataMiningSet : model.getDataMiningSets()) {
-			result.addDataMiningSet(new DataMiningSet(dataMiningSet));
-		}
-		return result;
-	}
-
-	/**
-	 * Copies simple information about model to the copy.
-	 * 
-	 * @param copy
-	 *          to this model data will be copied
-	 * @param original
-	 *          original model
-	 */
-	private void assignSimpleDataToCopy(Model copy, Model original) {
-		copy.setMapVersion(original.getMapVersion());
-		copy.setName(original.getName());
-
-		copy.setCreationDate(original.getCreationDate());
-
-		copy.setWidth(original.getWidth());
-		copy.setHeight(original.getHeight());
-		copy.setNotes(original.getNotes());
-		copy.setIdModel(original.getIdModel());
-		copy.setZoomLevels(original.getZoomLevels());
-		copy.setTileSize(original.getTileSize());
-
-		copy.addCreationWarnings(original.getCreationWarnings());
-	}
-
-	/**
-	 * Creates copy of the reaction that doesn't contain any references to the
-	 * original (so we have to substitute all references with the new ones...).
-	 * 
-	 * @param reaction
-	 *          original reaction
-	 * @return copy of the reaction
-	 */
-	private Reaction createCopy(Reaction reaction) {
-		Reaction copy = reaction.copy();
-		reaction.getNodes().clear();
-		for (AbstractNode node : copy.getNodes()) {
-			reaction.addNode(node);
-		}
-		copy.getNodes().clear();
-
-		for (AbstractNode node : reaction.getNodes()) {
-			AbstractNode nodeCopy = node.copy();
-			nodeCopy.setLine(new PolylineData(nodeCopy.getLine()));
-			copy.addNode(nodeCopy);
-		}
-
-		for (int i = 0; i < copy.getOperators().size(); i++) {
-			NodeOperator nodeCopy = copy.getOperators().get(i);
-			NodeOperator nodeOriginal = reaction.getOperators().get(i);
-			for (int j = 0; j < nodeCopy.getInputs().size(); j++) {
-				AbstractNode input = nodeCopy.getInputs().get(j);
-				int index1 = reaction.getOperators().indexOf(input);
-				int index2 = reaction.getNodes().indexOf(input);
-				if (index1 >= 0) {
-					nodeCopy.getInputs().set(j, copy.getOperators().get(index1));
-					copy.getOperators().get(index1).setNodeOperatorForInput(nodeCopy);
-
-					reaction.getOperators().get(index1).setNodeOperatorForInput(nodeOriginal);
-				} else if (index2 >= 0) {
-					nodeCopy.getInputs().set(j, copy.getNodes().get(index2));
-					copy.getNodes().get(index2).setNodeOperatorForInput(nodeCopy);
-
-					reaction.getNodes().get(index2).setNodeOperatorForInput(nodeOriginal);
-				} else {
-					throw new InvalidStateException("WTF");
-				}
-			}
-
-			for (int j = 0; j < nodeCopy.getOutputs().size(); j++) {
-				AbstractNode output = nodeCopy.getOutputs().get(j);
-				int index1 = reaction.getOperators().indexOf(output);
-				int index2 = reaction.getNodes().indexOf(output);
-				if (index1 >= 0) {
-					nodeCopy.getOutputs().set(j, copy.getOperators().get(index1));
-					copy.getOperators().get(index1).setNodeOperatorForOutput(nodeCopy);
-
-					reaction.getOperators().get(index1).setNodeOperatorForOutput(nodeOriginal);
-				} else if (index2 >= 0) {
-					nodeCopy.getOutputs().set(j, copy.getNodes().get(index2));
-					copy.getNodes().get(index2).setNodeOperatorForOutput(nodeCopy);
-
-					reaction.getNodes().get(index2).setNodeOperatorForOutput(nodeOriginal);
-				} else {
-					throw new InvalidStateException("WTF");
-				}
-			}
-		}
-
-		return copy;
-	}
-
-	/**
-	 * Updates references to elements and aliases in reaction to the objects taken
-	 * from model.
-	 * 
-	 * @param reaction
-	 *          references in this reaction will be updated
-	 * @param model
-	 *          references from this model will be taken
-	 */
-	private void updateReactionReferences(Reaction reaction, Model model) {
-		reaction.setModel(model);
-		for (ReactionNode rNode : reaction.getReactionNodes()) {
-			rNode.setAlias((SpeciesAlias) model.getAliasByAliasId(rNode.getAlias().getAliasId()));
-			rNode.setElement(model.getSpeciesBySpeciesId(((Species) rNode.getElement()).getElementId()));
-		}
-
-	}
-
-	/**
-	 * Updates information (like elements, parent aliases) in the alias with the
-	 * data from new model.
-	 * 
-	 * @param alias
-	 *          object to be updated
-	 * @param model
-	 *          data from this model will be used for update
-	 * @param originalModel
-	 *          original model from which alias copy was created
-	 */
-	private void updateAliasReferences(Alias alias, Model model, Model originalModel) {
-		if (alias instanceof CompartmentAlias) {
-			CompartmentAlias compartmentAlias = (CompartmentAlias) alias;
-			CompartmentAlias original = originalModel.getCompartmentAliasByCompartmentAliasId(alias.getAliasId());
-			for (Alias a : original.getAliases()) {
-				compartmentAlias.addAlias(model.getAliasByAliasId(a.getAliasId()));
-			}
-			String compartmentId = null;
-			if (original.getCompartment() != null) {
-				compartmentId = original.getCompartment().getElementId();
-			}
-			compartmentAlias.setCompartment(model.getCompartmentByCompartmentId(compartmentId));
-		}
-
-		if (alias instanceof ComplexAlias) {
-			ComplexAlias ca = (ComplexAlias) alias;
-			for (int i = 0; i < ca.getAliases().size(); i++) {
-				ca.getAliases().set(i, (SpeciesAlias) model.getAliasByAliasId(ca.getAliases().get(i).getAliasId()));
-			}
-		}
-		if (alias instanceof SpeciesAlias) {
-			SpeciesAlias originalAlias = (SpeciesAlias) originalModel.getAliasByAliasId(alias.getAliasId());
-			SpeciesAlias sa = (SpeciesAlias) alias;
-
-			if (sa.getComplexAlias() != null) {
-				sa.setComplexAlias((ComplexAlias) model.getAliasByAliasId(sa.getComplexAlias().getAliasId()));
-			}
-			sa.setSpecies(model.getSpeciesBySpeciesId(sa.getSpecies().getElementId()));
-
-			if (originalAlias.getParent() != null) {
-				Alias parent = null;
-				parent = model.getAliasByAliasId(originalAlias.getParent().getAliasId());
-				sa.setParent(parent);
-			}
-		}
-
-		if (alias.getParent() != null) {
-			alias.setParent(model.getAliasByAliasId(alias.getParent().getAliasId()));
-		}
-
-		alias.setModel(model);
-
-		if (alias.getCompartmentAlias() != null) {
-			alias.setCompartmentAlias(model.getCompartmentAliasByCompartmentAliasId(alias.getCompartmentAlias().getAliasId()));
-		}
-	}
-
-	/**
-	 * Updates information (like parent elements, aliases) in the element with the
-	 * data from new model.
-	 * 
-	 * @param element
-	 *          object to be updated
-	 * @param model
-	 *          data from this model will be used for update
-	 */
-	private void updateElementReferences(Element element, Model model) {
-
-		if (element.getParent() != null) {
-			element.setParent(model.getCompartmentByCompartmentId(((Compartment) element.getParent()).getElementId()));
-		}
-
-		element.setModel(model);
-
-		if (element.getComplex() != null) {
-			element.setComplex((ComplexSpecies) model.getSpeciesBySpeciesId(element.getComplex().getElementId()));
-		}
-
-		if (element instanceof Compartment) {
-			Set<Element> elements = ((Compartment) element).getElements();
-			Set<Element> newElements = new HashSet<Element>();
-			for (Element element2 : elements) {
-				if (element2 instanceof Compartment) {
-					newElements.add(model.getCompartmentByCompartmentId(element2.getElementId()));
-				} else {
-					newElements.add(model.getSpeciesBySpeciesId(((Species) element2).getElementId()));
-				}
-			}
-			((Compartment) element).getElements().clear();
-			((Compartment) element).getElements().addAll(newElements);
-		}
-
-		if (element instanceof ComplexSpecies) {
-			Set<Element> elements = ((ComplexSpecies) element).getElements();
-			Set<Element> newElements = new HashSet<Element>();
-			for (Element element2 : elements) {
-				newElements.add(model.getSpeciesBySpeciesId(((Species) element2).getElementId()));
-			}
-
-			((ComplexSpecies) element).getElements().clear();
-			((ComplexSpecies) element).getElements().addAll(newElements);
-		}
-
-	}
-
-}
+package lcsb.mapviewer.commands;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidClassException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelConnection;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.ComplexSpecies;
+import lcsb.mapviewer.model.map.species.Species;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Command that creates a new instance of the model with the same data.
+ * 
+ */
+
+public class CopyCommand extends NewModelCommand {
+	/**
+	 * Defaul class logger.
+	 */
+	private static Logger	logger	= Logger.getLogger(CopyCommand.class);
+
+	/**
+	 * Default constructor.
+	 * 
+	 * @param model
+	 *          {@link #model}
+	 */
+	public CopyCommand(Model model) {
+		super(model);
+	}
+
+	/**
+	 * Executed the operation.
+	 * 
+	 * @return copy of the model
+	 */
+	public Model execute() {
+		Map<Model, Model> copies = new HashMap<Model, Model>();
+
+		Model model = getModel();
+
+		if (model.getModelData().getParentModels().size() > 0) {
+			ModelSubmodelConnection parent = null;
+			for (SubmodelConnection connection : model.getModelData().getParentModels()) {
+				if (connection instanceof ModelSubmodelConnection) {
+					if (parent != null) {
+						throw new InvalidArgumentException("It looks like the model is a submodel, but has more than one parent...");
+					} else {
+						parent = (ModelSubmodelConnection) connection;
+					}
+				}
+			}
+			if (parent != null) {
+				logger.warn("Dirty copying of submodel");
+				CopyCommand copyParentCommand = new CopyCommand(parent.getParentModel().getModel());
+				Model copy = copyParentCommand.execute();
+				for (ModelSubmodelConnection submodel : copy.getSubmodelConnections()) {
+					if (submodel.getName().equals(parent.getName())) {
+						return submodel.getSubmodel().getModel();
+					}
+				}
+				throw new InvalidStateException("Problem with copying submodel of a model");
+			}
+		}
+
+		Model result = createNotNestedCopy(model);
+
+		copies.put(model, result);
+
+		for (ModelSubmodelConnection submodelConnection : model.getSubmodelConnections()) {
+			Model submodel = submodelConnection.getSubmodel().getModel();
+			Model submodelCopy = createNotNestedCopy(submodel);
+			copies.put(submodel, submodelCopy);
+		}
+		for (Model modelCopy : copies.values()) {
+			try {
+				assignModelCopies(modelCopy, copies);
+			} catch (InvalidModelException e) {
+				throw new InvalidArgumentException(e);
+			}
+		}
+		return result;
+
+	}
+
+	/**
+	 * Assign information about submodel to the copied links.
+	 * 
+	 * @param modelCopy
+	 *          copy of a model where substitution should be made
+	 * @param copies
+	 *          map with map copies
+	 * @throws InvalidModelException
+	 *           when there is inconsistency in data
+	 */
+	private void assignModelCopies(Model modelCopy, Map<Model, Model> copies) throws InvalidModelException {
+		for (ModelSubmodelConnection connection : modelCopy.getSubmodelConnections()) {
+			// copy connection reference
+			Model original = connection.getSubmodel().getModel();
+			Model copy = copies.get(original);
+			if (copy == null) {
+				throw new InvalidModelException("Original model contain reference to model that wasn't copied");
+			}
+			connection.setSubmodel(copy);
+
+			// copy connection parent reference
+			if (connection.getParentModel() != null) {
+				original = connection.getParentModel().getModel();
+				if (original != null) {
+					copy = copies.get(original);
+					if (copy == null) {
+						if (!copies.values().contains(original)) {
+							throw new InvalidModelException("Original model contain reference to model that wasn't copied");
+						}
+					} else {
+						connection.setParentModel(copy);
+					}
+				}
+			}
+		}
+		for (Alias alias : modelCopy.getAliases()) {
+			// if alias has connection to submodel
+			if (alias.getSubmodel() != null) {
+				AliasSubmodelConnection connection = alias.getSubmodel();
+				// copy information about submodel
+				Model original = connection.getSubmodel().getModel();
+				Model copy = copies.get(original);
+				if (copy == null) {
+					throw new InvalidModelException("Original model contain reference to model that wasn't copied");
+				}
+				connection.setSubmodel(copy);
+
+				// copy information about original alias
+				if (connection.getFromAlias() != null) {
+					connection.setFromAlias(modelCopy.getAliasByAliasId(connection.getFromAlias().getAliasId()));
+				}
+				// copy information about reference alias
+				if (connection.getToAlias() != null) {
+					connection.setToAlias(modelCopy.getAliasByAliasId(connection.getToAlias().getAliasId()));
+				}
+			}
+		}
+	}
+
+	/**
+	 * Creates copy of the model without modifing information about submodels
+	 * (information about original submodels will be left in the copy).
+	 * 
+	 * @param model
+	 *          original model to copy
+	 * @return copy of the model
+	 */
+	protected Model createNotNestedCopy(Model model) {
+		Model result = new ModelFullIndexed(null);
+		
+		result.setSbgnFormat(model.isSbgnFormat());
+		
+		for (Element element : model.getElements()) {
+			result.addElement(element);
+		}
+		for (Alias alias : model.getAliases()) {
+			if (alias instanceof CompartmentAlias) {
+				CompartmentAlias copy = ((CompartmentAlias) alias).copy();
+				copy.getAliases().clear();
+				result.addAlias(copy);
+			}
+
+		}
+
+		for (Alias alias : model.getAliases()) {
+			if (alias instanceof SpeciesAlias) {
+				SpeciesAlias copy = ((SpeciesAlias) alias).copy();
+				copy.setSpecies(result.getSpeciesBySpeciesId(((SpeciesAlias) alias).getSpecies().getElementId()));
+				CompartmentAlias ca = copy.getCompartmentAlias();
+				Alias parent = copy.getParent();
+				copy.setCompartmentAlias(null);
+				copy.setParent(null);
+
+				// the trick is that in addAlias also some connections are added, so
+				// lets clear info about parents
+
+				result.addAlias(copy);
+
+				if (ca != null) {
+					ca = result.getCompartmentAliasByCompartmentAliasId(ca.getAliasId());
+					copy.setCompartmentAlias(ca);
+				}
+				if (parent instanceof CompartmentAlias) {
+					ca = (CompartmentAlias) parent;
+					ca = result.getCompartmentAliasByCompartmentAliasId(ca.getAliasId());
+					copy.setParent(ca);
+				}
+			} else if (alias instanceof CompartmentAlias) {
+				// we already added compartment alias
+				continue;
+			} else {
+				throw new InvalidClassException("Don't know what to do with: " + alias.getClass());
+			}
+		}
+
+		for (Layer layer : model.getLayers()) {
+			result.addLayer(layer.copy());
+		}
+
+		for (Reaction reaction : model.getReactions()) {
+			result.addReaction(createCopy(reaction));
+		}
+
+		assignSimpleDataToCopy(result, model);
+		for (Layout layout : model.getLayouts()) {
+			result.addLayout(layout.copy());
+		}
+		result.setProject(model.getProject());
+
+		for (Element element : result.getElements()) {
+			updateElementReferences(element, model);
+		}
+		for (Alias alias : result.getAliases()) {
+			updateAliasReferences(alias, result, model);
+		}
+		for (Reaction reaction : result.getReactions()) {
+			updateReactionReferences(reaction, result);
+		}
+		for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+			result.addSubmodelConnection(connection.copy());
+		}
+		for (OverviewImage oi : model.getOverviewImages()) {
+			result.addOverviewImage(oi.copy());
+		}
+		for (DataMiningSet dataMiningSet : model.getDataMiningSets()) {
+			result.addDataMiningSet(new DataMiningSet(dataMiningSet));
+		}
+		return result;
+	}
+
+	/**
+	 * Copies simple information about model to the copy.
+	 * 
+	 * @param copy
+	 *          to this model data will be copied
+	 * @param original
+	 *          original model
+	 */
+	private void assignSimpleDataToCopy(Model copy, Model original) {
+		copy.setMapVersion(original.getMapVersion());
+		copy.setName(original.getName());
+
+		copy.setCreationDate(original.getCreationDate());
+
+		copy.setWidth(original.getWidth());
+		copy.setHeight(original.getHeight());
+		copy.setNotes(original.getNotes());
+		copy.setIdModel(original.getIdModel());
+		copy.setZoomLevels(original.getZoomLevels());
+		copy.setTileSize(original.getTileSize());
+
+		copy.addCreationWarnings(original.getCreationWarnings());
+	}
+
+	/**
+	 * Creates copy of the reaction that doesn't contain any references to the
+	 * original (so we have to substitute all references with the new ones...).
