Added NFKB1

AliSajid · May 26, 2020 · d0c5dbb · d0c5dbb
1 parent 97de77b
commit d0c5dbb
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Showing 253 changed files with 736 additions and 9 deletions.
diff --git a/analyse_data.R b/analyse_data.R
@@ -118,6 +118,7 @@ process_gene(all_results, "AGT")
 process_gene(all_results, "AGTR1")
 process_gene(all_results, "CTLA4")
 process_gene(all_results, "IL6R")
+process_gene(all_results, "NFKB1")
 #process_gene(all_results, "ACE")
 
 carbetocin <- all_results %>% 

diff --git a/figure3.R b/figure3.R
@@ -36,11 +36,13 @@ inf_genes <- c(
   "IL1RL2",
   "IL6",
   "IL6ST",
+  "IL6R",
   "TNF",
   "IL2",
   "IL2RA",
   "IL2RB",
-  "IL2RG"
+  "IL2RG",
+  "NFKB1"
 )
 
 imm_genes <- c("ARG1",
@@ -147,7 +149,7 @@ heatmap.2(
   all_results_cross_imm,
   dendrogram = "none",
   col = colors,
-  colsep = 1:4,
+  colsep = 1:5,
   rowsep = 1:5,
   trace = "none",
   cexRow = 3,

diff --git a/process_signatures.R b/process_signatures.R
@@ -39,7 +39,7 @@ genes <- c("IL1A", "IL1B", "IL2", "IL2RA", "IL2RB", "IL2RG", "IL6", "IL6R",  "TN
           "CD20", "CD3G", "CD11B", "TLR9", "TLR7", "ARG1",
           "CD40", "CD46", "CD44", "CD81", "CD83", "AGT", "AGTR1", "ACE", "ACE2",
           "DPP4", "ANPEP", "CEACAM1", "LAP3", "MMEL1", "CXCL1", "CXCL2", "CXCL3",
-          "CXCL5", "CXCL8", "CCL20", "HEY1", "MUC21", "CCL2", "TGFB1", "TGFBR1", "TGFBR2", "TGFBR3")
+          "CXCL5", "CXCL8", "CCL20", "HEY1", "MUC21", "CCL2", "TGFB1", "TGFBR1", "TGFBR2", "TGFBR3", "NFKB1")
 
 for (drug in drug_results) {
   name <- str_split(drug, "/")[[1]][4]

diff --git a/results/A549-result.csv b/results/A549-result.csv
@@ -15,6 +15,7 @@ Benazepril,CD19,A549,0.5088
 Captopril,CD40,A549,0.5433
 Captopril,CD83,A549,0.2885
 Captopril,TLR7,A549,0.2783
+Enalapril,NFKB1,A549,0.4537
 Enalapril,CEACAM1,A549,0.6395
 Fosinopril,HEY1,A549,0.4394
 Fosinopril,TLR7,A549,0.5027

diff --git a/results/MCF7-result.csv b/results/MCF7-result.csv
@@ -16,15 +16,18 @@ Desmopressin,CD83,MCF7,0.4198
 Desmopressin,TLR9,MCF7,0.4169
 Desmopressin,CXCL8,MCF7,-0.3421
 Desmopressin,IL1B,MCF7,0.3366
+Lopinavir,NFKB1,MCF7,0.481
 Benazepril,HEY1,MCF7,0.4016
 Benazepril,IL2RB,MCF7,0.597
+Captopril,NFKB1,MCF7,0.3425
 Captopril,IL2RA,MCF7,0.317
 Captopril,MMEL1,MCF7,0.5562
 Lisinopril,TGFBR2,MCF7,0.6395
 Lisinopril,CD46,MCF7,0.503
 Lisinopril,IL2RB,MCF7,0.6384
 Moexipril,IL2RA,MCF7,0.4224
 Olmesartan,IL1B,MCF7,0.5145
+Perindopril,NFKB1,MCF7,0.4558
 Ramipril,IL2RA,MCF7,0.4979
 Ramipril,IL1B,MCF7,-0.3077
 Ramipril,CD46,MCF7,0.4987

