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Matching_with_Covid19DM_Diagrams/grep_disease_maps.md

+### License Info
+
+This program is free software: you can redistribute it and/or modify it
+under the terms of the GNU General Public License as published by the
+Free Software Foundation, either version 3 of the License, or (at your
+option) any later version.
+
+This program is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
+Public License for more details.
+
+Please check <http://www.gnu.org/licenses/>.
+
+The code included in the present notebook is based on this
+[script](https://git-r3lab.uni.lu/computational-modelling-and-simulation/generegulationanalysis/-/blob/master/5_SBMLSearch/SourceCode/grep_disease_map.R)
+developed by Yusuke Hiki
+
+Introduction
+============
+
+The present script takes the output of our Footprint-based analysis and
+matches the results againts the content of [the Covid-19 Disease
+Maps](https://covid.pages.uni.lu/map_contents)
+
+    library(kableExtra)
+
+Results
+=======
+
+Reading Input files
+-------------------
+
+We first read the content ofthe Covid-19 Disease Maps which can be found
+in this
+[file](https://gitlab.lcsb.uni.lu/covid/models/-/blob/master/Resources/Expand%20the%20diagrams/COVID19_Disease_Map_bipartite_crosslinked_additional_HGNCs.tsv):
+
+    disease_map <- read.delim("https://gitlab.lcsb.uni.lu/covid/models/-/raw/master/Resources/Expand%20the%20diagrams/COVID19_Disease_Map_bipartite_crosslinked_additional_HGNCs.tsv")
+
+    # Extract row with HGNC symbol
+    disease_map_hgnc <- disease_map[ !is.na( disease_map$source_hgnc ), ]
+
+    # Get HGNC symbol list for each row
+    disease_map_gene_list <- strsplit( x=gsub( pattern="HGNC_SYMBOL:", replacement="", x=disease_map_hgnc$source_hgnc ), split=";" )
+
+We then read the output of our Footprint-based analyisis, namely
+CARNIVAL's output network. This file can be found
+[here](https://gitlab.lcsb.uni.lu/computational-modelling-and-simulation/footprint-based-analysis-and-causal-network-contextualisation-in-sars-cov-2-infected-a549-cell-line/-/tree/master/Carnival_Results).
+
+    carnival_results <- readRDS("InputFiles/carnival_results_withprogeny.rds")
+    carnival_nodes_hgnc <- unique(c(carnival_results$weightedSIF[,"Node1"], carnival_results$weightedSIF[,"Node2"]))
+
+Matching the results
+--------------------
+
+We finally match all our genes from the carnival network with all the
+genes from the different pathways included in the COVID19 Disease maps.
+
+    disease_map_hgnc_carnival_detected <- data.frame()
+
+
+    for( current_gene in  carnival_nodes_hgnc){
+      
+      # Get row index of disease map matched with target gene
+      index_matched <- which( unlist( lapply( X=disease_map_gene_list, FUN=function(x){ return( any(current_gene==x) ) } ) ) )
+      
+      # Extract the row
+      if( length( index_matched ) != 0 ){
+        disease_map_hgnc_carnival_detected_i <- cbind( disease_map_hgnc[ index_matched, ], hgnc_carnival=current_gene )
+        disease_map_hgnc_carnival_detected <- rbind( disease_map_hgnc_carnival_detected, disease_map_hgnc_carnival_detected_i )
+      }
+    }
+
+    disease_map_hgnc_carnival_detected <- unique( disease_map_hgnc_carnival_detected[ ,c("source_diagram", "hgnc_carnival") ] )
+    rownames(disease_map_hgnc_carnival_detected) <- NULL
+
+and We visualize the results.
+
+    disease_map_hgnc_carnival_detected %>% 
+      kbl(col.names = c("Covid19 DM Diagram", "Carnival nodes")) %>% 
+      kable_styling()
+
+<table class="table" style="margin-left: auto; margin-right: auto;">
+<thead>
+<tr>
+<th style="text-align:left;">
+Covid19 DM Diagram
+</th>
+<th style="text-align:left;">
+Carnival nodes
+</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td style="text-align:left;">
+C19DMap:PAMP signalling
+</td>
+<td style="text-align:left;">
+TICAM1
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:Orf3a protein interactions
+</td>
+<td style="text-align:left;">
+TICAM1
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:TGFbeta signalling
+</td>
+<td style="text-align:left;">
+MAPK3
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:Interferon 1 pathway
+</td>
+<td style="text-align:left;">
+TBK1
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:PAMP signalling
+</td>
+<td style="text-align:left;">
+TBK1
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:Pyrimidine deprivation
+</td>
+<td style="text-align:left;">
+TBK1
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:Interferon lambda pathway
+</td>
+<td style="text-align:left;">
+TBK1
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:Endoplasmatic Reticulum stress
+</td>
+<td style="text-align:left;">
+ATF6
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:Interferon 1 pathway
+</td>
+<td style="text-align:left;">
+IKBKE
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:PAMP signalling
+</td>
+<td style="text-align:left;">
+IKBKE
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:TGFbeta signalling
+</td>
+<td style="text-align:left;">
+SMAD1
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:Endoplasmatic Reticulum stress
+</td>
+<td style="text-align:left;">
+ATF4
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:Endoplasmatic Reticulum stress
+</td>
+<td style="text-align:left;">
+MBTPS1
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:Interferon 1 pathway
+</td>
+<td style="text-align:left;">
+IRF3
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:PAMP signalling
+</td>
+<td style="text-align:left;">
+IRF3
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:Pyrimidine deprivation
+</td>
+<td style="text-align:left;">
+IRF3
+</td>
+</tr>
+<tr>
+<td style="text-align:left;">
+C19DMap:Interferon lambda pathway
+</td>
+<td style="text-align:left;">
+IRF3
+</td>
+</tr>
+</tbody>
+</table>
+Session Info Details
+====================
+
+    ## R version 4.0.4 (2021-02-15)
+    ## Platform: x86_64-w64-mingw32/x64 (64-bit)
+    ## Running under: Windows 10 x64 (build 19042)
+    ## 
+    ## Matrix products: default
+    ## 
+    ## locale:
+    ## [1] LC_COLLATE=English_Germany.1252  LC_CTYPE=English_Germany.1252   
+    ## [3] LC_MONETARY=English_Germany.1252 LC_NUMERIC=C                    
+    ## [5] LC_TIME=English_Germany.1252    
+    ## 
+    ## attached base packages:
+    ## [1] stats     graphics  grDevices utils     datasets  methods   base     
+    ## 
+    ## other attached packages:
+    ## [1] kableExtra_1.3.4
+    ## 
+    ## loaded via a namespace (and not attached):
+    ##  [1] rstudioapi_0.13   knitr_1.33        xml2_1.3.2        magrittr_2.0.1   
+    ##  [5] rvest_1.0.0       munsell_0.5.0     colorspace_2.0-1  viridisLite_0.4.0
+    ##  [9] R6_2.5.1          rlang_0.4.11      highr_0.9         stringr_1.4.0    
+    ## [13] httr_1.4.2        tools_4.0.4       webshot_0.5.2     xfun_0.24        
+    ## [17] htmltools_0.5.1.1 systemfonts_1.0.2 yaml_2.2.1        digest_0.6.27    
+    ## [21] lifecycle_1.0.1   glue_1.4.2        evaluate_0.14     rmarkdown_2.9    
+    ## [25] stringi_1.6.2     compiler_4.0.4    scales_1.1.1      svglite_2.1.0