+	 * 
+	 * @param reaction
+	 *          original reaction
+	 * @return copy of the reaction
+	 */
+	private Reaction createCopy(Reaction reaction) {
+		Reaction copy = reaction.copy();
+		reaction.getNodes().clear();
+		for (AbstractNode node : copy.getNodes()) {
+			reaction.addNode(node);
+		}
+		copy.getNodes().clear();
+
+		for (AbstractNode node : reaction.getNodes()) {
+			AbstractNode nodeCopy = node.copy();
+			nodeCopy.setLine(new PolylineData(nodeCopy.getLine()));
+			copy.addNode(nodeCopy);
+		}
+
+		for (int i = 0; i < copy.getOperators().size(); i++) {
+			NodeOperator nodeCopy = copy.getOperators().get(i);
+			NodeOperator nodeOriginal = reaction.getOperators().get(i);
+			for (int j = 0; j < nodeCopy.getInputs().size(); j++) {
+				AbstractNode input = nodeCopy.getInputs().get(j);
+				int index1 = reaction.getOperators().indexOf(input);
+				int index2 = reaction.getNodes().indexOf(input);
+				if (index1 >= 0) {
+					nodeCopy.getInputs().set(j, copy.getOperators().get(index1));
+					copy.getOperators().get(index1).setNodeOperatorForInput(nodeCopy);
+
+					reaction.getOperators().get(index1).setNodeOperatorForInput(nodeOriginal);
+				} else if (index2 >= 0) {
+					nodeCopy.getInputs().set(j, copy.getNodes().get(index2));
+					copy.getNodes().get(index2).setNodeOperatorForInput(nodeCopy);
+
+					reaction.getNodes().get(index2).setNodeOperatorForInput(nodeOriginal);
+				} else {
+					throw new InvalidStateException("WTF");
+				}
+			}
+
+			for (int j = 0; j < nodeCopy.getOutputs().size(); j++) {
+				AbstractNode output = nodeCopy.getOutputs().get(j);
+				int index1 = reaction.getOperators().indexOf(output);
+				int index2 = reaction.getNodes().indexOf(output);
+				if (index1 >= 0) {
+					nodeCopy.getOutputs().set(j, copy.getOperators().get(index1));
+					copy.getOperators().get(index1).setNodeOperatorForOutput(nodeCopy);
+
+					reaction.getOperators().get(index1).setNodeOperatorForOutput(nodeOriginal);
+				} else if (index2 >= 0) {
+					nodeCopy.getOutputs().set(j, copy.getNodes().get(index2));
+					copy.getNodes().get(index2).setNodeOperatorForOutput(nodeCopy);
+
+					reaction.getNodes().get(index2).setNodeOperatorForOutput(nodeOriginal);
+				} else {
+					throw new InvalidStateException("WTF");
+				}
+			}
+		}
+
+		return copy;
+	}
+
+	/**
+	 * Updates references to elements and aliases in reaction to the objects taken
+	 * from model.
+	 * 
+	 * @param reaction
+	 *          references in this reaction will be updated
+	 * @param model
+	 *          references from this model will be taken
+	 */
+	private void updateReactionReferences(Reaction reaction, Model model) {
+		reaction.setModel(model);
+		for (ReactionNode rNode : reaction.getReactionNodes()) {
+			rNode.setAlias((SpeciesAlias) model.getAliasByAliasId(rNode.getAlias().getAliasId()));
+			rNode.setElement(model.getSpeciesBySpeciesId(((Species) rNode.getElement()).getElementId()));
+		}
+
+	}
+
+	/**
+	 * Updates information (like elements, parent aliases) in the alias with the
+	 * data from new model.
+	 * 
+	 * @param alias
+	 *          object to be updated
+	 * @param model
+	 *          data from this model will be used for update
+	 * @param originalModel
+	 *          original model from which alias copy was created
+	 */
+	private void updateAliasReferences(Alias alias, Model model, Model originalModel) {
+		if (alias instanceof CompartmentAlias) {
+			CompartmentAlias compartmentAlias = (CompartmentAlias) alias;
+			CompartmentAlias original = originalModel.getCompartmentAliasByCompartmentAliasId(alias.getAliasId());
+			for (Alias a : original.getAliases()) {
+				compartmentAlias.addAlias(model.getAliasByAliasId(a.getAliasId()));
+			}
+			String compartmentId = null;
+			if (original.getCompartment() != null) {
+				compartmentId = original.getCompartment().getElementId();
+			}
+			compartmentAlias.setCompartment(model.getCompartmentByCompartmentId(compartmentId));
+		}
+
+		if (alias instanceof ComplexAlias) {
+			ComplexAlias ca = (ComplexAlias) alias;
+			for (int i = 0; i < ca.getAliases().size(); i++) {
+				ca.getAliases().set(i, (SpeciesAlias) model.getAliasByAliasId(ca.getAliases().get(i).getAliasId()));
+			}
+		}
+		if (alias instanceof SpeciesAlias) {
+			SpeciesAlias originalAlias = (SpeciesAlias) originalModel.getAliasByAliasId(alias.getAliasId());
+			SpeciesAlias sa = (SpeciesAlias) alias;
+
+			if (sa.getComplexAlias() != null) {
+				sa.setComplexAlias((ComplexAlias) model.getAliasByAliasId(sa.getComplexAlias().getAliasId()));
+			}
+			sa.setSpecies(model.getSpeciesBySpeciesId(sa.getSpecies().getElementId()));
+
+			if (originalAlias.getParent() != null) {
+				Alias parent = null;
+				parent = model.getAliasByAliasId(originalAlias.getParent().getAliasId());
+				sa.setParent(parent);
+			}
+		}
+
+		if (alias.getParent() != null) {
+			alias.setParent(model.getAliasByAliasId(alias.getParent().getAliasId()));
+		}
+
+		alias.setModel(model);
+
+		if (alias.getCompartmentAlias() != null) {
+			alias.setCompartmentAlias(model.getCompartmentAliasByCompartmentAliasId(alias.getCompartmentAlias().getAliasId()));
+		}
+	}
+
+	/**
+	 * Updates information (like parent elements, aliases) in the element with the
+	 * data from new model.
+	 * 
+	 * @param element
+	 *          object to be updated
+	 * @param model
+	 *          data from this model will be used for update
+	 */
+	private void updateElementReferences(Element element, Model model) {
+
+		if (element.getParent() != null) {
+			element.setParent(model.getCompartmentByCompartmentId(((Compartment) element.getParent()).getElementId()));
+		}
+
+		element.setModel(model);
+
+		if (element.getComplex() != null) {
+			element.setComplex((ComplexSpecies) model.getSpeciesBySpeciesId(element.getComplex().getElementId()));
+		}
+
+		if (element instanceof Compartment) {
+			Set<Element> elements = ((Compartment) element).getElements();
+			Set<Element> newElements = new HashSet<Element>();
+			for (Element element2 : elements) {
+				if (element2 instanceof Compartment) {
+					newElements.add(model.getCompartmentByCompartmentId(element2.getElementId()));
+				} else {
+					newElements.add(model.getSpeciesBySpeciesId(((Species) element2).getElementId()));
+				}
+			}
+			((Compartment) element).getElements().clear();
+			((Compartment) element).getElements().addAll(newElements);
+		}
+
+		if (element instanceof ComplexSpecies) {
+			Set<Element> elements = ((ComplexSpecies) element).getElements();
+			Set<Element> newElements = new HashSet<Element>();
+			for (Element element2 : elements) {
+				newElements.add(model.getSpeciesBySpeciesId(((Species) element2).getElementId()));
+			}
+
+			((ComplexSpecies) element).getElements().clear();
+			((ComplexSpecies) element).getElements().addAll(newElements);
+		}
+
+	}
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
index ea5c114dce..c6b66f76d9 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -1,547 +1,547 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Species;
-
-import org.apache.log4j.Logger;
-
-/**
- * This {@link ModelCommand command} class allows to transform model into
- * multilevel (nested) component structure. Some artificial compartments will
- * appear. All compartments have information about children compartments. All
- * objects have information about parents.
- * 
- * 
- */
-public class CreateHierarchyCommand extends ModelCommand {
-	/**
-	 * Default class logger.
-	 */
-	@SuppressWarnings("unused")
-	private static Logger			 logger																					= Logger.getLogger(CreateHierarchyCommand.class);
-	/**
-	 * Natural logarithm of four.
-	 */
-	private static final double LOG_4																					 = Math.log(4);
-
-	/**
-	 * Top left corner x coordinate of the text associated with compratment.
-	 */
-	private static final double DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
-	/**
-	 * Top left corner y coordinate of the text associated with compratment.
-	 */
-	private static final double DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
-
-	/**
-	 * How many levels are possible.
-	 */
-	private int								 zoomLevels;
-	/**
-	 * What is the maximum zoom factor in the view.
-	 */
-	private double							maxZoomFactor;
-
-	/**
-	 * Default constructor that intializes data.
-	 * 
-	 * @param model
-	 *          model on which command will be executed
-	 * @param maxZoomFactor
-	 *          what is the maximum zoom out factor
-	 * @param zoomLevels
-	 *          how many levels are possible
-	 */
-	public CreateHierarchyCommand(Model model, int zoomLevels, double maxZoomFactor) {
-		super(model);
-		this.zoomLevels = zoomLevels;
-		this.maxZoomFactor = maxZoomFactor;
-	}
-
-	@Override
-	protected void undoImplementation() {
-		throw new NotImplementedException();
-	}
-
-	@Override
-	protected void executeImplementation() {
-		if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
-			throw new InvalidStateException("To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
-		}
-		Model model = getModel();
-		List<SpeciesAlias> compacts = new ArrayList<SpeciesAlias>();
-		for (Alias alias : model.getAliases()) {
-			if (alias instanceof ComplexAlias) {
-				if (((ComplexAlias) alias).getState().contains("brief")) {
-					compacts.add((SpeciesAlias) alias);
-					compacts.addAll(((ComplexAlias) alias).getAliases());
-				}
-			}
-		}
-		model.getAliases().removeAll(compacts);
-		clean();
-		createArtificials();
-		assignAliases();
-		orderConcludingComplex();
-		orderConcludingCompartments();
-
-		List<Alias> sortedAliases = model.getAliasesSortedBySize();
-		setParentingAndChildreningOfNonComplexChildrens(sortedAliases);
-		model.getAliases().addAll(compacts);
-		sortedAliases = model.getAliasesSortedBySize();
-		preSettingOfVisibilityLevel(sortedAliases, maxZoomFactor);
-		settingOfTransparencyLevel(sortedAliases);
-
-		assignSpeciesAccordingToAliasComplexes();
-
-		setStatus(ModelCommandStatus.EXECUTED);
-	}
-
-	/**
-	 * Fixes complexes assignment for species. The fix is based on
-	 * {@link SpeciesAlias#complexAlias} or {@link Alias#parent} fields.
-	 */
-	private void assignSpeciesAccordingToAliasComplexes() {
-		for (SpeciesAlias alias : getModel().getSpeciesAliases()) {
-			ComplexAlias complexAlias = null;
-			if (alias.getComplexAlias() != null) {
-				complexAlias = alias.getComplexAlias();
-			} else if (alias.getParent() instanceof ComplexAlias) {
-				complexAlias = (ComplexAlias) alias.getParent();
-			}
-			if (complexAlias != null) {
-
-				complexAlias = (ComplexAlias) getModel().getAliasByAliasId(complexAlias.getAliasId());
-				Species species = getModel().getSpeciesBySpeciesId(alias.getSpecies().getElementId());
-				ComplexSpecies complexSpecies = (ComplexSpecies) getModel().getSpeciesBySpeciesId(complexAlias.getSpecies().getElementId());
-				if (species.getComplex() != complexSpecies) {
-					species.setComplex(complexSpecies);
-					try {
-						complexSpecies.addElement(species);
-					} catch (InvalidArgumentException e) {
-						//this is thrown when species is already part of the complex
-					}
-				}
-			}
-		}
-
-	}
-
-	@Override
-	protected void redoImplementation() {
-		throw new NotImplementedException();
-	}
-
-	/**
-	 * Cleans hierarchical information from the model.
-	 */
-	protected void clean() {
-		for (Alias alias : getModel().getAliases()) {
-			alias.setParent(null);
-			if (alias instanceof ComplexAlias) {
-				((ComplexAlias) alias).getAliases().clear();
-			}
-		}
-		Set<ArtifitialCompartmentAlias> toRemove = new HashSet<ArtifitialCompartmentAlias>();
-		for (CompartmentAlias alias : getModel().getCompartmentsAliases()) {
-			alias.setParent(null);
-			alias.getAliases().clear();
-			if (alias instanceof ArtifitialCompartmentAlias) {
-				toRemove.add((ArtifitialCompartmentAlias) alias);
-			}
-		}
-		for (ArtifitialCompartmentAlias alias : toRemove) {
-			getModel().removeAlias(alias);
-		}
-	}
-
-	/**
-	 * Creates artifitial compartment alias for rectangles and texts object on
-	 * additional graphic layers.
-	 */
-	private void createArtificials() {
-		Model model = getModel();
-		int id = 0;
-		for (Layer layer : model.getLayers()) {
-			for (LayerRect rect : layer.getRectangles()) {
-				String title = "art" + id;
-				ArtifitialCompartmentAlias alias = new ArtifitialCompartmentAlias();
-				alias.setX(rect.getX());
-				alias.setY(rect.getY());
-				alias.setWidth(rect.getWidth());
-				alias.setHeight(rect.getHeight());
-				alias.setColor(rect.getColor());
-				alias.setAliasId("art" + (id++));
-				alias.setNamePoint(new Point2D.Double(rect.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, rect.getY()
-						+ DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
-
-				model.addAlias(alias);
-
-				Compartment compartment = new Compartment();
-				compartment.setName(title);
-				compartment.setElementId("ca_" + title);
-				alias.setCompartment(compartment);
-				model.addCompartment(compartment);
-			}
-			for (LayerText text : layer.getTexts()) {
-				ArtifitialCompartmentAlias alias = new ArtifitialCompartmentAlias();
-				alias.setX(text.getX());
-				alias.setY(text.getY());
-				alias.setWidth(text.getWidth());
-				alias.setHeight(text.getHeight());
-				alias.setColor(text.getColor());
-				alias.setAliasId((id++) + "");
-				alias.setTitle(text.getNotes().trim());
-				alias.setNamePoint(new Point2D.Double(text.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, text.getY()
-						+ DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
-
-				model.addAlias(alias);
-
-				Compartment compartment = new Compartment();
-				compartment.setName(text.getNotes().trim());
-				compartment.setElementId((id++) + "");
-				alias.setCompartment(compartment);
-				model.addCompartment(compartment);
-			}
-		}
-	}
-
-	/**
-	 * Assign aliases in hierarchical structure.
-	 */
-	private void assignAliases() {
-		assignToComplexes();
-		assignToCompartments();
-	}
-
-	/**
-	 * Checks if hierarchical structure of complexes is valid.
-	 */
-	private void orderConcludingComplex() {
-		orderingComplexesInCompartments();
-		orderingComplexesInComplexes();
-		List<Alias> list = new ArrayList<Alias>();
-		for (Alias alias : getModel().getAliases()) {
-			if (alias instanceof ComplexAlias) {
-				for (SpeciesAlias specAlias : ((ComplexAlias) alias).getAliases()) {
-					if (list.contains(specAlias)) {
-						throw new InvalidStateException("Some aliases are in few Complexes");
-					}
-				}
-				if (alias instanceof CompartmentAlias) {
-					for (Alias specAlias : ((CompartmentAlias) alias).getAliases()) {
-						if (list.contains(specAlias)) {
-							throw new InvalidStateException("Some aliases are in few Structures");
-						}
-					}
-				}
-			}
-		}
-		for (Alias alias : getModel().getAliases()) {
-			if (alias.getParent() != null) {
-				throw new InvalidStateException("WTF");
-			}
-		}
-		parentingInComplexes();
-	}
-
-	/**
-	 * Checks if hierarchical structure of compartments is valid.
-	 */
-	private void orderConcludingCompartments() {
-		for (CompartmentAlias compartment1 : getModel().getCompartmentsAliases()) {
-			for (CompartmentAlias compartment2 : getModel().getCompartmentsAliases()) {
-				if (!compartment1.equals(compartment2)) {
-					if (compartment1.contains(compartment2)) {
-						Set<Alias> duplicates = compartment2.getAliases();
-						compartment1.getAliases().removeAll(duplicates);
-					}
-				}
-			}
-		}
-	}
-
-	/**
-	 * Computes visibility levels for aliases based on the size.
