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

merged master into il6-amp

parents c807a0fb 4492ce99
Term id Term Definition Enrichment Corrected pvalue
GO:0070513 death domain binding 4/10 0.0089
GO:0097153 cysteine-type endopeptidase activity involved in apoptotic process 4/15 0.0207
GO:0032813 tumor necrosis factor receptor superfamily binding 5/46 0.0285
GO:0005123 death receptor binding 4/16 0.0333
GO:0051434 BH3 domain binding 3/5 0.0423
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Rank Gene Symbol Definition Systemic Processes Interactions Drugs
1 BAX "BCL2 associated X, apoptosis regulator" 13 8 0
2 CASP8 caspase 8 10 11 0
3 BAD BCL2 associated agonist of cell death 9 3 2
4 CASP9 caspase 9 8 5 1
5 FADD Fas associated via death domain 8 4 0
6 BID BH3 interacting domain death agonist 7 7 0
7 CASP3 caspase 3 6 8 13
8 BCL2 "BCL2, apoptosis regulator" 6 5 20
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Rank Cell line Perturbagen Dose(um) Duration(h) Enrichment Score Perturbed Genes
1 MCF7 bibu_1361_dihydrochloride 10.0 24 1/2 0.922 ATF4
2 PC3 ici-162,846 10.0 24 1/3 0.539 BAX
3 VCAP gefitinib 10.0 24 1/3 0.539 CASP3
4 PC3 leflunomide 10.0 24 1/4 0.346 ATF4
5 VCAP zd_7155_hydrochloride 10.0 6 1/5 0.230 BAX
6 PC3 meclocycline_sulfosalicylate 10.0 24 1/5 0.230 ATF4
7 MCF7 cv_1808 10.0 6 1/7 0.097 BAX
8 HEPG2 BRD-K23531129 10.0 6 2/29 0.088 ATF4, BAX
9 SKB BRD-K56196992 10.0 24 2/31 0.069 ATF4, BID
10 VCAP BRD-K58288048 10.0 24 4/128 0.060 BCL2, BCL2L1, BID, CASP3
11 MCF7 BRD-K72451865 10.0 24 3/72 0.060 BCL2, BCL2L1, BID
12 PC3 BRD-K83816656 10.0 24 2/33 0.051 BCL2L1, CASP3
13 MCF7 PF-562271 1.11 3 2/34 0.041 BAX, BCL2
14 MCF7 GW-5074 10 24 2/34 0.041 BAX, BCL2
15 MCF7 sorafenib 10 24 2/34 0.041 BCL2, MAP3K5
16 A375 BRD-U86222656 10.0 6 2/34 0.041 BID, CASP3
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Rank Cell line Perturbagen Dose(um) Duration(h) Enrichment Score Perturbed Genes
1 HS578T geldanamycin 10 3 4/63 0.853 ATF4, DDIT3, EIF2AK3, HSPA5
2 RMUGS (s)-(-)-bay_k_8644 10.0 6 3/36 0.827 ATF4, BCL2, BID
3 PC3 vidarabine 10.0 6 2/17 0.733 ATF4, BAX
4 BT20 geldanamycin 0.37 3 2/20 0.493 BCL2, HSPA5
5 BT20 geldanamycin 1.11 3 3/53 0.293 DDIT3, EIF2AK3, HSPA5
6 BT20 geldanamycin 10 3 3/54 0.267 ATF4, DDIT3, HSPA5
7 PC3 psoromic_acid 10.0 24 1/6 0.267 BCL2
8 MDAMB231 radicicol 10 3 3/54 0.267 ATF4, DDIT3, HSPA5
9 A549 BMS-777607 10 24 1/6 0.267 BAX
10 MCF10A radicicol 10 3 4/97 0.253 ATF4, DDIT3, EIF2AK3, HSPA5
11 SKBR3 geldanamycin 10 3 3/56 0.227 DDIT3, EIF2AK3, HSPA5
12 VCAP latanoprost 10.0 24 2/26 0.187 BAX, BID
13 LNCAP geldanamycin 1.11 3 3/59 0.173 DDIT3, EIF2AK3, HSPA5
14 LNCAP geldanamycin 3.33 3 3/59 0.173 DDIT3, EIF2AK3, HSPA5
15 MDAMB231 KIN001-043 10 24 4/107 0.160 ATF4, DDIT3, EIF2AK3, HSPA5
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Rank Cell line Perturbagen Dose(um) Duration(h) Enrichment Score Perturbed Genes
1 HS578T geldanamycin 10 3 4/86 0.817 ATF4, DDIT3, EIF2AK3, HSPA5
2 MCF7 sorafenib 10 24 4/93 0.718 ATF4, BCL2, DDIT3, MAP3K5
