Commit 4d6f3a23 authored by Jeremy Zucker's avatar Jeremy Zucker
Browse files

merged master into il6-amp

parents c807a0fb 4492ce99
Rank Cell line Perturbagen Dose(um) Duration(h) Enrichment Score Perturbed Genes
1 NPC BRD-K52911425 10.0 24 2/8 0.908 IKBKB, IKBKE
2 VCAP BRD-K58479490 10.0 6 1/2 0.908 ITCH
3 PC3 rimcazole_dihydrochloride 10.0 24 1/3 0.457 ITCH
4 VCAP c3930 10.0 6 2/13 0.386 IKBKB, IKBKE
5 ASC 1391-0741 10.0 24 2/14 0.326 IKBKB, IKBKE
6 VCAP ncgc00184891-01 10.0 24 2/14 0.326 IKBKB, ITCH
7 HT29 BRD-A62809825 10.0 6 1/4 0.228 ITCH
8 VCAP p5172 10.0 6 1/4 0.228 IKBKB
9 PC3 nefazodone_hydrochloride 10.0 24 1/4 0.228 ITCH
10 HT29 nutlin-3 44.4 6 1/4 0.228 ITCH
11 PC3 mestinon 10.0 24 1/4 0.228 TICAM1
12 A375 BRD-K88008216 10.0 6 2/18 0.152 IKBKB, IKBKE
13 VCAP geldanamycin 10.0 6 2/18 0.152 IKBKB, IKBKE
\ No newline at end of file
Rank Cell line Perturbagen Dose(um) Duration(h) Enrichment Score Perturbed Genes
1 VCAP mls-0391006 10.0 6 1/2 1.000 IKBKB
2 PC3 a3145 10.0 24 1/3 0.577 ITCH
3 HA1E 16beta-bromoandrosterone 11.1 24 2/19 0.260 IKBKB, IKBKE
4 HT29 bumetanide 10.0 6 1/5 0.235 ITCH
5 HA1E saracatinib 1.11 24 4/83 0.214 DDX58, IFIH1, IKBKB, IRF7
6 PC3 BRD-A98444709 10.0 6 1/6 0.148 ITCH
7 PC3 BRD-K82580504 10.0 24 1/6 0.148 ITCH
8 SKB BRD-K33164466 10.0 24 2/24 0.148 IKBKB, IKBKE
9 PC3 BRD-K00313977 10.0 6 1/6 0.148 ITCH
10 HT29 BRD-K00007652 10.0 6 3/59 0.112 IKBKB, IKBKE, ITCH
11 HA1E mebendazole 10.0 6 3/63 0.087 IKBKB, IKBKE, ITCH
\ No newline at end of file
Rank Cell line Perturbagen Dose(um) Duration(h) Enrichment Score Perturbed Genes
1 PC3 a3145 10.0 24 1/6 0.865 ITCH
2 PC3 mestinon 10.0 24 1/6 0.865 TICAM1
3 VCAP ncgc00184891-01 10.0 24 2/26 0.750 IKBKB, ITCH
4 VCAP rythmol 10.0 24 1/7 0.635 ITCH
5 VCAP ncgc00183913-01 10.0 24 2/30 0.558 IKBKB, ITCH
6 HT29 BRD-K66381707 10.0 6 2/30 0.558 ITCH, TICAM1
7 VCAP c3930 10.0 6 2/31 0.519 IKBKB, IKBKE
8 SKB BRD-K33164466 10.0 24 3/72 0.481 IKBKB, IKBKE, ITCH
9 ASC 1391-0741 10.0 24 2/36 0.346 IKBKB, IKBKE
10 VCAP ergonovine 10.0 6 1/9 0.346 ITCH
11 HA1E saracatinib 1.11 24 4/143 0.346 DDX58, IFIH1, IKBKB, IRF7
12 SW948 akt_inhibitor_x 24.0 6 4/147 0.308 IKBKE, ITCH, MAP2K6, TICAM1
13 HCC515 BRD-K00007652 10.0 6 3/83 0.308 IKBKB, IKBKE, ITCH
14 VCAP BRD-K47764688 10.0 24 3/84 0.308 IKBKB, IKBKE, ITCH
15 NPC BRD-K52911425 10.0 24 2/38 0.288 IKBKB, IKBKE
16 ASC BRD-K35483542 10.0 24 3/87 0.269 IKBKB, IKBKE, ITCH
17 HT29 bumetanide 10.0 6 1/10 0.231 ITCH
18 PHH s1118 10.0 24 2/40 0.231 IKBKB, IKBKE
19 PC3 BRD-K82580504 10.0 24 1/10 0.231 ITCH
20 VCAP BRD-K65404805 10.0 24 2/41 0.212 IKBKE, ITCH
21 VCAP geldanamycin 10.0 6 3/91 0.212 IKBKB, IKBKE, ITCH
22 PC3 sib_1893 10.0 24 2/42 0.192 CHUK, ITCH
23 HT29 BRD-K00007652 10.0 6 3/93 0.192 IKBKB, IKBKE, ITCH
24 HEPG2 mafenide_hydrochloride 10.0 6 3/93 0.192 IKBKE, ITCH, MAP3K7
25 HA1E bg_fa_0953 10.0 6 3/95 0.173 IKBKB, IKBKE, ITCH
\ No newline at end of file
Term id Term Definition Enrichment Corrected pvalue
GO:0002221 pattern recognition receptor signaling pathway 27/126 0.0007
GO:0002218 activation of innate immune response 28/248 0.0022
GO:0002224 toll-like receptor signaling pathway 22/97 0.0026