-	 * 
-	 * @param sortedAliases
-	 *          list of aliases
-	 * @param maxZoomFactor
-	 *          max scale used on the map
-	 */
-	private void preSettingOfVisibilityLevel(List<Alias> sortedAliases, double maxZoomFactor) {
-		for (Alias alias : sortedAliases) {
-			double rate = computeRate(alias, Configuration.MIN_VISIBLE_OBJECT_SIZE);
-			int logValue = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
-			if (alias.getParent() == null) {
-				logValue = 0;
-			}
-			if (logValue >= zoomLevels) {
-				if (alias.getParent() instanceof ComplexAlias) {
-					logValue = zoomLevels - 1;
-				} else {
-					logValue = zoomLevels;
-				}
-			}
-			alias.setVisibilityLevel(logValue);
-		}
-	}
-
-	/**
-	 * Sets transparency level in hierarchical view for compartment alias.
-	 * 
-	 * @param compartment
-	 *          comaprtment alias
-	 */
-	private void settingTransparencyLevelForCompartment(CompartmentAlias compartment) {
-		int maxVisibilityLevel = Integer.MAX_VALUE;
-		double rate = computeRate(compartment, Configuration.MAX_VISIBLE_OBJECT_SIZE);
-		maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
-		for (Alias child : compartment.getAliases()) {
-			maxVisibilityLevel = Math.min(maxVisibilityLevel, child.getVisibilityLevel());
-		}
-		if (maxVisibilityLevel >= zoomLevels) {
-			maxVisibilityLevel = zoomLevels;
-		}
-		if (maxVisibilityLevel <= 0) {
-			maxVisibilityLevel = 1;
-		}
-		compartment.setTransparencyLevel(maxVisibilityLevel);
-		for (Alias child : compartment.getAliases()) {
-			child.setVisibilityLevel(compartment.getTransparencyLevel());
-		}
-	}
-
-	/**
-	 * Sets transparency level in hierarchical view for complex alias.
-	 * 
-	 * @param complex
-	 *          complex alias
-	 */
-	private void settingTransparencyLevelForComplex(ComplexAlias complex) {
-		int maxVisibilityLevel = Integer.MAX_VALUE;
-		double rate = computeRate(complex, Configuration.MAX_VISIBLE_OBJECT_SIZE);
-		maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
-		for (Alias child : complex.getAliases()) {
-			maxVisibilityLevel = Math.min(maxVisibilityLevel, child.getVisibilityLevel());
-		}
-		if (maxVisibilityLevel >= zoomLevels) {
-			maxVisibilityLevel = zoomLevels;
-		}
-		if (maxVisibilityLevel <= 0) {
-			maxVisibilityLevel = 1;
-		}
-		complex.setTransparencyLevel(maxVisibilityLevel);
-		for (Alias child : complex.getAliases()) {
-			child.setVisibilityLevel(complex.getTransparencyLevel());
-		}
-	}
-
-	/**
-	 * Sets transparency level in hierarchical view for all elements.
-	 * 
-	 * @param sortedAliases
-	 *          list of aliases
-	 */
-	private void settingOfTransparencyLevel(List<Alias> sortedAliases) {
-		for (Alias alias : sortedAliases) {
-			if (alias instanceof CompartmentAlias) {
-				settingTransparencyLevelForCompartment((CompartmentAlias) alias);
-			} else if (alias instanceof ComplexAlias) {
-				settingTransparencyLevelForComplex((ComplexAlias) alias);
-			} else {
-				alias.setTransparencyLevel(0);
-			}
-		}
-	}
-
-	/**
-	 * Removes invalid compartment children.
-	 * 
-	 * @param sortedAliases
-	 *          list of aliases
-	 */
-	private void setChildrening(List<Alias> sortedAliases) {
-		for (Alias compartment : sortedAliases) {
-			if (compartment instanceof CompartmentAlias) {
-				Set<Alias> removable = new HashSet<Alias>();
-				for (Alias alias : ((CompartmentAlias) compartment).getAliases()) {
-					if (alias.getParent() != compartment) {
-						removable.add(alias);
-					}
-				}
-				((CompartmentAlias) compartment).getAliases().removeAll(removable);
-			}
-		}
-	}
-
-	/**
-	 * Sets parent for elements.
-	 * 
-	 * @param sortedAliases
-	 *          list of aliases
-	 */
-	private void setParentingOfNonComplexChildrens(List<Alias> sortedAliases) {
-		for (Alias alias : getModel().getAliases()) {
-			if (alias.getParent() == null) {
-				for (Alias complex : sortedAliases) {
-					if (complex instanceof ComplexAlias) {
-						if (((ComplexAlias) complex).getAliases().contains(alias)) {
-							alias.setParent(complex);
-						}
-					}
-				}
-				if (alias.getParent() == null) {
-					for (Alias compartment : sortedAliases) {
-						if (compartment instanceof CompartmentAlias) {
-							if (((CompartmentAlias) compartment).getAliases().contains(alias)) {
-								alias.setParent(compartment);
-							}
-						}
-					}
-				}
-			}
-		}
-	}
-
-	/**
-	 * Set parents for the elements in hierarchical view.
-	 * 
-	 * @param sortedAliases
-	 *          list of aliases
-	 */
-	private void setParentingAndChildreningOfNonComplexChildrens(List<Alias> sortedAliases) {
-		setParentingOfNonComplexChildrens(sortedAliases);
-		setChildrening(sortedAliases);
-	}
-
-	/**
-	 * Assign aliases to compartments.
-	 */
-	private void assignToCompartments() {
-		for (CompartmentAlias alias : getModel().getCompartmentsAliases()) {
-			for (CompartmentAlias alias2 : getModel().getCompartmentsAliases()) {
-				if (alias.contains(alias2)) {
-					alias.addAlias(alias2);
-				}
-			}
-			for (Alias alias2 : getModel().getAliases()) {
-				if (!(alias2 instanceof CompartmentAlias)) {
-					if (alias.contains(alias2)) {
-						alias.addAlias(alias2);
-					}
-				}
-			}
-		}
-	}
-
-	/**
-	 * Assign aliases to complexes.
-	 */
-	private void assignToComplexes() {
-		for (Alias alias : getModel().getAliases()) {
-			if (alias instanceof ComplexAlias) {
-				for (Alias alias2 : getModel().getAliases()) {
-					if (alias.contains(alias2) && !alias.equals(alias2)) {
-						((ComplexAlias) alias).getAliases().add((SpeciesAlias) alias2);
-					}
-				}
-			}
-		}
-	}
-
-	/**
-	 * Remove subchildren from complexes.
-	 */
-	private void orderingComplexesInComplexes() {
-		for (Alias complex1 : getModel().getAliases()) {
-			if (complex1 instanceof ComplexAlias) {
-				for (Alias complex2 : getModel().getAliases()) {
-					if (complex2 instanceof ComplexAlias) {
-						if (!complex1.equals(complex2)) {
-							if (complex1.contains(complex2)) {
-								List<SpeciesAlias> duplicates = ((ComplexAlias) complex2).getAliases();
-								((ComplexAlias) complex1).getAliases().removeAll(duplicates);
-							}
-						}
-					}
-				}
-			}
-		}
-	}
-
-	/**
-	 * Remove subchildren from compartments by complexes.
-	 */
-	private void orderingComplexesInCompartments() {
-		for (CompartmentAlias compartment : getModel().getCompartmentsAliases()) {
-			for (Alias complex : getModel().getAliases()) {
-				if (complex instanceof ComplexAlias) {
-					List<SpeciesAlias> duplicates = ((ComplexAlias) complex).getAliases();
-					compartment.getAliases().removeAll(duplicates);
-				}
-			}
-		}
-	}
-
-	/**
-	 * Sets proper parents after creating hierarchical structure.
-	 */
-	private void parentingInComplexes() {
-		for (Alias complex : getModel().getAliases()) {
-			if (complex instanceof ComplexAlias) {
-				for (Alias child : ((ComplexAlias) complex).getAliases()) {
-					if (child instanceof ComplexAlias) {
-						if (((ComplexAlias) child).getAliases().contains(complex)) {
-							if (complex.getParent() != null) {
-								throw new InvalidStateException(((SpeciesAlias) child).getSpecies().getName() + " has parent "
-										+ ((SpeciesAlias) child).getSpecies().getParent().getName() + " and now again try to add new parent "
-										+ ((SpeciesAlias) complex).getSpecies().getName());
-							}
-							child.setParent(complex);
-						}
-					}
-				}
-			}
-		}
-	}
-
-	/**
-	 * Computes the ratio between the minimal object that should be visible, and
-	 * alias visible on the top level.
-	 * 
-	 * @param alias
-	 *          alias for which computation is done
-	 * @param limit
-	 *          size of the minimal visibe object
-	 * @return ratio between the minimal object that should be visible, and alias
-	 *         visible on the top level
-	 */
-	private double computeRate(Alias alias, double limit) {
-		double length = alias.getWidth() / maxZoomFactor;
-		double height = alias.getHeight() / maxZoomFactor;
-		double size = length * height;
-		return (double) Math.ceil(limit / size);
-	}
-
-}
+package lcsb.mapviewer.commands;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.ComplexSpecies;
+import lcsb.mapviewer.model.map.species.Species;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This {@link ModelCommand command} class allows to transform model into
+ * multilevel (nested) component structure. Some artificial compartments will
+ * appear. All compartments have information about children compartments. All
+ * objects have information about parents.
+ * 
+ * 
+ */
+public class CreateHierarchyCommand extends ModelCommand {
+	/**
+	 * Default class logger.
+	 */
+	@SuppressWarnings("unused")
+	private static Logger			 logger																					= Logger.getLogger(CreateHierarchyCommand.class);
+	/**
+	 * Natural logarithm of four.
+	 */
+	private static final double LOG_4																					 = Math.log(4);
+
+	/**
+	 * Top left corner x coordinate of the text associated with compratment.
+	 */
+	private static final double DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
+	/**
+	 * Top left corner y coordinate of the text associated with compratment.
+	 */
+	private static final double DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
+
+	/**
+	 * How many levels are possible.
+	 */
+	private int								 zoomLevels;
+	/**
+	 * What is the maximum zoom factor in the view.
+	 */
+	private double							maxZoomFactor;
+
+	/**
+	 * Default constructor that intializes data.
+	 * 
+	 * @param model
+	 *          model on which command will be executed
+	 * @param maxZoomFactor
+	 *          what is the maximum zoom out factor
+	 * @param zoomLevels
+	 *          how many levels are possible
+	 */
+	public CreateHierarchyCommand(Model model, int zoomLevels, double maxZoomFactor) {
+		super(model);
+		this.zoomLevels = zoomLevels;
+		this.maxZoomFactor = maxZoomFactor;
+	}
+
+	@Override
+	protected void undoImplementation() {
+		throw new NotImplementedException();
+	}
+
+	@Override
+	protected void executeImplementation() {
+		if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
+			throw new InvalidStateException("To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
+		}
+		Model model = getModel();
+		List<SpeciesAlias> compacts = new ArrayList<SpeciesAlias>();
+		for (Alias alias : model.getAliases()) {
+			if (alias instanceof ComplexAlias) {
+				if (((ComplexAlias) alias).getState().contains("brief")) {
+					compacts.add((SpeciesAlias) alias);
+					compacts.addAll(((ComplexAlias) alias).getAliases());
+				}
+			}
+		}
+		model.getAliases().removeAll(compacts);
+		clean();
+		createArtificials();
+		assignAliases();
+		orderConcludingComplex();
+		orderConcludingCompartments();
+
+		List<Alias> sortedAliases = model.getAliasesSortedBySize();
+		setParentingAndChildreningOfNonComplexChildrens(sortedAliases);
+		model.getAliases().addAll(compacts);
+		sortedAliases = model.getAliasesSortedBySize();
+		preSettingOfVisibilityLevel(sortedAliases, maxZoomFactor);
+		settingOfTransparencyLevel(sortedAliases);
+
+		assignSpeciesAccordingToAliasComplexes();
+
+		setStatus(ModelCommandStatus.EXECUTED);
+	}
+
+	/**
+	 * Fixes complexes assignment for species. The fix is based on
+	 * {@link SpeciesAlias#complexAlias} or {@link Alias#parent} fields.
+	 */
+	private void assignSpeciesAccordingToAliasComplexes() {
+		for (SpeciesAlias alias : getModel().getSpeciesAliases()) {
+			ComplexAlias complexAlias = null;
+			if (alias.getComplexAlias() != null) {
+				complexAlias = alias.getComplexAlias();
+			} else if (alias.getParent() instanceof ComplexAlias) {
+				complexAlias = (ComplexAlias) alias.getParent();
+			}
+			if (complexAlias != null) {
+
+				complexAlias = (ComplexAlias) getModel().getAliasByAliasId(complexAlias.getAliasId());
+				Species species = getModel().getSpeciesBySpeciesId(alias.getSpecies().getElementId());
+				ComplexSpecies complexSpecies = (ComplexSpecies) getModel().getSpeciesBySpeciesId(complexAlias.getSpecies().getElementId());
+				if (species.getComplex() != complexSpecies) {
+					species.setComplex(complexSpecies);
+					try {
+						complexSpecies.addElement(species);
+					} catch (InvalidArgumentException e) {
+						//this is thrown when species is already part of the complex
+					}
+				}
+			}
+		}
+
+	}
+
+	@Override
+	protected void redoImplementation() {
+		throw new NotImplementedException();
+	}
+
+	/**
+	 * Cleans hierarchical information from the model.
+	 */
+	protected void clean() {
+		for (Alias alias : getModel().getAliases()) {
+			alias.setParent(null);
+			if (alias instanceof ComplexAlias) {
+				((ComplexAlias) alias).getAliases().clear();
+			}
+		}
+		Set<ArtifitialCompartmentAlias> toRemove = new HashSet<ArtifitialCompartmentAlias>();
+		for (CompartmentAlias alias : getModel().getCompartmentsAliases()) {
+			alias.setParent(null);
+			alias.getAliases().clear();
+			if (alias instanceof ArtifitialCompartmentAlias) {
+				toRemove.add((ArtifitialCompartmentAlias) alias);
+			}
+		}
+		for (ArtifitialCompartmentAlias alias : toRemove) {
+			getModel().removeAlias(alias);
+		}
+	}
+
+	/**
+	 * Creates artifitial compartment alias for rectangles and texts object on
+	 * additional graphic layers.
+	 */
+	private void createArtificials() {
+		Model model = getModel();
+		int id = 0;
+		for (Layer layer : model.getLayers()) {
+			for (LayerRect rect : layer.getRectangles()) {
+				String title = "art" + id;
+				ArtifitialCompartmentAlias alias = new ArtifitialCompartmentAlias();
+				alias.setX(rect.getX());
+				alias.setY(rect.getY());
+				alias.setWidth(rect.getWidth());
+				alias.setHeight(rect.getHeight());
+				alias.setColor(rect.getColor());
+				alias.setAliasId("art" + (id++));
+				alias.setNamePoint(new Point2D.Double(rect.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, rect.getY()
+						+ DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
+
+				model.addAlias(alias);
+
+				Compartment compartment = new Compartment();
+				compartment.setName(title);
+				compartment.setElementId("ca_" + title);
+				alias.setCompartment(compartment);
+				model.addCompartment(compartment);
+			}
+			for (LayerText text : layer.getTexts()) {
+				ArtifitialCompartmentAlias alias = new ArtifitialCompartmentAlias();
+				alias.setX(text.getX());
+				alias.setY(text.getY());
+				alias.setWidth(text.getWidth());
+				alias.setHeight(text.getHeight());
+				alias.setColor(text.getColor());
+				alias.setAliasId((id++) + "");
+				alias.setTitle(text.getNotes().trim());
+				alias.setNamePoint(new Point2D.Double(text.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, text.getY()
+						+ DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
+
+				model.addAlias(alias);
+
+				Compartment compartment = new Compartment();
+				compartment.setName(text.getNotes().trim());
+				compartment.setElementId((id++) + "");
+				alias.setCompartment(compartment);
+				model.addCompartment(compartment);
+			}
+		}
+	}
+
+	/**
+	 * Assign aliases in hierarchical structure.
+	 */
+	private void assignAliases() {
+		assignToComplexes();
+		assignToCompartments();
+	}
+
+	/**
+	 * Checks if hierarchical structure of complexes is valid.
+	 */
+	private void orderConcludingComplex() {
+		orderingComplexesInCompartments();
+		orderingComplexesInComplexes();
+		List<Alias> list = new ArrayList<Alias>();
+		for (Alias alias : getModel().getAliases()) {
+			if (alias instanceof ComplexAlias) {
+				for (SpeciesAlias specAlias : ((ComplexAlias) alias).getAliases()) {
+					if (list.contains(specAlias)) {
+						throw new InvalidStateException("Some aliases are in few Complexes");
+					}
+				}
+				if (alias instanceof CompartmentAlias) {
+					for (Alias specAlias : ((CompartmentAlias) alias).getAliases()) {
+						if (list.contains(specAlias)) {
+							throw new InvalidStateException("Some aliases are in few Structures");
+						}
+					}
+				}
+			}
+		}
+		for (Alias alias : getModel().getAliases()) {
+			if (alias.getParent() != null) {
+				throw new InvalidStateException("WTF");
+			}
+		}
+		parentingInComplexes();
+	}
+
+	/**
+	 * Checks if hierarchical structure of compartments is valid.