3 VCAP gefitinib 10.0 24 1/7 0.507 CASP3
4 PC3 leflunomide 10.0 24 1/7 0.507 ATF4
5 PC3 BRD-K83816656 10.0 24 3/66 0.465 BAX, BCL2L1, CASP3
6 BT20 geldanamycin 1.11 3 3/75 0.352 DDIT3, EIF2AK3, HSPA5
7 HS578T geldanamycin 3.33 3 4/137 0.324 ATF4, DDIT3, HSPA5, MAP3K5
8 A375 pelitinib 0.12 24 4/137 0.324 ATF4, BCL2L1, DDIT3, MAP3K5
9 LNCAP geldanamycin 3.33 3 3/79 0.310 DDIT3, EIF2AK3, HSPA5
10 BT20 geldanamycin 0.37 3 2/37 0.268 BCL2, HSPA5
11 LNCAP geldanamycin 10 3 3/91 0.197 DDIT3, EIF2AK3, HSPA5
12 VCAP latanoprost 10.0 24 2/43 0.169 BAX, BID
13 BT20 geldanamycin 10 3 3/98 0.155 ATF4, DDIT3, HSPA5
14 A375 QL-XII-47 1.11 24 4/175 0.155 ATF4, DDIT3, EIF2AK3, MAP3K5
15 BT20 radicicol 10 3 3/98 0.155 ATF4, DDIT3, HSPA5
16 RMUGS (s)-(-)-bay_k_8644 10.0 6 3/102 0.127 ATF4, BCL2, BID
17 LNCAP geldanamycin 1.11 3 3/102 0.127 DDIT3, EIF2AK3, HSPA5
18 PC3 vidarabine 10.0 6 2/46 0.113 ATF4, BAX
19 BT20 radicicol 3.33 3 2/47 0.113 DDIT3, HSPA5
20 VCAP zd_7155_hydrochloride 10.0 6 1/12 0.099 BAX
21 MCF10A radicicol 10 3 4/189 0.099 ATF4, DDIT3, EIF2AK3, HSPA5
22 HME1 geldanamycin 10 3 3/106 0.099 ATF4, BCL2, DDIT3
23 A549 methylstat 10 24 2/48 0.099 ATF4, DDIT3
24 HEPG2 s1095 10.0 6 3/108 0.099 ATF4, BAX, CASP3
25 A375 ABT-737 10 24 3/108 0.099 DDIT3, EIF2AK3, HSPA5
26 A549 BMS-777607 10 24 1/12 0.099 BAX
27 MDAMB231 radicicol 10 3 3/108 0.099 ATF4, DDIT3, HSPA5
28 PC3 ABT-737 10 24 4/189 0.099 ATF4, DDIT3, EIF2AK3, HSPA5
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Term id Term Definition Enrichment Corrected pvalue
GO:0005851 eukaryotic translation initiation factor 2B complex 6/6 0.0033
GO:0097136 Bcl-2 family protein complex 4/7 0.0059
GO:0031968 organelle outer membrane 10/210 0.0119
GO:0019867 outer membrane 10/212 0.0161
GO:0005741 mitochondrial outer membrane 9/186 0.0204
GO:1990604 IRE1-TRAF2-ASK1 complex 3/4 0.0235
GO:0005850 eukaryotic translation initiation factor 2 complex 3/5 0.0274
GO:0005789 endoplasmic reticulum membrane 18/1077 0.0283
GO:0042175 nuclear outer membrane-endoplasmic reticulum membrane network 18/1100 0.0292
GO:0031264 death-inducing signaling complex 3/9 0.0386
GO:0044432 endoplasmic reticulum part 19/1362 0.0412
GO:1990617 CHOP-ATF4 complex 2/2 0.0425
GO:1990597 AIP1-IRE1 complex 2/3 0.0498
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Term id Term Definition Enrichment Corrected pvalue
GO:0003743 translation initiation factor activity 9/57 0.004
GO:0045182 translation regulator activity 12/152 0.0083
GO:0004694 eukaryotic translation initiation factor 2alpha kinase activity 4/4 0.0132
GO:0008135 "translation factor activity, RNA binding" 9/100 0.0159
GO:0090079 "translation regulator activity, nucleic acid binding" 9/123 0.0215
GO:0097199 cysteine-type endopeptidase activity involved in apoptotic signaling pathway 4/8 0.0269
GO:0051400 BH domain binding 4/10 0.0289
GO:0019899 enzyme binding 31/2205 0.0344
GO:0097153 cysteine-type endopeptidase activity involved in apoptotic process 4/15 0.0381
GO:0005123 death receptor binding 4/16 0.0404