GO:0035666 TRIF-dependent toll-like receptor signaling pathway 14/29 0.0042
GO:0002756 MyD88-independent toll-like receptor signaling pathway 14/31 0.0045
GO:0002758 innate immune response-activating signal transduction 27/227 0.0046
GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling 23/183 0.0058
GO:0002833 positive regulation of response to biotic stimulus 28/351 0.0076
GO:0045089 positive regulation of innate immune response 28/332 0.0083
GO:0043122 regulation of I-kappaB kinase/NF-kappaB signaling 24/236 0.0083
GO:0007249 I-kappaB kinase/NF-kappaB signaling 16/69 0.0109
GO:0002764 immune response-regulating signaling pathway 33/570 0.0111
GO:0045088 regulation of innate immune response 29/443 0.0125
GO:0032479 regulation of type I interferon production 18/127 0.0132
GO:0043902 positive regulation of multi-organism process 29/494 0.0133
GO:0002753 cytoplasmic pattern recognition receptor signaling pathway 13/35 0.014
GO:0031349 positive regulation of defense response 29/473 0.0148
GO:0002831 regulation of response to biotic stimulus 29/509 0.0148
GO:0051090 regulation of DNA-binding transcription factor activity 27/433 0.0171
GO:0051403 stress-activated MAPK cascade 16/106 0.0171
GO:0032727 positive regulation of interferon-alpha production 10/23 0.0186
GO:0032728 positive regulation of interferon-beta production 11/32 0.0189
GO:0032103 positive regulation of response to external stimulus 30/602 0.019
GO:0032648 regulation of interferon-beta production 12/50 0.0215
GO:0032481 positive regulation of type I interferon production 14/79 0.0221
GO:0031098 stress-activated protein kinase signaling cascade 17/141 0.0224
GO:0043900 regulation of multi-organism process 32/768 0.0232
GO:0051092 positive regulation of NF-kappaB transcription factor activity 17/152 0.0246
GO:0002757 immune response-activating signal transduction 27/534 0.0247
GO:0032647 regulation of interferon-alpha production 10/29 0.026
GO:0050776 regulation of immune response 37/1113 0.027
GO:0002253 activation of immune response 28/603 0.0287
GO:0035872 "nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway" 9/28 0.0297
GO:0070423 nucleotide-binding oligomerization domain containing signaling pathway 9/27 0.0298
GO:0009615 response to virus 20/285 0.0303
GO:0051091 positive regulation of DNA-binding transcription factor activity 19/263 0.0304
GO:0031347 regulation of defense response 31/788 0.0315
GO:0032480 negative regulation of type I interferon production 9/45 0.0332
GO:0007254 JNK cascade 12/83 0.0333
GO:0001819 positive regulation of cytokine production 21/446 0.0339
GO:0050778 positive regulation of immune response 30/826 0.0341
GO:1902533 positive regulation of intracellular signal transduction 31/1031 0.035
GO:0060759 regulation of response to cytokine stimulus 15/178 0.0354
GO:0001817 regulation of cytokine production 26/710 0.0385
GO:0002684 positive regulation of immune system process 32/1118 0.0423
GO:0060760 positive regulation of response to cytokine stimulus 9/55 0.0429
GO:0002682 regulation of immune system process 38/1659 0.0434
GO:0000165 MAPK cascade 17/366 0.0443
GO:0051607 defense response to virus 14/196 0.0451
GO:0034162 toll-like receptor 9 signaling pathway 6/17 0.0452