+	 */
+	private void orderConcludingCompartments() {
+		for (CompartmentAlias compartment1 : getModel().getCompartmentsAliases()) {
+			for (CompartmentAlias compartment2 : getModel().getCompartmentsAliases()) {
+				if (!compartment1.equals(compartment2)) {
+					if (compartment1.contains(compartment2)) {
+						Set<Alias> duplicates = compartment2.getAliases();
+						compartment1.getAliases().removeAll(duplicates);
+					}
+				}
+			}
+		}
+	}
+
+	/**
+	 * Computes visibility levels for aliases based on the size.
+	 * 
+	 * @param sortedAliases
+	 *          list of aliases
+	 * @param maxZoomFactor
+	 *          max scale used on the map
+	 */
+	private void preSettingOfVisibilityLevel(List<Alias> sortedAliases, double maxZoomFactor) {
+		for (Alias alias : sortedAliases) {
+			double rate = computeRate(alias, Configuration.MIN_VISIBLE_OBJECT_SIZE);
+			int logValue = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
+			if (alias.getParent() == null) {
+				logValue = 0;
+			}
+			if (logValue >= zoomLevels) {
+				if (alias.getParent() instanceof ComplexAlias) {
+					logValue = zoomLevels - 1;
+				} else {
+					logValue = zoomLevels;
+				}
+			}
+			alias.setVisibilityLevel(logValue);
+		}
+	}
+
+	/**
+	 * Sets transparency level in hierarchical view for compartment alias.
+	 * 
+	 * @param compartment
+	 *          comaprtment alias
+	 */
+	private void settingTransparencyLevelForCompartment(CompartmentAlias compartment) {
+		int maxVisibilityLevel = Integer.MAX_VALUE;
+		double rate = computeRate(compartment, Configuration.MAX_VISIBLE_OBJECT_SIZE);
+		maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
+		for (Alias child : compartment.getAliases()) {
+			maxVisibilityLevel = Math.min(maxVisibilityLevel, child.getVisibilityLevel());
+		}
+		if (maxVisibilityLevel >= zoomLevels) {
+			maxVisibilityLevel = zoomLevels;
+		}
+		if (maxVisibilityLevel <= 0) {
+			maxVisibilityLevel = 1;
+		}
+		compartment.setTransparencyLevel(maxVisibilityLevel);
+		for (Alias child : compartment.getAliases()) {
+			child.setVisibilityLevel(compartment.getTransparencyLevel());
+		}
+	}
+
+	/**
+	 * Sets transparency level in hierarchical view for complex alias.
+	 * 
+	 * @param complex
+	 *          complex alias
+	 */
+	private void settingTransparencyLevelForComplex(ComplexAlias complex) {
+		int maxVisibilityLevel = Integer.MAX_VALUE;
+		double rate = computeRate(complex, Configuration.MAX_VISIBLE_OBJECT_SIZE);
+		maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
+		for (Alias child : complex.getAliases()) {
+			maxVisibilityLevel = Math.min(maxVisibilityLevel, child.getVisibilityLevel());
+		}
+		if (maxVisibilityLevel >= zoomLevels) {
+			maxVisibilityLevel = zoomLevels;
+		}
+		if (maxVisibilityLevel <= 0) {
+			maxVisibilityLevel = 1;
+		}
+		complex.setTransparencyLevel(maxVisibilityLevel);
+		for (Alias child : complex.getAliases()) {
+			child.setVisibilityLevel(complex.getTransparencyLevel());
+		}
+	}
+
+	/**
+	 * Sets transparency level in hierarchical view for all elements.
+	 * 
+	 * @param sortedAliases
+	 *          list of aliases
+	 */
+	private void settingOfTransparencyLevel(List<Alias> sortedAliases) {
+		for (Alias alias : sortedAliases) {
+			if (alias instanceof CompartmentAlias) {
+				settingTransparencyLevelForCompartment((CompartmentAlias) alias);
+			} else if (alias instanceof ComplexAlias) {
+				settingTransparencyLevelForComplex((ComplexAlias) alias);
+			} else {
+				alias.setTransparencyLevel(0);
+			}
+		}
+	}
+
+	/**
+	 * Removes invalid compartment children.
+	 * 
+	 * @param sortedAliases
+	 *          list of aliases
+	 */
+	private void setChildrening(List<Alias> sortedAliases) {
+		for (Alias compartment : sortedAliases) {
+			if (compartment instanceof CompartmentAlias) {
+				Set<Alias> removable = new HashSet<Alias>();
+				for (Alias alias : ((CompartmentAlias) compartment).getAliases()) {
+					if (alias.getParent() != compartment) {
+						removable.add(alias);
+					}
+				}
+				((CompartmentAlias) compartment).getAliases().removeAll(removable);
+			}
+		}
+	}
+
+	/**
+	 * Sets parent for elements.
+	 * 
+	 * @param sortedAliases
+	 *          list of aliases
+	 */
+	private void setParentingOfNonComplexChildrens(List<Alias> sortedAliases) {
+		for (Alias alias : getModel().getAliases()) {
+			if (alias.getParent() == null) {
+				for (Alias complex : sortedAliases) {
+					if (complex instanceof ComplexAlias) {
+						if (((ComplexAlias) complex).getAliases().contains(alias)) {
+							alias.setParent(complex);
+						}
+					}
+				}
+				if (alias.getParent() == null) {
+					for (Alias compartment : sortedAliases) {
+						if (compartment instanceof CompartmentAlias) {
+							if (((CompartmentAlias) compartment).getAliases().contains(alias)) {
+								alias.setParent(compartment);
+							}
+						}
+					}
+				}
+			}
+		}
+	}
+
+	/**
+	 * Set parents for the elements in hierarchical view.
+	 * 
+	 * @param sortedAliases
+	 *          list of aliases
+	 */
+	private void setParentingAndChildreningOfNonComplexChildrens(List<Alias> sortedAliases) {
+		setParentingOfNonComplexChildrens(sortedAliases);
+		setChildrening(sortedAliases);
+	}
+
+	/**
+	 * Assign aliases to compartments.
+	 */
+	private void assignToCompartments() {
+		for (CompartmentAlias alias : getModel().getCompartmentsAliases()) {
+			for (CompartmentAlias alias2 : getModel().getCompartmentsAliases()) {
+				if (alias.contains(alias2)) {
+					alias.addAlias(alias2);
+				}
+			}
+			for (Alias alias2 : getModel().getAliases()) {
+				if (!(alias2 instanceof CompartmentAlias)) {
+					if (alias.contains(alias2)) {
+						alias.addAlias(alias2);
+					}
+				}
+			}
+		}
+	}
+
+	/**
+	 * Assign aliases to complexes.
+	 */
+	private void assignToComplexes() {
+		for (Alias alias : getModel().getAliases()) {
+			if (alias instanceof ComplexAlias) {
+				for (Alias alias2 : getModel().getAliases()) {
+					if (alias.contains(alias2) && !alias.equals(alias2)) {
+						((ComplexAlias) alias).getAliases().add((SpeciesAlias) alias2);
+					}
+				}
+			}
+		}
+	}
+
+	/**
+	 * Remove subchildren from complexes.
+	 */
+	private void orderingComplexesInComplexes() {
+		for (Alias complex1 : getModel().getAliases()) {
+			if (complex1 instanceof ComplexAlias) {
+				for (Alias complex2 : getModel().getAliases()) {
+					if (complex2 instanceof ComplexAlias) {
+						if (!complex1.equals(complex2)) {
+							if (complex1.contains(complex2)) {
+								List<SpeciesAlias> duplicates = ((ComplexAlias) complex2).getAliases();
+								((ComplexAlias) complex1).getAliases().removeAll(duplicates);
+							}
+						}
+					}
+				}
+			}
+		}
+	}
+
+	/**
+	 * Remove subchildren from compartments by complexes.
+	 */
+	private void orderingComplexesInCompartments() {
+		for (CompartmentAlias compartment : getModel().getCompartmentsAliases()) {
+			for (Alias complex : getModel().getAliases()) {
+				if (complex instanceof ComplexAlias) {
+					List<SpeciesAlias> duplicates = ((ComplexAlias) complex).getAliases();
+					compartment.getAliases().removeAll(duplicates);
+				}
+			}
+		}
+	}
+
+	/**
+	 * Sets proper parents after creating hierarchical structure.
+	 */
+	private void parentingInComplexes() {
+		for (Alias complex : getModel().getAliases()) {
+			if (complex instanceof ComplexAlias) {
+				for (Alias child : ((ComplexAlias) complex).getAliases()) {
+					if (child instanceof ComplexAlias) {
+						if (((ComplexAlias) child).getAliases().contains(complex)) {
+							if (complex.getParent() != null) {
+								throw new InvalidStateException(((SpeciesAlias) child).getSpecies().getName() + " has parent "
+										+ ((SpeciesAlias) child).getSpecies().getParent().getName() + " and now again try to add new parent "
+										+ ((SpeciesAlias) complex).getSpecies().getName());
+							}
+							child.setParent(complex);
+						}
+					}
+				}
+			}
+		}
+	}
+
+	/**
+	 * Computes the ratio between the minimal object that should be visible, and
+	 * alias visible on the top level.
+	 * 
+	 * @param alias
+	 *          alias for which computation is done
+	 * @param limit
+	 *          size of the minimal visibe object
+	 * @return ratio between the minimal object that should be visible, and alias
+	 *         visible on the top level
+	 */
+	private double computeRate(Alias alias, double limit) {
+		double length = alias.getWidth() / maxZoomFactor;
+		double height = alias.getHeight() / maxZoomFactor;
+		double size = length * height;
+		return (double) Math.ceil(limit / size);
+	}
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
index e9c57cea48..dfdd85384d 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -1,341 +1,341 @@
-package lcsb.mapviewer.commands;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.GenericColorSchema;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-
-public class ColorModelCommandTest extends CommandTestFunctions {
-	Logger logger = Logger.getLogger(ColorModelCommandTest.class);
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	/**
-	 * Test if all elements were copied - if not hibernate will complain
-	 * 
-	 * @throws Exception
-	 * 
-	 */
-	@Test
-	public void testColorFullModel() throws Exception {
-		ModelComparator comparator = new ModelComparator();
-		try {
-			Model model = getModelForFile("testFiles/sample.xml", false);
-			Model model2 = getModelForFile("testFiles/sample.xml", false);
-			Model coloredModel = new CopyCommand(model).execute();
-
-			List<ColorSchema> schemas = new ArrayList<>();
-			ColorSchema schema = new GenericColorSchema();
-			schema.setName("CNC");
-			schema.setValue(-1.0);
-			schemas.add(schema);
-			ColorModelCommand factory = new ColorModelCommand(coloredModel, schemas);
-
-			assertFalse(Color.RED.equals(coloredModel.getAliasByAliasId("sa14").getColor()));
-
-			factory.execute();
-
-			assertEquals(0, comparator.compare(model, model2));
-
-			assertFalse(comparator.compare(model, coloredModel) == 0);
-
-			assertEquals(Color.RED, coloredModel.getAliasByAliasId("sa14").getColor());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testColoring2() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/coloring_model.xml", true);
-			Collection<ColorSchema> schemas = new ArrayList<>();
-			ColorSchema schema = new GenericColorSchema();
-			schema.setGeneralIdentifier("HGNC:11138");
-			schema.setValue(1.0);
-			schemas.add(schema);
-			schema = new GenericColorSchema();
-			schema.setGeneralIdentifier("CHEBI:CHEBI:15377");
-			schema.setValue(1.0);
-			schemas.add(schema);
-			schema = new GenericColorSchema();
-			schema.setGeneralIdentifier("CHEBI:CHEBI:15376");
-			schema.setValue(1.0);
-			schemas.add(schema);
-
-			ColorModelCommand factory = new ColorModelCommand(model, schemas);
-			Collection<ColorSchema> missing = factory.getMissingSchema();
-
-			assertEquals(1, missing.size());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testReactionColoring1() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
-			Reaction re4 = model.getReactionByReactionId("re4");
-			Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
-
-			ColorModelCommand factory = new ColorModelCommand(model, schemas);
-			assertFalse(Color.BLACK.equals(re4.getNodes().get(0).getLine().getColor()));
-
-			factory.execute();
-			re4 = model.getReactionByReactionId("re4");
-
-			assertEquals(Color.BLACK, re4.getNodes().get(0).getLine().getColor());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testReactionColoring2() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
-			Reaction re1 = model.getReactionByReactionId("re1");
-			Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
-			ColorSchema schema = new GenericColorSchema();
-			schema.setReactionIdentifier("re1");
-			schema.setColor(Color.RED);
-			schemas.add(schema);
-
-			ColorModelCommand factory = new ColorModelCommand(model, schemas);
-			assertEquals(Color.BLACK, re1.getNodes().get(0).getLine().getColor());
-
-			factory.execute();
-			re1 = model.getReactionByReactionId("re1");
-
-			assertEquals(Color.RED, re1.getNodes().get(0).getLine().getColor());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testReactionColoring3() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
-			Reaction re2 = model.getReactionByReactionId("re2");
-			Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
-			ColorSchema schema = new GenericColorSchema();
-			schema.setReactionIdentifier("re2");
-			schema.setValue(-1.0);
-			schemas.add(schema);
-
-			ColorModelCommand factory = new ColorModelCommand(model, schemas);
-			assertEquals(Color.BLACK, re2.getNodes().get(0).getLine().getColor());
-
-			factory.execute();
-			re2 = model.getReactionByReactionId("re2");
-
-			assertEquals(Color.RED, re2.getNodes().get(0).getLine().getColor());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testReactionColoring4() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
-			Reaction re3 = model.getReactionByReactionId("re3");
-			Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
-			ColorSchema schema = new GenericColorSchema();
-			Pair<MiriamType, String> pair = new Pair<MiriamType, String>(MiriamType.PUBMED, "12345");
-			List<Pair<MiriamType, String>> identifiers = new ArrayList<Pair<MiriamType, String>>();
-			identifiers.add(pair);
-
-			schema.setIdentifierColumns(identifiers);
-			schema.setValue(-1.0);
-			schemas.add(schema);
-
-			ColorModelCommand factory = new ColorModelCommand(model, schemas);
-
-			assertEquals(Color.BLACK, re3.getNodes().get(0).getLine().getColor());
-
-			factory.execute();
-			re3 = model.getReactionByReactionId("re3");
-
-			assertEquals(Color.RED, re3.getNodes().get(0).getLine().getColor());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testColoringComplexModel() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/sample.xml", false);
-			Model model2 = getModelForFile("testFiles/sample.xml", false);
-
-			model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, "BLA"));
-
-			Collection<ColorSchema> schemas = new ArrayList<>();
-			Model coloredModel = new CopyCommand(model).execute();
-			new ColorModelCommand(coloredModel, schemas).execute();
-
-			Model coloredModel2 = coloredModel.getSubmodelConnections().iterator().next().getSubmodel().getModel();
-			Model coloredModel3 = coloredModel.getSubmodelByConnectionName("BLA");
-
-			assertFalse(coloredModel2.getAliasByAliasId("sa2").getColor().equals(model2.getAliasByAliasId("sa2").getColor()));
-			assertFalse(coloredModel3.getAliasByAliasId("sa2").getColor().equals(model2.getAliasByAliasId("sa2").getColor()));
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testColoredAliases() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/sample.xml", false);
-			Collection<ColorSchema> schemas = new ArrayList<>();
-			ColorSchema schema = new GenericColorSchema();
-			schema.setName("CNC");
-			schema.setColor(Color.BLUE);
-			schemas.add(schema);
-			schema = new GenericColorSchema();
-			schema.setName("BDH1");
-			schema.setColor(Color.BLUE);
-			schemas.add(schema);
-			ColorModelCommand factory = new ColorModelCommand(model, schemas);
-
-			Map<Object, ColorSchema> map = factory.getModifiedElements();
-			assertEquals(2, map.size());
-			for (Map.Entry<Object, ColorSchema> entry : map.entrySet()) {
-				assertTrue(entry.getKey() instanceof Alias);
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testColoredReactions() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/sample.xml", false);
-			Collection<ColorSchema> schemas = new ArrayList<>();
-			ColorSchema schema = new GenericColorSchema();
-			schema.setReactionIdentifier("re1");
-			schema.setLineWidth(3.0);
-			schema.setColor(Color.BLUE);
-			schema.setName("");
-			schema.setReverseReaction(true);
-			schemas.add(schema);
-			ColorModelCommand factory = new ColorModelCommand(model, schemas);
-
-			Map<Object, ColorSchema> map = factory.getModifiedElements();
-			assertEquals(0, map.size());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-	
-	@Test
-	public void testColoredReactions2() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/sample.xml", false);
-			Collection<ColorSchema> schemas = new ArrayList<>();
-			ColorSchema schema = new GenericColorSchema();
-			schema.setReactionIdentifier("re1");
-			schema.setLineWidth(3.0);
-			schema.setColor(Color.BLUE);
-			schema.setName(null);
-			schema.setReverseReaction(true);
-			schemas.add(schema);
-			ColorModelCommand factory = new ColorModelCommand(model, schemas);
-
-			Map<Object, ColorSchema> map = factory.getModifiedElements();
-			assertEquals(1, map.size());
-			for (Map.Entry<Object, ColorSchema> entry : map.entrySet()) {
-				assertTrue(entry.getKey() instanceof Reaction);
-				assertEquals("re1", ((Reaction) entry.getKey()).getIdReaction());
-				assertEquals(entry.getValue(), schema);
-			}
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-	
-	@Test
-	public void testAliasMatchWithReactionId() throws Exception {
-		try {
-			GenericColorSchema colorSchema = new GenericColorSchema();
-			colorSchema.setName(null);
-			colorSchema.setReactionIdentifier("1");
-			
-			Alias alias = new SpeciesAlias();
-			Protein protein = new GenericProtein();
-			protein.setName("test");
-			alias.setElement(protein);
-			
-			List<ColorSchema> schemas = new ArrayList<>();
-			schemas.add(colorSchema);
-
-			ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas);
-
-			assertFalse(factory.match(alias, colorSchema));
-			
-			colorSchema.setReactionIdentifier(null);
-			assertTrue(factory.match(alias, colorSchema));
-			
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-		
-	}
-	
-}
+package lcsb.mapviewer.commands;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.GenericColorSchema;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+
+public class ColorModelCommandTest extends CommandTestFunctions {
+	Logger logger = Logger.getLogger(ColorModelCommandTest.class);
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	/**
+	 * Test if all elements were copied - if not hibernate will complain
+	 * 
+	 * @throws Exception
+	 * 
+	 */
+	@Test
+	public void testColorFullModel() throws Exception {