diff --git a/results/NFKB1-crosstab.csv b/results/NFKB1-crosstab.csv
@@ -0,0 +1,6 @@
+cellline,Benazepril,Bupropion,Captopril,Carbetocin,Chloroquine,Desmopressin,Enalapril,Fosinopril,Hydroxychloroquine,Lisinopril,Lopinavir,Moexipril,Olmesartan,Perindopril,Quinapril,Ramipril,Telmisartan,Valsartan
+A549,NA,NA,NA,NA,NA,NA,0.4537,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+MCF7,NA,NA,0.3425,NA,NA,NA,NA,NA,NA,NA,0.481,NA,NA,0.4558,NA,NA,NA,NA
+PC3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.588,NA,NA,NA
+SW480,NA,NA,NA,NA,NA,NA,NA,0.391,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+VCAP,-0.5286,-0.5066,NA,0.6352,0.7148,0.4042,NA,NA,-0.5427,0.4945,NA,0.4869,0.6398,NA,NA,0.5349,0.6292,0.5569
diff --git a/results/NFKB1.csv b/results/NFKB1.csv
@@ -0,0 +1,19 @@
+perturbagen,cellline,similarity
+Enalapril,A549,0.4537
+Captopril,MCF7,0.3425
+Perindopril,MCF7,0.4558
+Lopinavir,MCF7,0.481
+Quinapril,PC3,0.588
+Fosinopril,SW480,0.391
+Hydroxychloroquine,VCAP,-0.5427
+Benazepril,VCAP,-0.5286
+Bupropion,VCAP,-0.5066
+Desmopressin,VCAP,0.4042
+Moexipril,VCAP,0.4869
+Lisinopril,VCAP,0.4945
+Ramipril,VCAP,0.5349
+Valsartan,VCAP,0.5569
+Telmisartan,VCAP,0.6292
+Carbetocin,VCAP,0.6352
+Olmesartan,VCAP,0.6398
+Chloroquine,VCAP,0.7148
diff --git a/results/PC3-result.csv b/results/PC3-result.csv
@@ -40,6 +40,7 @@ Perindopril,IL2RA,PC3,0.478
 Perindopril,CCL2,PC3,0.6252
 Quinapril,IL2RB,PC3,0.5928
 Quinapril,CCL2,PC3,0.5278
+Quinapril,NFKB1,PC3,0.588
 Quinapril,IL6R,PC3,0.55
 Quinapril,IL2RA,PC3,0.4976
 Ramipril,CCL2,PC3,0.5367