GO:0032101 regulation of response to external stimulus 31/1102 0.0459
GO:0007252 I-kappaB phosphorylation 6/12 0.0462
GO:0001959 regulation of cytokine-mediated signaling pathway 13/167 0.0474
GO:0032757 positive regulation of interleukin-8 production 8/48 0.0482
GO:0045357 regulation of interferon-beta biosynthetic process 5/9 0.0487
GO:0030522 intracellular receptor signaling pathway 13/164 0.0488
\ No newline at end of file
Term id Term Definition Enrichment Corrected pvalue
GO:0035631 CD40 receptor complex 6/11 0.0052
GO:0097342 ripoptosome 5/6 0.0085
GO:0031264 death-inducing signaling complex 5/9 0.0159
GO:0010008 endosome membrane 14/472 0.0213
GO:0044440 endosomal part 14/520 0.0238
GO:0008385 IkappaB kinase complex 4/9 0.0335
GO:0044445 cytosolic part 10/252 0.0394
GO:0005768 endosome 15/902 0.0446
GO:0031265 CD95 death-inducing signaling complex 3/6 0.0481
\ No newline at end of file
Term id Term Definition Enrichment Corrected pvalue
GO:0032813 tumor necrosis factor receptor superfamily binding 9/46 0.0063
GO:0044389 ubiquitin-like protein ligase binding 15/306 0.0091
GO:0031625 ubiquitin protein ligase binding 14/288 0.0143
GO:0005164 tumor necrosis factor receptor binding 7/32 0.021
GO:0004674 protein serine/threonine kinase activity 16/448 0.0279
GO:0004708 MAP kinase kinase activity 5/16 0.034
GO:0004672 protein kinase activity 16/617 0.0388
GO:0004712 protein serine/threonine/tyrosine kinase activity 6/43 0.0448
GO:0008384 IkappaB kinase activity 3/3 0.0457
\ No newline at end of file
Rank Gene Symbol Definition Systemic Processes Interactions Drugs
1 CHUK conserved helix-loop-helix ubiquitous kinase 9 14 5
2 IRAK1 interleukin 1 receptor associated kinase 1 9 9 0
3 MYD88 "MYD88, innate immune signal transduction adaptor" 9 11 0
4 IKBKG inhibitor of nuclear factor kappa B kinase subunit gamma 8 18 7
5 DDX58 DExD/H-box helicase 58 8 7 0
6 IKBKB inhibitor of nuclear factor kappa B kinase subunit beta 8 15 9
7 TLR3 toll like receptor 3 8 11 1
8 TLR7 toll like receptor 7 8 1 11
9 IKBKE inhibitor of nuclear factor kappa B kinase subunit epsilon 7 13 0
10 TICAM1 toll like receptor adaptor molecule 1 7 12 0
11 TBK1 TANK binding kinase 1 7 14 0
12 MAP3K7 mitogen-activated protein kinase kinase kinase 7 7 19 0
13 RIPK1 receptor interacting serine/threonine kinase 1 7 15 0
14 TRAF6 TNF receptor associated factor 6 7 24 0
15 TLR8 toll like receptor 8 7 0 4
16 MAVS mitochondrial antiviral signaling protein 7 19 0
17 IFIH1 interferon induced with helicase C domain 1 6 1 0
18 ITCH itchy E3 ubiquitin protein ligase 6 8 0
19 FADD Fas associated via death domain 6 11 0
20 IRAK4 interleukin 1 receptor associated kinase 4 6 4 1
21 IRF3 interferon regulatory factor 3 6 13 0
22 IRF7 interferon regulatory factor 7 6 8 0
23 UBE2N ubiquitin conjugating enzyme E2 N 6 5 0
24 MAPK14 mitogen-activated protein kinase 14 5 11 62
25 TRADD TNFRSF1A associated via death domain 5 6 0
26 TRAF2 TNF receptor associated factor 2 5 22 0
27 TRIM25 tripartite motif containing 25 5 10 0
28 CASP8 caspase 8 5 12 0
29 MAP2K6 mitogen-activated protein kinase kinase 6 5 6 1
\ No newline at end of file
......@@ -93,23 +93,50 @@ construct_overview <- function(elements) {