+		ModelComparator comparator = new ModelComparator();
+		try {
+			Model model = getModelForFile("testFiles/sample.xml", false);
+			Model model2 = getModelForFile("testFiles/sample.xml", false);
+			Model coloredModel = new CopyCommand(model).execute();
+
+			List<ColorSchema> schemas = new ArrayList<>();
+			ColorSchema schema = new GenericColorSchema();
+			schema.setName("CNC");
+			schema.setValue(-1.0);
+			schemas.add(schema);
+			ColorModelCommand factory = new ColorModelCommand(coloredModel, schemas);
+
+			assertFalse(Color.RED.equals(coloredModel.getAliasByAliasId("sa14").getColor()));
+
+			factory.execute();
+
+			assertEquals(0, comparator.compare(model, model2));
+
+			assertFalse(comparator.compare(model, coloredModel) == 0);
+
+			assertEquals(Color.RED, coloredModel.getAliasByAliasId("sa14").getColor());
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testColoring2() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/coloring_model.xml", true);
+			Collection<ColorSchema> schemas = new ArrayList<>();
+			ColorSchema schema = new GenericColorSchema();
+			schema.setGeneralIdentifier("HGNC:11138");
+			schema.setValue(1.0);
+			schemas.add(schema);
+			schema = new GenericColorSchema();
+			schema.setGeneralIdentifier("CHEBI:CHEBI:15377");
+			schema.setValue(1.0);
+			schemas.add(schema);
+			schema = new GenericColorSchema();
+			schema.setGeneralIdentifier("CHEBI:CHEBI:15376");
+			schema.setValue(1.0);
+			schemas.add(schema);
+
+			ColorModelCommand factory = new ColorModelCommand(model, schemas);
+			Collection<ColorSchema> missing = factory.getMissingSchema();
+
+			assertEquals(1, missing.size());
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testReactionColoring1() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+			Reaction re4 = model.getReactionByReactionId("re4");
+			Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
+
+			ColorModelCommand factory = new ColorModelCommand(model, schemas);
+			assertFalse(Color.BLACK.equals(re4.getNodes().get(0).getLine().getColor()));
+
+			factory.execute();
+			re4 = model.getReactionByReactionId("re4");
+
+			assertEquals(Color.BLACK, re4.getNodes().get(0).getLine().getColor());
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testReactionColoring2() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+			Reaction re1 = model.getReactionByReactionId("re1");
+			Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
+			ColorSchema schema = new GenericColorSchema();
+			schema.setReactionIdentifier("re1");
+			schema.setColor(Color.RED);
+			schemas.add(schema);
+
+			ColorModelCommand factory = new ColorModelCommand(model, schemas);
+			assertEquals(Color.BLACK, re1.getNodes().get(0).getLine().getColor());
+
+			factory.execute();
+			re1 = model.getReactionByReactionId("re1");
+
+			assertEquals(Color.RED, re1.getNodes().get(0).getLine().getColor());
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testReactionColoring3() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+			Reaction re2 = model.getReactionByReactionId("re2");
+			Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
+			ColorSchema schema = new GenericColorSchema();
+			schema.setReactionIdentifier("re2");
+			schema.setValue(-1.0);
+			schemas.add(schema);
+
+			ColorModelCommand factory = new ColorModelCommand(model, schemas);
+			assertEquals(Color.BLACK, re2.getNodes().get(0).getLine().getColor());
+
+			factory.execute();
+			re2 = model.getReactionByReactionId("re2");
+
+			assertEquals(Color.RED, re2.getNodes().get(0).getLine().getColor());
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testReactionColoring4() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+			Reaction re3 = model.getReactionByReactionId("re3");
+			Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
+			ColorSchema schema = new GenericColorSchema();
+			Pair<MiriamType, String> pair = new Pair<MiriamType, String>(MiriamType.PUBMED, "12345");
+			List<Pair<MiriamType, String>> identifiers = new ArrayList<Pair<MiriamType, String>>();
+			identifiers.add(pair);
+
+			schema.setIdentifierColumns(identifiers);
+			schema.setValue(-1.0);
+			schemas.add(schema);
+
+			ColorModelCommand factory = new ColorModelCommand(model, schemas);
+
+			assertEquals(Color.BLACK, re3.getNodes().get(0).getLine().getColor());
+
+			factory.execute();
+			re3 = model.getReactionByReactionId("re3");
+
+			assertEquals(Color.RED, re3.getNodes().get(0).getLine().getColor());
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testColoringComplexModel() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/sample.xml", false);
+			Model model2 = getModelForFile("testFiles/sample.xml", false);
+
+			model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, "BLA"));
+
+			Collection<ColorSchema> schemas = new ArrayList<>();
+			Model coloredModel = new CopyCommand(model).execute();
+			new ColorModelCommand(coloredModel, schemas).execute();
+
+			Model coloredModel2 = coloredModel.getSubmodelConnections().iterator().next().getSubmodel().getModel();
+			Model coloredModel3 = coloredModel.getSubmodelByConnectionName("BLA");
+
+			assertFalse(coloredModel2.getAliasByAliasId("sa2").getColor().equals(model2.getAliasByAliasId("sa2").getColor()));
+			assertFalse(coloredModel3.getAliasByAliasId("sa2").getColor().equals(model2.getAliasByAliasId("sa2").getColor()));
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testColoredAliases() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/sample.xml", false);
+			Collection<ColorSchema> schemas = new ArrayList<>();
+			ColorSchema schema = new GenericColorSchema();
+			schema.setName("CNC");
+			schema.setColor(Color.BLUE);
+			schemas.add(schema);
+			schema = new GenericColorSchema();
+			schema.setName("BDH1");
+			schema.setColor(Color.BLUE);
+			schemas.add(schema);
+			ColorModelCommand factory = new ColorModelCommand(model, schemas);
+
+			Map<Object, ColorSchema> map = factory.getModifiedElements();
+			assertEquals(2, map.size());
+			for (Map.Entry<Object, ColorSchema> entry : map.entrySet()) {
+				assertTrue(entry.getKey() instanceof Alias);
+			}
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testColoredReactions() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/sample.xml", false);
+			Collection<ColorSchema> schemas = new ArrayList<>();
+			ColorSchema schema = new GenericColorSchema();
+			schema.setReactionIdentifier("re1");
+			schema.setLineWidth(3.0);
+			schema.setColor(Color.BLUE);
+			schema.setName("");
+			schema.setReverseReaction(true);
+			schemas.add(schema);
+			ColorModelCommand factory = new ColorModelCommand(model, schemas);
+
+			Map<Object, ColorSchema> map = factory.getModifiedElements();
+			assertEquals(0, map.size());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+	
+	@Test
+	public void testColoredReactions2() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/sample.xml", false);
+			Collection<ColorSchema> schemas = new ArrayList<>();
+			ColorSchema schema = new GenericColorSchema();
+			schema.setReactionIdentifier("re1");
+			schema.setLineWidth(3.0);
+			schema.setColor(Color.BLUE);
+			schema.setName(null);
+			schema.setReverseReaction(true);
+			schemas.add(schema);
+			ColorModelCommand factory = new ColorModelCommand(model, schemas);
+
+			Map<Object, ColorSchema> map = factory.getModifiedElements();
+			assertEquals(1, map.size());
+			for (Map.Entry<Object, ColorSchema> entry : map.entrySet()) {
+				assertTrue(entry.getKey() instanceof Reaction);
+				assertEquals("re1", ((Reaction) entry.getKey()).getIdReaction());
+				assertEquals(entry.getValue(), schema);
+			}
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+	
+	@Test
+	public void testAliasMatchWithReactionId() throws Exception {
+		try {
+			GenericColorSchema colorSchema = new GenericColorSchema();
+			colorSchema.setName(null);
+			colorSchema.setReactionIdentifier("1");
+			
+			Alias alias = new SpeciesAlias();
+			Protein protein = new GenericProtein();
+			protein.setName("test");
+			alias.setElement(protein);
+			
+			List<ColorSchema> schemas = new ArrayList<>();
+			schemas.add(colorSchema);
+
+			ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas);
+
+			assertFalse(factory.match(alias, colorSchema));
+			
+			colorSchema.setReactionIdentifier(null);
+			assertTrue(factory.match(alias, colorSchema));
+			
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+		
+	}
+	
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
index 3ceabb3643..ebbeaf037e 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.commands;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Protein;
-
-import org.apache.log4j.Logger;
-
-public abstract class CommandTestFunctions {
-	public double										 EPSILON = 1e-6;
-
-	Logger														logger	= Logger.getLogger(CommandTestFunctions.class);
-
-	private static Map<String, Model> models	= new HashMap<String, Model>();
-
-	protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
-		if (!fromCache) {
-			logger.debug("File without cache: " + fileName);
-			Model result = new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
-			result.setName(null);
-			return result;
-		}
-		Model result = models.get(fileName);
-		if (result == null) {
-			logger.debug("File to cache: " + fileName);
-
-			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
-			result.setName(null);
-			models.put(fileName, result);
-		}
-		return result;
-	}
-
-	protected Model createSimpleModel() {
-		Model model = new ModelFullIndexed(null);
-		Compartment compartment = new Compartment();
-		model.addCompartment(compartment);
-
-		ComplexSpecies complex = new ComplexSpecies();
-		complex.setElementId("complex_id");
-
-		Protein protein = new Protein();
-		protein.setNotes(null);
-		protein.setParent(compartment);
-		protein.setElementId("species_id");
-		List<String> list = new ArrayList<>();
-		list.add("synonym");
-		protein.addSynonyms(list);
-		List<String> list2 = new ArrayList<>();
-		list2.add("f_symbol");
-		protein.setFormerSymbols(list2);
-		complex.addElement(protein);
-
-		model.addElement(protein);
-		model.addElement(complex);
-
-		ComplexAlias complexAlias = new ComplexAlias();
-		complexAlias.setAliasId("complex_alias_id");
-		complexAlias.setSpecies(complex);
-		model.addAlias(complexAlias);
-
-		SpeciesAlias alias = new SpeciesAlias();
-		alias.setAliasId("alias_id");
-		alias.setSpecies(protein);
-		complexAlias.addAlias(alias);
-
-		model.addAlias(alias);
-
-		return model;
-	}
-
-}
+package lcsb.mapviewer.commands;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.ComplexSpecies;
+import lcsb.mapviewer.model.map.species.Protein;
+
+import org.apache.log4j.Logger;
+
+public abstract class CommandTestFunctions {
+	public double										 EPSILON = 1e-6;
+
+	Logger														logger	= Logger.getLogger(CommandTestFunctions.class);
+
+	private static Map<String, Model> models	= new HashMap<String, Model>();
+
+	protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
+		if (!fromCache) {
+			logger.debug("File without cache: " + fileName);
+			Model result = new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
+			result.setName(null);
+			return result;
+		}
+		Model result = models.get(fileName);
+		if (result == null) {
+			logger.debug("File to cache: " + fileName);
+
+			CellDesignerXmlParser parser = new CellDesignerXmlParser();
+			result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
+			result.setName(null);
+			models.put(fileName, result);
+		}
+		return result;
+	}
+
+	protected Model createSimpleModel() {
+		Model model = new ModelFullIndexed(null);
+		Compartment compartment = new Compartment();
+		model.addCompartment(compartment);
+
+		ComplexSpecies complex = new ComplexSpecies();
+		complex.setElementId("complex_id");
+
+		Protein protein = new Protein();
+		protein.setNotes(null);
+		protein.setParent(compartment);
+		protein.setElementId("species_id");
+		List<String> list = new ArrayList<>();
+		list.add("synonym");
+		protein.addSynonyms(list);
+		List<String> list2 = new ArrayList<>();
+		list2.add("f_symbol");
+		protein.setFormerSymbols(list2);
+		complex.addElement(protein);
+
+		model.addElement(protein);
+		model.addElement(complex);
+
+		ComplexAlias complexAlias = new ComplexAlias();
+		complexAlias.setAliasId("complex_alias_id");
+		complexAlias.setSpecies(complex);
+		model.addAlias(complexAlias);
+
+		SpeciesAlias alias = new SpeciesAlias();
+		alias.setAliasId("alias_id");
+		alias.setSpecies(protein);
+		complexAlias.addAlias(alias);
+
+		model.addAlias(alias);
+
+		return model;
+	}
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
index aef0f6d491..032b83c900 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -1,344 +1,344 @@
-package lcsb.mapviewer.commands;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Protein;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CopyCommandTest extends CommandTestFunctions {
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testCopyModel() {
-		try {
-			Model model = getModelForFile("testFiles/sample.xml", false);
-			Model copy = new CopyCommand(model).execute();
-
-			ModelComparator comparator = new ModelComparator();
-
-			assertEquals(0, comparator.compare(model, copy));
-		} catch (Exception e) {
-			e.printStackTrace();
-			fail("exception occurred");
-		}
-	}
-
-	@Test
-	public void testCopyCustomModel() {
-		try {
-			Model model = new ModelFullIndexed(null);
-			Compartment compartment = new Compartment();
-			model.addCompartment(compartment);
-
-			Protein protein = new Protein();
-			protein.setNotes(null);
-			protein.setParent(compartment);
-			protein.setElementId("A");
-
-			model.addElement(protein);
-
-			Model copy = new CopyCommand(model).execute();
-
-			ModelComparator comparator = new ModelComparator();
-
-			assertEquals(0, comparator.compare(model, copy));
-		} catch (Exception e) {
-			e.printStackTrace();
-			fail("exception occurred");
-		}
-	}
-
-	@Test
-	public void testCopyCustomModel2() {
-		try {
-			Model model = new ModelFullIndexed(null);
-			Compartment compartment = new Compartment();
-			model.addCompartment(compartment);
-
-			ComplexSpecies complex = new ComplexSpecies();
-			complex.setElementId("id");
-
-			Protein protein = new Protein();
-			protein.setNotes(null);
-			protein.setParent(compartment);
-			protein.setElementId("A");
-			complex.addElement(protein);
-
-			model.addElement(protein);
-			model.addElement(complex);
-
-			ComplexAlias complexAlias = new ComplexAlias();
-			complexAlias.setAliasId("id2");
-			complexAlias.setSpecies(complex);
-			model.addAlias(complexAlias);
-
-			SpeciesAlias alias = new SpeciesAlias();
-			alias.setAliasId("B");
-			alias.setSpecies(protein);
-			complexAlias.addAlias(alias);
-
-			model.addAlias(alias);
-
-			Model copy = new CopyCommand(model).execute();
-
-			ModelComparator comparator = new ModelComparator();
-
-			assertEquals(0, comparator.compare(model, copy));
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			fail("exception occurred");
-		}
-	}
-
-	@Test
-	public void testCopyModel3() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/complex_with_state.xml", true);
-
-			Model copy = new CopyCommand(model).execute();
-
-			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(copy);
-
-			InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-			Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
-			ModelComparator comparator = new ModelComparator();
-
-			// check if after conversion to xml everything works
-			assertEquals(0, comparator.compare(copy, copy2));
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testCopyModel4() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/problematic_description.xml", true);
-
-			Model copy = new CopyCommand(model).execute();
-
-			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(copy);
-
-			InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-			Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
-			ModelComparator comparator = new ModelComparator();
-
-			// check if after conversion to xml everything works
-			assertEquals(0, comparator.compare(copy, copy2));
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testCopyModelWithArtifitialAliases() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-			logger.debug(model.getName());
-			new CreateHierarchyCommand(model, 2, 2).execute();
-
-			Model copy = new CopyCommand(model).execute();
-
-			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(copy);
-
-			InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-			Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
-			ModelComparator comparator = new ModelComparator();
-
-			new CreateHierarchyCommand(copy2, 2, 2).execute();
-
-			// check if after conversion to xml everything works
-			assertEquals(0, comparator.compare(copy, copy2));
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testCopyModelWithSubmodels() throws Exception {
-		try {
-			Model model = getModel();
-			Model model2 = getModel();
-			model2.setNotes("ASDSA");
-			model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
-			Model copy = new CopyCommand(model).execute();
-
-			ModelComparator comparator = new ModelComparator();
-
-			assertEquals(0, comparator.compare(model, copy));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testCopySubmodel() throws Exception {
-		try {
-			Model model = getModel();
-			Model model2 = getModel();
-			model2.setNotes("ASDSA");
-			model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS, "name a"));
-
-			Model model3 = getModel();
-			model3.setNotes("ASDSA");
-			model.addSubmodelConnection(new ModelSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name b"));
-			Alias alias = model2.getAliasByAliasId("a_id");
-			alias.setSubmodel(new AliasSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name c"));
-			Model copy = new CopyCommand(model2).execute();
-
-			ModelComparator comparator = new ModelComparator();
-
-			assertEquals(0, comparator.compare(model2, copy));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testCopyModelWithSubmodels2() throws Exception {
-		try {
-			Model model = getModel();