diff --git a/results/SW480-result.csv b/results/SW480-result.csv
@@ -1,4 +1,5 @@
 perturbagen,treatment,cellline,similarity
 Desmopressin,TGFB1,SW480,0.3834
+Fosinopril,NFKB1,SW480,0.391
 Moexipril,TGFB1,SW480,0.4997
 Hydroxychloroquine,TGFB1,SW480,0.3533
diff --git a/results/VCAP-result.csv b/results/VCAP-result.csv
@@ -1,6 +1,8 @@
 perturbagen,treatment,cellline,similarity
 Bupropion,CTLA4,VCAP,0.6138
 Bupropion,CCL2,VCAP,0.5719
+Bupropion,NFKB1,VCAP,-0.5066
+Carbetocin,NFKB1,VCAP,0.6352
 Carbetocin,TGFBR1,VCAP,0.6333
 Carbetocin,ANPEP,VCAP,0.6297
 Carbetocin,CD19,VCAP,0.591
@@ -9,10 +11,12 @@ Carbetocin,CTLA4,VCAP,0.6643
 Carbetocin,CD44,VCAP,0.6581
 Chloroquine,DPP4,VCAP,0.6728
 Chloroquine,MMEL1,VCAP,0.5906
+Chloroquine,NFKB1,VCAP,0.7148
 Chloroquine,TGFBR1,VCAP,0.6603
 Chloroquine,CTLA4,VCAP,0.7058
 Chloroquine,CD44,VCAP,0.6615
 Desmopressin,TLR7,VCAP,0.4236
+Desmopressin,NFKB1,VCAP,0.4042
 Desmopressin,IL6,VCAP,0.3946
 Desmopressin,DPP4,VCAP,0.4858
 Lopinavir,TGFBR1,VCAP,0.4843
@@ -22,6 +26,7 @@ Lopinavir,CD44,VCAP,0.5937
 Benazepril,DPP4,VCAP,0.6218
 Benazepril,TNF,VCAP,0.5046
 Benazepril,CCL2,VCAP,0.4552
+Benazepril,NFKB1,VCAP,-0.5286
 Benazepril,TGFBR2,VCAP,0.7592
 Benazepril,ANPEP,VCAP,0.61
 Benazepril,CD81,VCAP,0.6016
@@ -38,14 +43,17 @@ Fosinopril,ANPEP,VCAP,0.4619
 Fosinopril,CTLA4,VCAP,0.6632
 Fosinopril,CD44,VCAP,0.5987
 Lisinopril,CTLA4,VCAP,-0.6095
+Lisinopril,NFKB1,VCAP,0.4945
 Lisinopril,IL2RA,VCAP,0.4337
 Moexipril,CTLA4,VCAP,0.5986
 Moexipril,CD44,VCAP,0.5512
+Moexipril,NFKB1,VCAP,0.4869
 Olmesartan,CD44,VCAP,-0.627
 Olmesartan,TGFBR2,VCAP,0.7789
 Olmesartan,TGFBR1,VCAP,0.6981
 Olmesartan,ANPEP,VCAP,0.6633
 Olmesartan,CTLA4,VCAP,-0.6509
+Olmesartan,NFKB1,VCAP,0.6398
 Perindopril,CTLA4,VCAP,0.7345
 Perindopril,CD44,VCAP,0.6901
 Quinapril,TGFBR3,VCAP,0.2476
@@ -57,6 +65,7 @@ Quinapril,CD81,VCAP,0.6068
 Quinapril,TGFBR1,VCAP,0.5104
 Ramipril,CD44,VCAP,0.5535
 Ramipril,CTLA4,VCAP,0.623
+Ramipril,NFKB1,VCAP,0.5349
 Ramipril,TGFBR1,VCAP,0.505
 Ramipril,ANPEP,VCAP,0.4758
 Telmisartan,TGFBR3,VCAP,0.2831
@@ -65,12 +74,15 @@ Telmisartan,CTLA4,VCAP,0.6948
 Telmisartan,CD44,VCAP,0.6699
 Telmisartan,TGFBR2,VCAP,0.6993
 Telmisartan,ANPEP,VCAP,0.65
+Telmisartan,NFKB1,VCAP,0.6292
 Telmisartan,TGFBR1,VCAP,0.6077
 Telmisartan,CD19,VCAP,0.5179
+Valsartan,NFKB1,VCAP,0.5569
 Valsartan,CTLA4,VCAP,0.6682
 Valsartan,CD44,VCAP,0.5687
 Valsartan,TGFBR1,VCAP,0.5515
 Hydroxychloroquine,ANPEP,VCAP,0.4177
 Hydroxychloroquine,CTLA4,VCAP,0.6821
+Hydroxychloroquine,NFKB1,VCAP,-0.5427
 Hydroxychloroquine,CD19,VCAP,-0.5097
 Hydroxychloroquine,TGFBR1,VCAP,-0.4898
diff --git a/results/all_averaged.csv b/results/all_averaged.csv
@@ -26,6 +26,7 @@ Benazepril,IL6,0.5861
 Benazepril,IL6R,0.5221
 Benazepril,LAP3,0.3453
 Benazepril,MMEL1,0.4087
+Benazepril,NFKB1,-0.5286
 Benazepril,TGFB1,0.4451
 Benazepril,TGFBR1,0.5742
 Benazepril,TGFBR2,0.7592
@@ -59,6 +60,7 @@ Bupropion,IL6,-0.5782
 Bupropion,IL6R,0.5525
 Bupropion,LAP3,0.5045
 Bupropion,MMEL1,0.5556
+Bupropion,NFKB1,-0.5066
 Bupropion,TGFB1,0.5543
 Bupropion,TGFBR1,0.5068
 Bupropion,TGFBR2,0.6332
@@ -92,6 +94,7 @@ Captopril,IL6,0.669
 Captopril,IL6R,0.5329
 Captopril,LAP3,0.5539
 Captopril,MMEL1,0.5562
+Captopril,NFKB1,0.3425
 Captopril,TGFB1,0.5423
 Captopril,TGFBR1,0.3697
 Captopril,TGFBR2,0.7026