GO:0051434 BH3 domain binding 3/5 0.0484
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Term id Term Definition Enrichment Corrected pvalue
GO:0070059 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress 15/33 0.0008
GO:0034976 response to endoplasmic reticulum stress 27/243 0.0011
GO:0097193 intrinsic apoptotic signaling pathway 19/149 0.0019
GO:0034620 cellular response to unfolded protein 17/121 0.0024
GO:0043558 regulation of translational initiation in response to stress 8/10 0.0038
GO:0097190 apoptotic signaling pathway 22/282 0.0051
GO:0035967 cellular response to topologically incorrect protein 17/141 0.0055
GO:1905897 regulation of response to endoplasmic reticulum stress 14/83 0.0055
GO:0006986 response to unfolded protein 17/157 0.0069
GO:0006984 ER-nucleus signaling pathway 10/36 0.0076
GO:0035966 response to topologically incorrect protein 17/179 0.0077
GO:0043555 regulation of translation in response to stress 8/17 0.0081
GO:1900101 regulation of endoplasmic reticulum unfolded protein response 9/26 0.0094
GO:1900103 positive regulation of endoplasmic reticulum unfolded protein response 7/14 0.012
GO:1905898 positive regulation of response to endoplasmic reticulum stress 9/38 0.0121
GO:0030968 endoplasmic reticulum unfolded protein response 13/100 0.0123
GO:0036500 ATF6-mediated unfolded protein response 6/9 0.0131
GO:0006446 regulation of translational initiation 10/78 0.0137
GO:0043280 positive regulation of cysteine-type endopeptidase activity involved in apoptotic process 12/125 0.0141
GO:0042594 response to starvation 14/187 0.0157
GO:2001056 positive regulation of cysteine-type endopeptidase activity 12/142 0.016
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process 10/85 0.0164
GO:0009267 cellular response to starvation 12/148 0.0165
GO:0009266 response to temperature stimulus 13/175 0.0168
GO:0010952 positive regulation of peptidase activity 13/190 0.0197
GO:1990440 positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress 5/11 0.0197
GO:1990928 response to amino acid starvation 8/47 0.0198
GO:0070997 neuron death 8/52 0.0203
GO:0046902 regulation of mitochondrial membrane permeability 9/77 0.0216
GO:1901030 positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway 7/36 0.0219
GO:1902235 regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway 7/33 0.022
GO:0010950 positive regulation of endopeptidase activity 12/171 0.0232
GO:0001836 release of cytochrome c from mitochondria 6/22 0.0233
GO:0036499 PERK-mediated unfolded protein response 5/12 0.0238
GO:0043525 positive regulation of neuron apoptotic process 8/60 0.0252
GO:0080135 regulation of cellular response to stress 24/746 0.0252
GO:0033554 cellular response to stress 39/1695 0.0266
GO:0006915 apoptotic process 27/920 0.0268
GO:1903894 regulation of IRE1-mediated unfolded protein response 5/13 0.027
GO:0090559 regulation of membrane permeability 9/87 0.0271
GO:2001235 positive regulation of apoptotic signaling pathway 12/183 0.0293
GO:0010942 positive regulation of cell death 23/729 0.0297