-			Model model2 = getModel();
-			model2.setNotes("ASDSA2");
-
-			model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
-			model.getAliasByAliasId("a_id").setSubmodel(new AliasSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
-			Model copy = new CopyCommand(model).execute();
-
-			ModelComparator comparator = new ModelComparator();
-
-			assertEquals(0, comparator.compare(model, copy));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-
-	@Test
-	public void testCopyModelWithName() throws Exception {
-		try {
-			Model model = getModel();
-			model.setName("ASDSA2");
-
-			Model copy = new CopyCommand(model).execute();
-
-			ModelComparator comparator = new ModelComparator();
-
-			assertEquals(0, comparator.compare(model, copy));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testCopyModelWithSubmodelsThrowException() throws Exception {
-		try {
-			Model model = getModel();
-			Model model2 = getModel();
-			model2.setNotes("ASDSA2");
-
-			model.getAliasByAliasId("a_id").setSubmodel(new AliasSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
-			try {
-				new CopyCommand(model).execute();
-				fail("Exception expected");
-			} catch (InvalidArgumentException e) {
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	private Model getModel() {
-		Model model = new ModelFullIndexed(null);
-		model.setNotes("Some description");
-		Protein protein = new Protein();
-		protein.setName("ad");
-		protein.setElementId("A");
-		model.addElement(protein);
-
-		SpeciesAlias alias = new SpeciesAlias(protein);
-		alias.setAliasId("a_id");
-		model.addAlias(alias);
-
-		Compartment compartment = new Compartment("default");
-		model.addCompartment(compartment);
-
-		Layer layer = new Layer();
-		layer.setName("layer name");
-		model.addLayer(layer);
-
-		model.addReaction(new Reaction());
-		return model;
-	}
-
-	@Test
-	public void testCopyModelWithImages() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/sample.xml", false);
-			OverviewImage oi = new OverviewImage();
-			OverviewModelLink oml = new OverviewModelLink();
-			oml.setLinkedModel(model);
-			oml.setPolygon("1,2");
-			oi.addLink(oml);
-			model.addOverviewImage(oi);
-			Model copy = new CopyCommand(model).execute();
-
-			ModelComparator comparator = new ModelComparator();
-
-			assertEquals(0, comparator.compare(model, copy));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-
-}
+package lcsb.mapviewer.commands;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.ComplexSpecies;
+import lcsb.mapviewer.model.map.species.Protein;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CopyCommandTest extends CommandTestFunctions {
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testCopyModel() {
+		try {
+			Model model = getModelForFile("testFiles/sample.xml", false);
+			Model copy = new CopyCommand(model).execute();
+
+			ModelComparator comparator = new ModelComparator();
+
+			assertEquals(0, comparator.compare(model, copy));
+		} catch (Exception e) {
+			e.printStackTrace();
+			fail("exception occurred");
+		}
+	}
+
+	@Test
+	public void testCopyCustomModel() {
+		try {
+			Model model = new ModelFullIndexed(null);
+			Compartment compartment = new Compartment();
+			model.addCompartment(compartment);
+
+			Protein protein = new Protein();
+			protein.setNotes(null);
+			protein.setParent(compartment);
+			protein.setElementId("A");
+
+			model.addElement(protein);
+
+			Model copy = new CopyCommand(model).execute();
+
+			ModelComparator comparator = new ModelComparator();
+
+			assertEquals(0, comparator.compare(model, copy));
+		} catch (Exception e) {
+			e.printStackTrace();
+			fail("exception occurred");
+		}
+	}
+
+	@Test
+	public void testCopyCustomModel2() {
+		try {
+			Model model = new ModelFullIndexed(null);
+			Compartment compartment = new Compartment();
+			model.addCompartment(compartment);
+
+			ComplexSpecies complex = new ComplexSpecies();
+			complex.setElementId("id");
+
+			Protein protein = new Protein();
+			protein.setNotes(null);
+			protein.setParent(compartment);
+			protein.setElementId("A");
+			complex.addElement(protein);
+
+			model.addElement(protein);
+			model.addElement(complex);
+
+			ComplexAlias complexAlias = new ComplexAlias();
+			complexAlias.setAliasId("id2");
+			complexAlias.setSpecies(complex);
+			model.addAlias(complexAlias);
+
+			SpeciesAlias alias = new SpeciesAlias();
+			alias.setAliasId("B");
+			alias.setSpecies(protein);
+			complexAlias.addAlias(alias);
+
+			model.addAlias(alias);
+
+			Model copy = new CopyCommand(model).execute();
+
+			ModelComparator comparator = new ModelComparator();
+
+			assertEquals(0, comparator.compare(model, copy));
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			fail("exception occurred");
+		}
+	}
+
+	@Test
+	public void testCopyModel3() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/complex_with_state.xml", true);
+
+			Model copy = new CopyCommand(model).execute();
+
+			CellDesignerXmlParser parser = new CellDesignerXmlParser();
+			String xml = parser.toXml(copy);
+
+			InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+			Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+			ModelComparator comparator = new ModelComparator();
+
+			// check if after conversion to xml everything works
+			assertEquals(0, comparator.compare(copy, copy2));
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testCopyModel4() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/problematic_description.xml", true);
+
+			Model copy = new CopyCommand(model).execute();
+
+			CellDesignerXmlParser parser = new CellDesignerXmlParser();
+			String xml = parser.toXml(copy);
+
+			InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+			Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+			ModelComparator comparator = new ModelComparator();
+
+			// check if after conversion to xml everything works
+			assertEquals(0, comparator.compare(copy, copy2));
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testCopyModelWithArtifitialAliases() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+			logger.debug(model.getName());
+			new CreateHierarchyCommand(model, 2, 2).execute();
+
+			Model copy = new CopyCommand(model).execute();
+
+			CellDesignerXmlParser parser = new CellDesignerXmlParser();
+			String xml = parser.toXml(copy);
+
+			InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+			Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+			ModelComparator comparator = new ModelComparator();
+
+			new CreateHierarchyCommand(copy2, 2, 2).execute();
+
+			// check if after conversion to xml everything works
+			assertEquals(0, comparator.compare(copy, copy2));
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testCopyModelWithSubmodels() throws Exception {
+		try {
+			Model model = getModel();
+			Model model2 = getModel();
+			model2.setNotes("ASDSA");
+			model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+			Model copy = new CopyCommand(model).execute();
+
+			ModelComparator comparator = new ModelComparator();
+
+			assertEquals(0, comparator.compare(model, copy));
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testCopySubmodel() throws Exception {
+		try {
+			Model model = getModel();
+			Model model2 = getModel();
+			model2.setNotes("ASDSA");
+			model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS, "name a"));
+
+			Model model3 = getModel();
+			model3.setNotes("ASDSA");
+			model.addSubmodelConnection(new ModelSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name b"));
+			Alias alias = model2.getAliasByAliasId("a_id");
+			alias.setSubmodel(new AliasSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name c"));
+			Model copy = new CopyCommand(model2).execute();
+
+			ModelComparator comparator = new ModelComparator();
+
+			assertEquals(0, comparator.compare(model2, copy));
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testCopyModelWithSubmodels2() throws Exception {
+		try {
+			Model model = getModel();
+			Model model2 = getModel();
+			model2.setNotes("ASDSA2");
+
+			model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+			model.getAliasByAliasId("a_id").setSubmodel(new AliasSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+			Model copy = new CopyCommand(model).execute();
+
+			ModelComparator comparator = new ModelComparator();
+
+			assertEquals(0, comparator.compare(model, copy));
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+
+	@Test
+	public void testCopyModelWithName() throws Exception {
+		try {
+			Model model = getModel();
+			model.setName("ASDSA2");
+
+			Model copy = new CopyCommand(model).execute();
+
+			ModelComparator comparator = new ModelComparator();
+
+			assertEquals(0, comparator.compare(model, copy));
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testCopyModelWithSubmodelsThrowException() throws Exception {
+		try {
+			Model model = getModel();
+			Model model2 = getModel();
+			model2.setNotes("ASDSA2");
+
+			model.getAliasByAliasId("a_id").setSubmodel(new AliasSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+			try {
+				new CopyCommand(model).execute();
+				fail("Exception expected");
+			} catch (InvalidArgumentException e) {
+			}
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	private Model getModel() {
+		Model model = new ModelFullIndexed(null);
+		model.setNotes("Some description");
+		Protein protein = new Protein();
+		protein.setName("ad");
+		protein.setElementId("A");
+		model.addElement(protein);
+
+		SpeciesAlias alias = new SpeciesAlias(protein);
+		alias.setAliasId("a_id");
+		model.addAlias(alias);
+
+		Compartment compartment = new Compartment("default");
+		model.addCompartment(compartment);
+
+		Layer layer = new Layer();
+		layer.setName("layer name");
+		model.addLayer(layer);
+
+		model.addReaction(new Reaction());
+		return model;
+	}
+
+	@Test
+	public void testCopyModelWithImages() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/sample.xml", false);
+			OverviewImage oi = new OverviewImage();
+			OverviewModelLink oml = new OverviewModelLink();
+			oml.setLinkedModel(model);
+			oml.setPolygon("1,2");
+			oi.addLink(oml);
+			model.addOverviewImage(oi);
+			Model copy = new CopyCommand(model).execute();
+
+			ModelComparator comparator = new ModelComparator();
+
+			assertEquals(0, comparator.compare(model, copy));
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
index f4f23f6a5c..4669b97eff 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
@@ -1,285 +1,285 @@
-package lcsb.mapviewer.commands;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-import java.util.HashSet;
-import java.util.Set;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.model.Model;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CreateHierarchyCommandTest extends CommandTestFunctions {
-	Logger	logger	= Logger.getLogger(CreateHierarchyCommandTest.class);
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testCyclicComplexes() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/cyclic_hierarchy_problem.xml", false);
-
-			new CreateHierarchyCommand(model, 8, 80).execute();
-
-			Alias alias = model.getAliasByAliasId("sa5033");
-
-			Set<Alias> parents = new HashSet<Alias>();
-			while (alias.getParent() instanceof ComplexAlias) {
-				assertFalse("Cyclic nesting", parents.contains(alias.getParent()));
-				alias = alias.getParent();
-				parents.add(alias);
-			}
-
-			Set<Integer> levels = new HashSet<Integer>();
-			for (Alias a : model.getAliases()) {
-				levels.add(a.getVisibilityLevel());
-			}
-			assertTrue(levels.size() > 2);
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testCreateHierachy() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
-			new CreateHierarchyCommand(model, 2, 2).execute();
-			// check if second call will throw an exception...
-			new CreateHierarchyCommand(model, 2, 2).execute();
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testCreateHierachy2() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
-			new CreateHierarchyCommand(model, 2, 2).execute();
-
-			boolean artifitial = false;
-			for (CompartmentAlias a : model.getCompartmentsAliases()) {
-				if (a instanceof ArtifitialCompartmentAlias) {
-					artifitial = true;
-					assertNotNull(a.getCompartment());
-				}
-			}
-			assertTrue("No hierarchical structure element found", artifitial);
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testRecreateHierachy() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
-			int size0 = model.getCompartments().size();
-			int aliasSize0 = model.getCompartmentsAliases().size();
-
-			new CreateHierarchyCommand(model, 2, 2).execute();
-
-			int size = model.getCompartments().size();
-			int aliasSize = model.getCompartmentsAliases().size();
-
-			assertTrue(size0 != size);
-			assertTrue(aliasSize0 != aliasSize);
-			new CreateHierarchyCommand(model, 2, 2).execute();
-
-			int size2 = model.getCompartments().size();
-			int aliasSize2 = model.getCompartmentsAliases().size();
-
-			assertEquals(size, size2);
-			assertEquals(aliasSize, aliasSize2);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testCreateComponentsMinVisibility() throws Exception {
-		try {
-			double zoomFactor = 39.0625;
-			int levels = 6;
-
-			Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml", false);
-
-			new CreateHierarchyCommand(model, levels, zoomFactor).execute();
-
-			for (Alias alias : model.getAliases()) {
-				if (alias.getParent() == null) {
-					assertTrue("Alias " + alias.getAliasId() + " is not visible at levels highers than " + alias.getVisibilityLevel(), alias.getVisibilityLevel() <= 1);
-				}
-			}
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testCreateComponentsMaxVisibility() throws Exception {
-		try {
-			double zoomFactor = 39.0625;
-			int levels = 6;
-
-			Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml", false);
-
-			new CreateHierarchyCommand(model, levels, zoomFactor).execute();
-
-			for (Alias alias : model.getAliases()) {
-				assertTrue(
-						"Alias " + alias.getAliasId() + " is not visible even at the bottom level (visibility: " + alias.getVisibilityLevel() + ") ",
-						alias.getVisibilityLevel() <= levels);
-			}
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testCompactComplexesInNestedView() throws Exception {
-		Model model;
-		try {
-			model = getModelForFile("testFiles/problematic/compact_complex_view_problem.xml", false);
-			Alias alias = model.getAliasByAliasId("sa1");
-			Object parent1 = alias.getParent();
-			new CreateHierarchyCommand(model, 3, 16).execute();
-			Object parent2 = alias.getParent();
-			assertEquals(parent1, parent2);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testRecallHierachyCreation() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
-			CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
-			command.execute();
-			try {
-				command.execute();
-				fail("Exception expected");
-			} catch (InvalidStateException e) {
-
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testClear() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
-			CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
-			command.clean();
-			for (Alias alias : model.getAliases()) {
-				assertNull(alias.getParent());
-				if (alias instanceof ComplexAlias) {
-					assertTrue(((ComplexAlias) alias).getAliases().isEmpty());
-				}
-			}
-			for (CompartmentAlias alias : model.getCompartmentsAliases()) {
-				assertNull(alias.getParent());
-				assertTrue(alias.getAliases().isEmpty());
-			}
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testNestedProblem() throws Exception {
-		try {
-			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			Model model = parser.createModel(new ConverterParams().filename("testFiles/nested_test.xml").sizeAutoAdjust(true));
-
-			double zoomFactor = Math.max(model.getHeight(), model.getWidth()) / (256);
-			int zoomLevels = (int) Math.ceil(Math.log(zoomFactor) / Math.log(2));
-
-			CreateHierarchyCommand command = new CreateHierarchyCommand(model, zoomLevels, zoomFactor);
-			command.execute();
-
-			for (Alias alias : model.getAliases()) {
-				Alias parentAlias = alias.getParent();
-				if (parentAlias != null) {
-					assertTrue(alias.getVisibilityLevel() >= parentAlias.getVisibilityLevel());
-				}
-			}
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testDisconnectedChildInComplex() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/problematic/disconnected_child_in_complex.xml", false);
-
-			new CreateHierarchyCommand(model, 8, 80).execute();
-			
-			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xmlString = parser.toXml(model);
-		//	logger.debug(xmlString);
-			
-			InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
-
-			parser.createModel(new ConverterParams().inputStream(stream));
-
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-
-
-}
+package lcsb.mapviewer.commands;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+import java.util.HashSet;
+import java.util.Set;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.model.Model;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CreateHierarchyCommandTest extends CommandTestFunctions {
+	Logger	logger	= Logger.getLogger(CreateHierarchyCommandTest.class);
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testCyclicComplexes() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/cyclic_hierarchy_problem.xml", false);
+
+			new CreateHierarchyCommand(model, 8, 80).execute();
+
+			Alias alias = model.getAliasByAliasId("sa5033");
+
+			Set<Alias> parents = new HashSet<Alias>();
+			while (alias.getParent() instanceof ComplexAlias) {
+				assertFalse("Cyclic nesting", parents.contains(alias.getParent()));
+				alias = alias.getParent();
+				parents.add(alias);
+			}
+
+			Set<Integer> levels = new HashSet<Integer>();
+			for (Alias a : model.getAliases()) {
+				levels.add(a.getVisibilityLevel());
+			}
+			assertTrue(levels.size() > 2);
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testCreateHierachy() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+			new CreateHierarchyCommand(model, 2, 2).execute();
+			// check if second call will throw an exception...