@@ -125,6 +128,7 @@ Carbetocin,IL6,0.7417
 Carbetocin,IL6R,-0.5156
 Carbetocin,LAP3,0.4177
 Carbetocin,MMEL1,0.4872
+Carbetocin,NFKB1,0.6352
 Carbetocin,TGFB1,-0.5532
 Carbetocin,TGFBR1,0.6333
 Carbetocin,TGFBR2,-0.7065
@@ -158,6 +162,7 @@ Chloroquine,IL6,0.634
 Chloroquine,IL6R,0.5543
 Chloroquine,LAP3,0.6284
 Chloroquine,MMEL1,0.5906
+Chloroquine,NFKB1,0.7148
 Chloroquine,TGFB1,0.593
 Chloroquine,TGFBR1,0.6603
 Chloroquine,TGFBR2,0.6871
@@ -191,6 +196,7 @@ Desmopressin,IL6,0.3946
 Desmopressin,IL6R,-0.334
 Desmopressin,LAP3,0.2498
 Desmopressin,MMEL1,0.3615
+Desmopressin,NFKB1,0.4042
 Desmopressin,TGFB1,0.3834
 Desmopressin,TGFBR1,0.4118
 Desmopressin,TGFBR2,0.4872
@@ -224,6 +230,7 @@ Enalapril,IL6,0.6952
 Enalapril,IL6R,0.5889
 Enalapril,LAP3,0.6565
 Enalapril,MMEL1,0.5704
+Enalapril,NFKB1,0.4537
 Enalapril,TGFB1,0.5467
 Enalapril,TGFBR1,0.5409
 Enalapril,TGFBR2,0.6791
@@ -257,6 +264,7 @@ Fosinopril,IL6,0.6454
 Fosinopril,IL6R,0.4779
 Fosinopril,LAP3,0.6139
 Fosinopril,MMEL1,0.5654
+Fosinopril,NFKB1,0.391
 Fosinopril,TGFB1,-0.4146
 Fosinopril,TGFBR1,0.4543
 Fosinopril,TGFBR2,0.7256
@@ -289,6 +297,7 @@ Hydroxychloroquine,IL6,-0.351
 Hydroxychloroquine,IL6R,0.5236
 Hydroxychloroquine,LAP3,0.5314
 Hydroxychloroquine,MMEL1,0.3073
+Hydroxychloroquine,NFKB1,-0.5427
 Hydroxychloroquine,TGFB1,0.3533
 Hydroxychloroquine,TGFBR1,-0.4898
 Hydroxychloroquine,TGFBR2,0.6384
@@ -322,6 +331,7 @@ Lisinopril,IL6,-0.5781
 Lisinopril,IL6R,0.5034
 Lisinopril,LAP3,-0.5185
 Lisinopril,MMEL1,0.4176
+Lisinopril,NFKB1,0.4945
 Lisinopril,TGFB1,0.5787
 Lisinopril,TGFBR1,0.5298
 Lisinopril,TGFBR2,0.6395
@@ -355,6 +365,7 @@ Lopinavir,IL6,0.6681
 Lopinavir,IL6R,0.5377
 Lopinavir,LAP3,0.5966
 Lopinavir,MMEL1,0.51
+Lopinavir,NFKB1,0.481
 Lopinavir,TGFB1,-0.5261
 Lopinavir,TGFBR1,0.4843
 Lopinavir,TGFBR2,0.588
@@ -386,6 +397,7 @@ Moexipril,IL6,0.6033
 Moexipril,IL6R,0.4607
 Moexipril,LAP3,0.5427
 Moexipril,MMEL1,0.4393
+Moexipril,NFKB1,0.4869
 Moexipril,TGFB1,0.4997
 Moexipril,TGFBR1,0.4433
 Moexipril,TGFBR2,0.6453
@@ -419,6 +431,7 @@ Olmesartan,IL6,-0.7271
 Olmesartan,IL6R,0.6291
 Olmesartan,LAP3,0.5087
 Olmesartan,MMEL1,0.4633
+Olmesartan,NFKB1,0.6398
 Olmesartan,TGFB1,0.5815
 Olmesartan,TGFBR1,0.6981
 Olmesartan,TGFBR2,0.7789
@@ -452,6 +465,7 @@ Perindopril,IL6,0.6697
 Perindopril,IL6R,0.6224
 Perindopril,LAP3,0.5696
 Perindopril,MMEL1,0.5261
+Perindopril,NFKB1,0.4558
 Perindopril,TGFB1,0.5251
 Perindopril,TGFBR1,0.4756
 Perindopril,TGFBR2,0.749
@@ -485,6 +499,7 @@ Quinapril,IL6,-0.5652
 Quinapril,IL6R,0.55
 Quinapril,LAP3,0.5462
 Quinapril,MMEL1,0.4357
+Quinapril,NFKB1,0.588
 Quinapril,TGFB1,0.5074
 Quinapril,TGFBR1,0.5104
 Quinapril,TGFBR2,0.6436
@@ -519,6 +534,7 @@ Ramipril,IL6,0.5307
 Ramipril,IL6R,0.4893
 Ramipril,LAP3,0.5558
 Ramipril,MMEL1,0.4791
+Ramipril,NFKB1,0.5349
 Ramipril,TGFB1,0.356
 Ramipril,TGFBR1,0.505
 Ramipril,TGFBR2,0.6371
@@ -552,6 +568,7 @@ Telmisartan,IL6,0.6184
 Telmisartan,IL6R,0.5448
 Telmisartan,LAP3,0.6373
 Telmisartan,MMEL1,0.5711
+Telmisartan,NFKB1,0.6292
 Telmisartan,TGFB1,0.5226
 Telmisartan,TGFBR1,0.6077
 Telmisartan,TGFBR2,0.6993
@@ -586,6 +603,7 @@ Valsartan,IL6,0.6727
 Valsartan,IL6R,0.5232
 Valsartan,LAP3,0.5678
 Valsartan,MMEL1,0.5875
+Valsartan,NFKB1,0.5569
 Valsartan,TGFB1,0.582
 Valsartan,TGFBR1,0.5515
 Valsartan,TGFBR2,0.6864