GO:1901028 regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway 7/45 0.0299
GO:0008219 cell death 29/1085 0.0304
GO:0032055 negative regulation of translation in response to stress 4/6 0.0315
GO:0012501 programmed cell death 28/1050 0.0342
GO:0043065 positive regulation of apoptotic process 22/670 0.0343
GO:0043068 positive regulation of programmed cell death 22/678 0.0353
GO:1903896 positive regulation of IRE1-mediated unfolded protein response 4/8 0.0356
GO:0045947 negative regulation of translational initiation 5/19 0.0359
GO:1901214 regulation of neuron death 15/323 0.036
GO:0071496 cellular response to external stimulus 15/332 0.0362
GO:0043281 regulation of cysteine-type endopeptidase activity involved in apoptotic process 12/210 0.0386
GO:0009411 response to UV 10/139 0.0398
GO:0046660 female sex differentiation 9/110 0.0399
GO:0043496 regulation of protein homodimerization activity 5/22 0.0408
GO:0008585 female gonad development 8/91 0.0408
GO:0031669 cellular response to nutrient levels 12/230 0.0415
GO:2000116 regulation of cysteine-type endopeptidase activity 12/234 0.0418
GO:2001242 regulation of intrinsic apoptotic signaling pathway 10/169 0.0434
GO:0032469 endoplasmic reticulum calcium ion homeostasis 5/23 0.0435
GO:0046545 development of primary female sexual characteristics 8/96 0.045
GO:0006983 ER overload response 4/12 0.0465
GO:0031668 cellular response to extracellular stimulus 12/261 0.0468
GO:1903573 negative regulation of response to endoplasmic reticulum stress 6/44 0.0479
GO:0009628 response to abiotic stimulus 28/1163 0.048
GO:0007006 mitochondrial membrane organization 9/135 0.0487
GO:0071287 cellular response to manganese ion 4/13 0.0492
GO:0032058 positive regulation of translational initiation in response to stress 3/4 0.0496
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Rank Gene Symbol Definition Systemic Processes Interactions Drugs
1 BAX "BCL2 associated X, apoptosis regulator" 10 8 0
2 BCL2 "BCL2, apoptosis regulator" 10 11 20
3 HSPA5 heat shock protein family A (Hsp70) member 5 9 4 2
4 EIF2S1 eukaryotic translation initiation factor 2 subunit alpha 9 7 0
5 BAK1 BCL2 antagonist/killer 1 9 4 0
6 EIF2AK3 eukaryotic translation initiation factor 2 alpha kinase 3 8 3 0
7 ATF4 activating transcription factor 4 8 2 0
8 BCL2L1 BCL2 like 1 7 11 2
9 BBC3 BCL2 binding component 3 6 2 0
10 BCL2L11 BCL2 like 11 6 4 0
11 EIF2AK4 eukaryotic translation initiation factor 2 alpha kinase 4 6 0 0
12 CASP8 caspase 8 6 12 0
13 EIF2B5 eukaryotic translation initiation factor 2B subunit epsilon 5 4 0
14 BID BH3 interacting domain death agonist 5 8 0
15 MAP3K5 mitogen-activated protein kinase kinase kinase 5 5 3 0
16 TRAF2 TNF receptor associated factor 2 5 6 0
17 DDIT3 DNA damage inducible transcript 3 5 3 1
18 CASP3 caspase 3 5 7 13
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Term id Term Definition Enrichment Corrected pvalue
GO:0034340 response to type I interferon 15/71 0.0007
GO:0009615 response to virus 18/285 0.0022