+			new CreateHierarchyCommand(model, 2, 2).execute();
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testCreateHierachy2() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+			new CreateHierarchyCommand(model, 2, 2).execute();
+
+			boolean artifitial = false;
+			for (CompartmentAlias a : model.getCompartmentsAliases()) {
+				if (a instanceof ArtifitialCompartmentAlias) {
+					artifitial = true;
+					assertNotNull(a.getCompartment());
+				}
+			}
+			assertTrue("No hierarchical structure element found", artifitial);
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testRecreateHierachy() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+			int size0 = model.getCompartments().size();
+			int aliasSize0 = model.getCompartmentsAliases().size();
+
+			new CreateHierarchyCommand(model, 2, 2).execute();
+
+			int size = model.getCompartments().size();
+			int aliasSize = model.getCompartmentsAliases().size();
+
+			assertTrue(size0 != size);
+			assertTrue(aliasSize0 != aliasSize);
+			new CreateHierarchyCommand(model, 2, 2).execute();
+
+			int size2 = model.getCompartments().size();
+			int aliasSize2 = model.getCompartmentsAliases().size();
+
+			assertEquals(size, size2);
+			assertEquals(aliasSize, aliasSize2);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testCreateComponentsMinVisibility() throws Exception {
+		try {
+			double zoomFactor = 39.0625;
+			int levels = 6;
+
+			Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml", false);
+
+			new CreateHierarchyCommand(model, levels, zoomFactor).execute();
+
+			for (Alias alias : model.getAliases()) {
+				if (alias.getParent() == null) {
+					assertTrue("Alias " + alias.getAliasId() + " is not visible at levels highers than " + alias.getVisibilityLevel(), alias.getVisibilityLevel() <= 1);
+				}
+			}
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testCreateComponentsMaxVisibility() throws Exception {
+		try {
+			double zoomFactor = 39.0625;
+			int levels = 6;
+
+			Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml", false);
+
+			new CreateHierarchyCommand(model, levels, zoomFactor).execute();
+
+			for (Alias alias : model.getAliases()) {
+				assertTrue(
+						"Alias " + alias.getAliasId() + " is not visible even at the bottom level (visibility: " + alias.getVisibilityLevel() + ") ",
+						alias.getVisibilityLevel() <= levels);
+			}
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testCompactComplexesInNestedView() throws Exception {
+		Model model;
+		try {
+			model = getModelForFile("testFiles/problematic/compact_complex_view_problem.xml", false);
+			Alias alias = model.getAliasByAliasId("sa1");
+			Object parent1 = alias.getParent();
+			new CreateHierarchyCommand(model, 3, 16).execute();
+			Object parent2 = alias.getParent();
+			assertEquals(parent1, parent2);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testRecallHierachyCreation() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+			CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
+			command.execute();
+			try {
+				command.execute();
+				fail("Exception expected");
+			} catch (InvalidStateException e) {
+
+			}
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testClear() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+
+			CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
+			command.clean();
+			for (Alias alias : model.getAliases()) {
+				assertNull(alias.getParent());
+				if (alias instanceof ComplexAlias) {
+					assertTrue(((ComplexAlias) alias).getAliases().isEmpty());
+				}
+			}
+			for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+				assertNull(alias.getParent());
+				assertTrue(alias.getAliases().isEmpty());
+			}
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testNestedProblem() throws Exception {
+		try {
+			CellDesignerXmlParser parser = new CellDesignerXmlParser();
+			Model model = parser.createModel(new ConverterParams().filename("testFiles/nested_test.xml").sizeAutoAdjust(true));
+
+			double zoomFactor = Math.max(model.getHeight(), model.getWidth()) / (256);
+			int zoomLevels = (int) Math.ceil(Math.log(zoomFactor) / Math.log(2));
+
+			CreateHierarchyCommand command = new CreateHierarchyCommand(model, zoomLevels, zoomFactor);
+			command.execute();
+
+			for (Alias alias : model.getAliases()) {
+				Alias parentAlias = alias.getParent();
+				if (parentAlias != null) {
+					assertTrue(alias.getVisibilityLevel() >= parentAlias.getVisibilityLevel());
+				}
+			}
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testDisconnectedChildInComplex() throws Exception {
+		try {
+			Model model = getModelForFile("testFiles/problematic/disconnected_child_in_complex.xml", false);
+
+			new CreateHierarchyCommand(model, 8, 80).execute();
+			
+			CellDesignerXmlParser parser = new CellDesignerXmlParser();
+			String xmlString = parser.toXml(model);
+		//	logger.debug(xmlString);
+			
+			InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
+
+			parser.createModel(new ConverterParams().inputStream(stream));
+
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/Project.java b/model/src/main/java/lcsb/mapviewer/model/Project.java
index 8058df51cc..ba235988a1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/Project.java
+++ b/model/src/main/java/lcsb/mapviewer/model/Project.java
@@ -1,368 +1,368 @@
-package lcsb.mapviewer.model;
-
-import java.io.Serializable;
-import java.util.HashSet;
-import java.util.Set;
-
-import javax.persistence.Basic;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-
-/**
- * Top level structure in the system. It describes single project and contains
- * all data in it.
- * 
- * @author Piotr Gawron
- * 
- */
-@Entity
-@Table(name = "project_table")
-public class Project implements Serializable {
-
-	/**
-	 * Default class logger.
-	 */
-	@SuppressWarnings("unused")
-	private static Logger			logger					 = Logger.getLogger(Project.class);
-
-	/**
-		 * 
-		 */
-	private static final long	serialVersionUID = 1L;
-
-	/**
-	 * Unique database identifier.
-	 */
-	@Id
-	@GeneratedValue(strategy = GenerationType.IDENTITY)
-	@Column(name = "idDb", unique = true, nullable = false)
-	private int								id;
-
-	/**
-	 * Project identifier defined by the user (some meaningful string).
-	 */
-	@Column(name = "project_id", unique = true, nullable = false)
-	private String						projectId;
-
-	/**
-	 * Project disease.
-	 */
-	@Cascade({ CascadeType.ALL })
-	@OneToOne
-	private MiriamData				disease;
-
-	/**
-	 * Name of the project.
-	 */
-	private String						name;
-
-	/**
-	 * Directory where the images on the server will be stored for this project.
-	 */
-	private String						directory;
-
-	/**
-	 * Status of the project used during uploading the project to the system.
-	 */
-	private ProjectStatus			status					 = ProjectStatus.UNKNOWN;
-
-	/**
-	 * Progress of single step of project uploading.
-	 */
-	private double						progress				 = 0;
-
-	/**
-	 * Errors connected with the project.
-	 */
-	private String						errors					 = null;
-
-	/**
-	 * Map models in the project.
-	 */
-	@Cascade({ CascadeType.ALL })
-	@OneToMany(mappedBy = "project", orphanRemoval = true)
-	private Set<ModelData>		models					 = new HashSet<ModelData>();
-
-	/**
-	 * Here we store input file.
-	 */
-	@Basic(fetch = FetchType.LAZY)
-	private byte[]						inputData;
-
-	/**
-	 * Here we store input file.
-	 */
-	private String						inputFileName;
-
-	/**
-	 * Organism associated with the project.
-	 */
-	@Cascade({ CascadeType.ALL })
-	@OneToOne
-	private MiriamData				organism;
-
-	/**
-	 * Default constructor.
-	 */
-	public Project() {
-	}
-
-	/**
-	 * Constructor with the project name in the parameter.
-	 * 
-	 * @param projectName
-	 *          name of the project
-	 */
-	public Project(String projectName) {
-		this.projectId = projectName;
-	}
-
-	/**
-	 * Adds map model to the project.
-	 * 
-	 * @param model
-	 *          map to be added
-	 */
-	public void addModel(ModelData model) {
-		models.add(model);
-		model.setProject(this);
-	}
-
-	/**
-	 * Adds map model to the project.
-	 * 
-	 * @param model
-	 *          map to be added
-	 */
-	public void addModel(Model model) {
-		models.add(model.getModelData());
-		model.setProject(this);
-	}
-
-	/**
-	 * Removes map model from the project.
-	 * 
-	 * @param model
-	 *          map model to remove
-	 */
-	public void removeModel(ModelData model) {
-		models.remove(model);
-	}
-
-	/**
-	 * @return the id
-	 * @see #id
-	 */
-	public int getId() {
-		return id;
-	}
-
-	/**
-	 * @param id
-	 *          the id to set
-	 * @see #id
-	 */
-	public void setId(int id) {
-		this.id = id;
-	}
-
-	/**
-	 * @return user defined project identifier
-	 * @see #projectId
-	 */
-	public String getProjectId() {
-		return projectId;
-	}
-
-	/**
-	 * @param projectId
-	 *          user defined project identifier
-	 * @see #projectId
-	 */
-	public void setProjectId(String projectId) {
-		this.projectId = projectId;
-	}
-
-	/**
-	 * @return the status
-	 * @see #status
-	 */
-	public ProjectStatus getStatus() {
-		return status;
-	}
-
-	/**
-	 * @param status
-	 *          the status to set
-	 * @see #status
-	 */
-	public void setStatus(ProjectStatus status) {
-		this.status = status;
-	}
-
-	/**
-	 * @return the progress
-	 * @see #progress
-	 */
-	public double getProgress() {
-		return progress;
-	}
-
-	/**
-	 * @param progress
-	 *          the progress to set
-	 * @see #progress
-	 */
-	public void setProgress(double progress) {
-		this.progress = progress;
-	}
-
-	/**
-	 * @return the models
-	 * @see #models
-	 */
-	public Set<ModelData> getModels() {
-		return models;
-	}
-
-	/**
-	 * @param models
-	 *          the models to set
-	 * @see #models
-	 */
-	public void setModels(Set<ModelData> models) {
-		this.models = models;
-	}
-
-	/**
-	 * @return the errors
-	 * @see #errors
-	 */
-	public String getErrors() {
-		return errors;
-	}
-
-	/**
-	 * @param errors
-	 *          the errors to set
-	 * @see #errors
-	 */
-	public void setErrors(String errors) {
-		this.errors = errors;
-	}
-
-	/**
-	 * @return the directory
-	 * @see #directory
-	 */
-	public String getDirectory() {
-		return directory;
-	}
-
-	/**
-	 * @param directory
-	 *          the directory to set
-	 * @see #directory
-	 */
-	public void setDirectory(String directory) {
-		this.directory = directory;
-	}
-
-	/**
-	 * @return the name
-	 * @see #name
-	 */
-	public String getName() {
-		return name;
-	}
-
-	/**
-	 * @param name
-	 *          the name to set
-	 * @see #name
-	 */
-	public void setName(String name) {
-		this.name = name;
-	}
-
-	/**
-	 * @return disease
-	 */
-	public MiriamData getDisease() {
-		return disease;
-	}
-
-	/**
-	 * @param disease
-	 *          the disease
-	 */
-	public void setDisease(MiriamData disease) {
-		this.disease = disease;
-	}
-
-	/**
-	 * @return the inputData
-	 * @see #inputData
-	 */
-	public byte[] getInputData() {
-		return inputData;
-	}
-
-	/**
-	 * @param inputData
-	 *          the inputData to set
-	 * @see #inputData
-	 */
-	public void setInputData(byte[] inputData) {
-		this.inputData = inputData;
-	}
-
-	/**
-	 * @return the inputFileName
-	 * @see #inputFileName
-	 */
-	public String getInputFileName() {
-		return inputFileName;
-	}
-
-	/**
-	 * @param inputFileName
-	 *          the inputFileName to set
-	 * @see #inputFileName
-	 */
-	public void setInputFileName(String inputFileName) {
-		this.inputFileName = inputFileName;
-	}
-
-	/**
-	 * @param organism
-	 *          the organism to set
-	 * @see #organism
-	 */
-	public void setOrganism(MiriamData organism) {
-		this.organism = organism;
-	}
-
-	/**
-	 * @return the organism
-	 * @see #organism
-	 */
-	public MiriamData getOrganism() {
-		return organism;
-	}
-}
+package lcsb.mapviewer.model;
+
+import java.io.Serializable;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.persistence.Basic;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.OneToMany;
+import javax.persistence.OneToOne;
+import javax.persistence.Table;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+
+/**
+ * Top level structure in the system. It describes single project and contains
+ * all data in it.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+@Entity
+@Table(name = "project_table")
+public class Project implements Serializable {
+
+	/**
+	 * Default class logger.
+	 */
+	@SuppressWarnings("unused")
+	private static Logger			logger					 = Logger.getLogger(Project.class);
+
+	/**
+		 * 
+		 */
+	private static final long	serialVersionUID = 1L;
+
+	/**
+	 * Unique database identifier.
+	 */
+	@Id
+	@GeneratedValue(strategy = GenerationType.IDENTITY)
+	@Column(name = "idDb", unique = true, nullable = false)
+	private int								id;
+
+	/**
+	 * Project identifier defined by the user (some meaningful string).
+	 */
+	@Column(name = "project_id", unique = true, nullable = false)
+	private String						projectId;
+
+	/**
+	 * Project disease.
+	 */
+	@Cascade({ CascadeType.ALL })
+	@OneToOne
+	private MiriamData				disease;
+
+	/**
+	 * Name of the project.
+	 */
+	private String						name;
+
+	/**
+	 * Directory where the images on the server will be stored for this project.
+	 */
+	private String						directory;
+
+	/**
+	 * Status of the project used during uploading the project to the system.
+	 */
+	private ProjectStatus			status					 = ProjectStatus.UNKNOWN;
+
+	/**
+	 * Progress of single step of project uploading.
+	 */
+	private double						progress				 = 0;
+
+	/**
+	 * Errors connected with the project.
+	 */
+	private String						errors					 = null;
+
+	/**
+	 * Map models in the project.
+	 */
+	@Cascade({ CascadeType.ALL })
+	@OneToMany(mappedBy = "project", orphanRemoval = true)
+	private Set<ModelData>		models					 = new HashSet<ModelData>();
+
+	/**
+	 * Here we store input file.
+	 */
+	@Basic(fetch = FetchType.LAZY)
+	private byte[]						inputData;
+
+	/**
+	 * Here we store input file.
+	 */
+	private String						inputFileName;
+
+	/**
+	 * Organism associated with the project.
+	 */
+	@Cascade({ CascadeType.ALL })
+	@OneToOne
+	private MiriamData				organism;
+
+	/**
+	 * Default constructor.
+	 */
+	public Project() {
+	}
+
+	/**
+	 * Constructor with the project name in the parameter.
+	 * 
+	 * @param projectName
+	 *          name of the project
+	 */
+	public Project(String projectName) {
+		this.projectId = projectName;
+	}
+
+	/**
+	 * Adds map model to the project.
+	 * 
+	 * @param model
+	 *          map to be added
+	 */
+	public void addModel(ModelData model) {
+		models.add(model);
+		model.setProject(this);
+	}
+
+	/**
+	 * Adds map model to the project.
+	 * 
+	 * @param model
+	 *          map to be added
+	 */
+	public void addModel(Model model) {
+		models.add(model.getModelData());
+		model.setProject(this);
+	}
+
+	/**
+	 * Removes map model from the project.