### Resource: url to the xml content of the diagram
### Type: what kind of file do we integrate
### Name: under which name the diaram is to be shown in the build
res <- read.csv(url("https://git-r3lab.uni.lu/covid/models/raw/master/Integration/MINERVA_build/resources.csv"),
header = T, stringsAsFactors = F)
regular_build = T
if(regular_build) {
### Regular build
res <- read.csv(url("https://git-r3lab.uni.lu/covid/models/raw/master/Integration/MINERVA_build/resources.csv"),
header = T, stringsAsFactors = F)
} else {
### WikiPathways testbuild
wps <- readLines("https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/pathways.txt")
res <- data.frame(Include = "Yes",
Resource = paste0("https://raw.githubusercontent.com/wikipathways/SARS-CoV-2-WikiPathways/master/gpml/", wps, ".gpml"),
Type = "GPML",
Name = wps)
}
### Filter only these to be included
res <- res[res$Include == "Yes",]
### Define the output dir
outdir <- "_notgit/output/"
### Just to simplify later writes
outdir_submaps <- paste0(outdir,"submaps/")
### Create output directory if not existing.
if(!dir.exists("output/")) { dir.create("output/") }
if(!dir.exists(outdir)) { dir.create(outdir) }
### Create submaps directory if not existing.
if(!dir.exists("output/submaps/")) { dir.create("output/submaps/") }
if(!dir.exists(outdir_submaps)) { dir.create(outdir_submaps) }
### For all resources
for(r in 1:nrow(res)) {
### Process the 'resources' table, all should be network-accessible (raw git)
message(paste0("Processing: ", res[r,]$Resource))
con <- url(res[r,]$Resource)
rls <- paste(readLines(con), collapse = "\n")
conread <-try(readLines(con), silent = T)
### Try retrieving a resource, end gracefully
if(class(conread) == "try-error") {
message(paste0("Cannot read from ", res[r,]$Resource))
close(con)
message(conread)
next
}
rls <- paste(conread, collapse = "\n")
close(con)
fin_cont <- NULL
### Depending on the type, process differently
......@@ -125,7 +152,7 @@ for(r in 1:nrow(res)) {
}
### Write the result to a file
write_xml(fin_cont, file = paste0("output/submaps/",res[r,]$Name,".xml"))
write_xml(fin_cont, file = paste0(outdir_submaps,res[r,]$Name,".xml"))
message("Done.\n\n")
}
......@@ -142,7 +169,7 @@ if(reconstruct_overview) {
ovw <- gsub("width=\"90.0\" height=\"30.0\"", "width=\"190.0\" height=\"40.0\"", ovw)
ovw <- gsub("color=\"FFCC99FF\"", "color=\"FFCCFFFF\"", ovw)
cat(ovw, file = paste0("output/overview.xml"))
cat(ovw, file = paste0(outdir,"overview.xml"))
}
if(reconstruct_mapping) {
......@@ -164,8 +191,8 @@ if(reconstruct_mapping) {
}
### Write to file, read in as an xml structure
cat(mapping, file = "output/submaps/mapping.xml", sep = "\n")
mapn <- read_xml("output/submaps/mapping.xml")
cat(mapping, file = paste0(outdir_submaps, "mapping.xml"), sep = "\n")
mapn <- read_xml(paste0(outdir_submaps, "mapping.xml"))
### Remove all reactions whose baseReactant species is a placeholder
for(sp in xml_find_all(mapn, "//cd:species", ns_cd)) {
......@@ -177,5 +204,5 @@ if(reconstruct_mapping) {
}
### Write down the trimmed file
write_xml(mapn, "output/submaps/mapping.xml")
write_xml(mapn, paste0(outdir_submaps, "mapping.xml"))
}
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