+	 * 
+	 * @param model
+	 *          map model to remove
+	 */
+	public void removeModel(ModelData model) {
+		models.remove(model);
+	}
+
+	/**
+	 * @return the id
+	 * @see #id
+	 */
+	public int getId() {
+		return id;
+	}
+
+	/**
+	 * @param id
+	 *          the id to set
+	 * @see #id
+	 */
+	public void setId(int id) {
+		this.id = id;
+	}
+
+	/**
+	 * @return user defined project identifier
+	 * @see #projectId
+	 */
+	public String getProjectId() {
+		return projectId;
+	}
+
+	/**
+	 * @param projectId
+	 *          user defined project identifier
+	 * @see #projectId
+	 */
+	public void setProjectId(String projectId) {
+		this.projectId = projectId;
+	}
+
+	/**
+	 * @return the status
+	 * @see #status
+	 */
+	public ProjectStatus getStatus() {
+		return status;
+	}
+
+	/**
+	 * @param status
+	 *          the status to set
+	 * @see #status
+	 */
+	public void setStatus(ProjectStatus status) {
+		this.status = status;
+	}
+
+	/**
+	 * @return the progress
+	 * @see #progress
+	 */
+	public double getProgress() {
+		return progress;
+	}
+
+	/**
+	 * @param progress
+	 *          the progress to set
+	 * @see #progress
+	 */
+	public void setProgress(double progress) {
+		this.progress = progress;
+	}
+
+	/**
+	 * @return the models
+	 * @see #models
+	 */
+	public Set<ModelData> getModels() {
+		return models;
+	}
+
+	/**
+	 * @param models
+	 *          the models to set
+	 * @see #models
+	 */
+	public void setModels(Set<ModelData> models) {
+		this.models = models;
+	}
+
+	/**
+	 * @return the errors
+	 * @see #errors
+	 */
+	public String getErrors() {
+		return errors;
+	}
+
+	/**
+	 * @param errors
+	 *          the errors to set
+	 * @see #errors
+	 */
+	public void setErrors(String errors) {
+		this.errors = errors;
+	}
+
+	/**
+	 * @return the directory
+	 * @see #directory
+	 */
+	public String getDirectory() {
+		return directory;
+	}
+
+	/**
+	 * @param directory
+	 *          the directory to set
+	 * @see #directory
+	 */
+	public void setDirectory(String directory) {
+		this.directory = directory;
+	}
+
+	/**
+	 * @return the name
+	 * @see #name
+	 */
+	public String getName() {
+		return name;
+	}
+
+	/**
+	 * @param name
+	 *          the name to set
+	 * @see #name
+	 */
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	/**
+	 * @return disease
+	 */
+	public MiriamData getDisease() {
+		return disease;
+	}
+
+	/**
+	 * @param disease
+	 *          the disease
+	 */
+	public void setDisease(MiriamData disease) {
+		this.disease = disease;
+	}
+
+	/**
+	 * @return the inputData
+	 * @see #inputData
+	 */
+	public byte[] getInputData() {
+		return inputData;
+	}
+
+	/**
+	 * @param inputData
+	 *          the inputData to set
+	 * @see #inputData
+	 */
+	public void setInputData(byte[] inputData) {
+		this.inputData = inputData;
+	}
+
+	/**
+	 * @return the inputFileName
+	 * @see #inputFileName
+	 */
+	public String getInputFileName() {
+		return inputFileName;
+	}
+
+	/**
+	 * @param inputFileName
+	 *          the inputFileName to set
+	 * @see #inputFileName
+	 */
+	public void setInputFileName(String inputFileName) {
+		this.inputFileName = inputFileName;
+	}
+
+	/**
+	 * @param organism
+	 *          the organism to set
+	 * @see #organism
+	 */
+	public void setOrganism(MiriamData organism) {
+		this.organism = organism;
+	}
+
+	/**
+	 * @return the organism
+	 * @see #organism
+	 */
+	public MiriamData getOrganism() {
+		return organism;
+	}
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java b/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java
index b796d5bbc3..9e3151fa16 100644
--- a/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java
+++ b/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java
@@ -1,110 +1,110 @@
-package lcsb.mapviewer.model;
-
-/**
- * Defines possible statuses when uploading project into system.
- * 
- * @author Piotr Gawron
- * 
- */
-public enum ProjectStatus {
-	
-	/**
-	 * Unknown status.
-	 */
-	UNKNOWN("uninitialized"),
-	
-	/**
-	 * Data are parsed by the CellDesigner parser.
-	 */
-	PARSING_DATA("Parsing data"),
-	
-	/**
-	 * Model is annotated by the annotation tool.
-	 */
-	ANNOTATING("Annotating"),
-	
-	/**
-	 * Model is being uploaded to the database.
-	 */
-	UPLOADING_TO_DB("Uploading to db"),
-	
-	/**
-	 * Model is being extended (
-	 * {@link lcsb.mapviewer.services.utils.IPostLoadModification
-	 * IPostLoadModification} is processing).
-	 */
-	EXTENDING_MODEL("Data mining"),
-	
-	/**
-	 * Images for the projects are being generated.
-	 */
-	GENERATING_IMAGES("Generating images"),
-	
-	/**
-	 * Data that are linked to pubmed articles are being cached.
-	 */
-	CACHING("Caching pubmed data"),
-	
-	/**
-	 * Project is ready to use.
-	 */
-	DONE("Ok"),
-	
-	/**
-	 * There was problem during project creation.
-	 */
-	FAIL("Failure"),
-	
-	/**
-	 * Data that are linked to miriam are being cached.
-	 */
-	CACHING_MIRIAM("Caching miriam data"),
-
-	/**
-	 * Miriam data validation.
-	 */
-	VALIDATING_MIRIAM("Validating miriam data"),
-	
-	/**
-	 * Removing of the project.
-	 */
-	REMOVING("Project removing"),
-
-	/**
-	 * All chemicals that can be found by map elements are cached.
-	 */
-	CACHING_CHEMICAL("Caching chemical data"),
-
-	/**
-	 * All drugs that can be found by map elements are cached.
-	 */
-	CACHING_DRUG("Caching drug data"),
-
-	/**
-	 * All mirna that can be found by map elements are cached.
-	 */
-	CACHING_MI_RNA("Caching miRNA data");
-
-	/**
-	 * Message used to present the status on the client side.
-	 */
-	private String	readableString;
-
-	/**
-	 * Default constructor of the enum with {@link #readableString} parameter.
-	 * 
-	 * @param readableForm
-	 *          {@link #readableString}
-	 */
-	ProjectStatus(String readableForm) {
-		this.readableString = readableForm;
-	}
-
-	/**
-	 * @return {@link #readableString}
-	 */
-	public String toString() {
-		return readableString;
-	}
-
-}
+package lcsb.mapviewer.model;
+
+/**
+ * Defines possible statuses when uploading project into system.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public enum ProjectStatus {
+	
+	/**
+	 * Unknown status.
+	 */
+	UNKNOWN("uninitialized"),
+	
+	/**
+	 * Data are parsed by the CellDesigner parser.
+	 */
+	PARSING_DATA("Parsing data"),
+	
+	/**
+	 * Model is annotated by the annotation tool.
+	 */
+	ANNOTATING("Annotating"),
+	
+	/**
+	 * Model is being uploaded to the database.
+	 */
+	UPLOADING_TO_DB("Uploading to db"),
+	
+	/**
+	 * Model is being extended (
+	 * {@link lcsb.mapviewer.services.utils.IPostLoadModification
+	 * IPostLoadModification} is processing).
+	 */
+	EXTENDING_MODEL("Data mining"),
+	
+	/**
+	 * Images for the projects are being generated.
+	 */
+	GENERATING_IMAGES("Generating images"),
+	
+	/**
+	 * Data that are linked to pubmed articles are being cached.
+	 */
+	CACHING("Caching pubmed data"),
+	
+	/**
+	 * Project is ready to use.
+	 */
+	DONE("Ok"),
+	
+	/**
+	 * There was problem during project creation.
+	 */
+	FAIL("Failure"),
+	
+	/**
+	 * Data that are linked to miriam are being cached.
+	 */
+	CACHING_MIRIAM("Caching miriam data"),
+
+	/**
+	 * Miriam data validation.
+	 */
+	VALIDATING_MIRIAM("Validating miriam data"),
+	
+	/**
+	 * Removing of the project.
+	 */
+	REMOVING("Project removing"),
+
+	/**
+	 * All chemicals that can be found by map elements are cached.
+	 */
+	CACHING_CHEMICAL("Caching chemical data"),
+
+	/**
+	 * All drugs that can be found by map elements are cached.
+	 */
+	CACHING_DRUG("Caching drug data"),
+
+	/**
+	 * All mirna that can be found by map elements are cached.
+	 */
+	CACHING_MI_RNA("Caching miRNA data");
+
+	/**
+	 * Message used to present the status on the client side.
+	 */
+	private String	readableString;
+
+	/**
+	 * Default constructor of the enum with {@link #readableString} parameter.
+	 * 
+	 * @param readableForm
+	 *          {@link #readableString}
+	 */
+	ProjectStatus(String readableForm) {
+		this.readableString = readableForm;
+	}
+
+	/**
+	 * @return {@link #readableString}
+	 */
+	public String toString() {
+		return readableString;
+	}
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/AllTests.java b/model/src/test/java/lcsb/mapviewer/AllTests.java
index ab3bed5138..95fc537883 100644
--- a/model/src/test/java/lcsb/mapviewer/AllTests.java
+++ b/model/src/test/java/lcsb/mapviewer/AllTests.java
@@ -1,16 +1,16 @@
-package lcsb.mapviewer;
-
-import lcsb.mapviewer.model.AllModelTests;
-import lcsb.mapviewer.modelutils.map.AllMapUtilTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllModelTests.class,//
-		AllMapUtilTests.class,//
-})
-public class AllTests {
-
-}
+package lcsb.mapviewer;
+
+import lcsb.mapviewer.model.AllModelTests;
+import lcsb.mapviewer.modelutils.map.AllMapUtilTests;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllModelTests.class,//
+		AllMapUtilTests.class,//
+})
+public class AllTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java b/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java
index fc9832424e..a99c4fe2df 100644
--- a/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java
+++ b/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import org.junit.After;
-import org.junit.Before;
-
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-
-public class ModelTestFunctions {
-
-	private EventStorageLoggerAppender appender;
-
-	@Before
-	public final void _setUp() throws Exception {
-		Logger.getRootLogger().removeAppender(appender);
-		appender = new EventStorageLoggerAppender();
-		Logger.getRootLogger().addAppender(appender);
-	}
-
-	@After
-	public final void _tearDown() throws Exception {
-		Logger.getRootLogger().removeAppender(appender);
-	}
-
-	protected List<LoggingEvent> getWarnings() {
-		return appender.getWarnings();
-	}
-
-}
+package lcsb.mapviewer;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.junit.After;
+import org.junit.Before;
+
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+
+public class ModelTestFunctions {
+
+	private EventStorageLoggerAppender appender;
+
+	@Before
+	public final void _setUp() throws Exception {
+		Logger.getRootLogger().removeAppender(appender);
+		appender = new EventStorageLoggerAppender();
+		Logger.getRootLogger().addAppender(appender);
+	}
+
+	@After
+	public final void _tearDown() throws Exception {
+		Logger.getRootLogger().removeAppender(appender);
+	}
+
+	protected List<LoggingEvent> getWarnings() {
+		return appender.getWarnings();
+	}
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java b/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
index 9387ffa40a..bd4e35c210 100644
--- a/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
@@ -1,24 +1,24 @@
-package lcsb.mapviewer.model;
-
-import lcsb.mapviewer.model.cache.AllCacheTests;
-import lcsb.mapviewer.model.graphics.AllGraphicsTests;
-import lcsb.mapviewer.model.log.AllLogTests;
-import lcsb.mapviewer.model.map.AllMapTests;
-import lcsb.mapviewer.model.user.AllUserTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllCacheTests.class, //
-		AllGraphicsTests.class, //
-		AllLogTests.class, //
-		AllMapTests.class, //
-		AllUserTests.class, //
-		ProjectStatusTest.class, //
-		ProjectTest.class,//
-})
-public class AllModelTests {
-
-}
+package lcsb.mapviewer.model;
+
+import lcsb.mapviewer.model.cache.AllCacheTests;
+import lcsb.mapviewer.model.graphics.AllGraphicsTests;
+import lcsb.mapviewer.model.log.AllLogTests;
+import lcsb.mapviewer.model.map.AllMapTests;
+import lcsb.mapviewer.model.user.AllUserTests;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllCacheTests.class, //
+		AllGraphicsTests.class, //
+		AllLogTests.class, //
+		AllMapTests.class, //
+		AllUserTests.class, //
+		ProjectStatusTest.class, //
+		ProjectTest.class,//
+})
+public class AllModelTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java b/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java
index 0d4cdcdfeb..3a966d4e01 100644
--- a/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.model;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ProjectStatusTest {
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testValidValues() {
-		for (ProjectStatus type : ProjectStatus.values()) {
-			assertNotNull(type);
-
-			// for coverage tests
-			ProjectStatus.valueOf(type.name());
-			type.toString();
-		}
-	}
-
-}
+package lcsb.mapviewer.model;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ProjectStatusTest {
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testValidValues() {
+		for (ProjectStatus type : ProjectStatus.values()) {
+			assertNotNull(type);
+
+			// for coverage tests
+			ProjectStatus.valueOf(type.name());
+			type.toString();
+		}
+	}
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java b/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
index 4952f2e507..917ebae588 100644
--- a/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
@@ -1,130 +1,130 @@
-package lcsb.mapviewer.model;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-public class ProjectTest {
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testSerialization() {
-		try {
-			SerializationUtils.serialize(new Project());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testProject() {
-		try {
-			Project project = new Project("str");
-			assertNotNull(project);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testAddModel() {
-		try {
-			Model model = new ModelFullIndexed(null);
-			Model model2 = new ModelFullIndexed(null);
-			Project project = new Project();
-			assertEquals(0, project.getModels().size());
-			project.addModel(model);
-			assertEquals(1, project.getModels().size());
-			project.addModel(model);
-			assertEquals(1, project.getModels().size());
-			project.addModel(model2.getModelData());
-			assertEquals(2, project.getModels().size());
-			project.removeModel(model2.getModelData());
-			assertEquals(1, project.getModels().size());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testGetters() {
-		try {
-			MiriamData organism = new MiriamData();
-			int id = 5;
-			String projectId = "str";
-			ProjectStatus status = ProjectStatus.ANNOTATING;
-			double progress = 4.5;
-			Set<ModelData> models = new HashSet<>();
-			String errors = "eerStr";
-			String directory = "dir";
-			String name = "name3";
-			MiriamData disease = new MiriamData();
-			Project project = new Project("str");
-
-			project.setId(id);
-			assertEquals(id, project.getId());
-
-			project.setProjectId(projectId);
-			assertEquals(projectId, project.getProjectId());
-
-			project.setStatus(status);
-			assertEquals(status, project.getStatus());
-
-			project.setProgress(progress);
-			assertEquals(progress, project.getProgress(), Configuration.EPSILON);
-
-			project.setModels(models);
-			assertEquals(models, project.getModels());
-
-			project.setErrors(errors);
-			assertEquals(errors, project.getErrors());
-
-			project.setDirectory(directory);
-			assertEquals(directory, project.getDirectory());
-
-			project.setName(name);
-			assertEquals(name, project.getName());
-
-			project.setDisease(disease);
-			assertEquals(disease, project.getDisease());
-
-			String inputFileName = "x";
-			byte[] inputData = new byte[] { 1, 2 };
-			project.setInputData(inputData);
-			assertEquals(inputData, project.getInputData());
-
-			project.setInputFileName(inputFileName);
-			assertEquals(inputFileName, project.getInputFileName());
-
-			project.setOrganism(organism);
-			assertEquals(organism, project.getOrganism());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-}
+package lcsb.mapviewer.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+public class ProjectTest {
+
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void testSerialization() {
+		try {
+			SerializationUtils.serialize(new Project());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testProject() {
+		try {
+			Project project = new Project("str");
+			assertNotNull(project);
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testAddModel() {
+		try {
+			Model model = new ModelFullIndexed(null);
+			Model model2 = new ModelFullIndexed(null);
+			Project project = new Project();
+			assertEquals(0, project.getModels().size());
+			project.addModel(model);
+			assertEquals(1, project.getModels().size());
+			project.addModel(model);
+			assertEquals(1, project.getModels().size());
+			project.addModel(model2.getModelData());
+			assertEquals(2, project.getModels().size());
+			project.removeModel(model2.getModelData());
+			assertEquals(1, project.getModels().size());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+	@Test
+	public void testGetters() {
+		try {
+			MiriamData organism = new MiriamData();
+			int id = 5;
+			String projectId = "str";
+			ProjectStatus status = ProjectStatus.ANNOTATING;
+			double progress = 4.5;
+			Set<ModelData> models = new HashSet<>();
+			String errors = "eerStr";
+			String directory = "dir";
+			String name = "name3";
+			MiriamData disease = new MiriamData();
+			Project project = new Project("str");
+
+			project.setId(id);
+			assertEquals(id, project.getId());
+
+			project.setProjectId(projectId);
+			assertEquals(projectId, project.getProjectId());
+
+			project.setStatus(status);
+			assertEquals(status, project.getStatus());
+
+			project.setProgress(progress);
+			assertEquals(progress, project.getProgress(), Configuration.EPSILON);
+
+			project.setModels(models);
+			assertEquals(models, project.getModels());
+
+			project.setErrors(errors);
+			assertEquals(errors, project.getErrors());
+
+			project.setDirectory(directory);
+			assertEquals(directory, project.getDirectory());
+
+			project.setName(name);
+			assertEquals(name, project.getName());
+
+			project.setDisease(disease);
+			assertEquals(disease, project.getDisease());
+
+			String inputFileName = "x";
+			byte[] inputData = new byte[] { 1, 2 };
+			project.setInputData(inputData);
+			assertEquals(inputData, project.getInputData());
+
+			project.setInputFileName(inputFileName);
+			assertEquals(inputFileName, project.getInputFileName());
+
+			project.setOrganism(organism);
+			assertEquals(organism, project.getOrganism());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+}
-- 
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