GO:0019221 cytokine-mediated signaling pathway 24/680 0.0023
GO:0002224 toll-like receptor signaling pathway 12/97 0.0042
GO:0034097 response to cytokine 28/1110 0.0061
GO:0045088 regulation of innate immune response 17/443 0.0066
GO:0002221 pattern recognition receptor signaling pathway 12/126 0.0067
GO:0071345 cellular response to cytokine stimulus 26/1018 0.0067
GO:0002758 innate immune response-activating signal transduction 13/227 0.0095
GO:0007249 I-kappaB kinase/NF-kappaB signaling 9/69 0.0098
GO:0051707 response to other organism 27/1301 0.0112
GO:0051403 stress-activated MAPK cascade 10/106 0.0123
GO:0043207 response to external biotic stimulus 27/1303 0.0127
GO:0002218 activation of innate immune response 13/248 0.0136
GO:0002831 regulation of response to biotic stimulus 17/509 0.0158
GO:0009607 response to biotic stimulus 27/1326 0.0161
GO:0043900 regulation of multi-organism process 20/768 0.0176
GO:0045087 innate immune response 20/750 0.0183
GO:0002833 positive regulation of response to biotic stimulus 14/351 0.019
GO:0045089 positive regulation of innate immune response 14/332 0.0193
GO:0070498 interleukin-1-mediated signaling pathway 9/98 0.0207
GO:0031098 stress-activated protein kinase signaling cascade 10/141 0.0223
GO:0007252 I-kappaB phosphorylation 5/12 0.0225
GO:0051607 defense response to virus 11/196 0.0227
GO:0035666 TRIF-dependent toll-like receptor signaling pathway 6/29 0.0248
GO:0038095 Fc-epsilon receptor signaling pathway 10/167 0.0256
GO:0002756 MyD88-independent toll-like receptor signaling pathway 6/31 0.0287
GO:0002764 immune response-regulating signaling pathway 16/570 0.0296
GO:0002753 cytoplasmic pattern recognition receptor signaling pathway 6/35 0.0296
GO:0043902 positive regulation of multi-organism process 15/494 0.0313
GO:0035994 response to muscle stretch 5/19 0.0331
GO:0098542 defense response to other organism 20/935 0.0335
GO:0031347 regulation of defense response 18/788 0.0339
GO:0051090 regulation of DNA-binding transcription factor activity 14/433 0.0346
GO:0060333 interferon-gamma-mediated signaling pathway 7/71 0.0378
GO:0032103 positive regulation of response to external stimulus 15/602 0.0378
GO:0071347 cellular response to interleukin-1 9/178 0.0391
GO:0050776 regulation of immune response 21/1113 0.0393
GO:0038093 Fc receptor signaling pathway 10/232 0.0399
GO:0031349 positive regulation of defense response 14/473 0.0406
GO:0070423 nucleotide-binding oligomerization domain containing signaling pathway 5/27 0.0427
GO:0006952 defense response 23/1319 0.043
GO:0032479 regulation of type I interferon production 8/127 0.0433
GO:0035872 "nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway" 5/28 0.0463
GO:0002755 MyD88-dependent toll-like receptor signaling pathway 5/34 0.0463
GO:0051092 positive regulation of NF-kappaB transcription factor activity 8/152 0.0475
GO:0070555 response to interleukin-1 9/207 0.0491
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Term id Term Definition Enrichment Corrected pvalue
GO:0008385 IkappaB kinase complex 4/9 0.0062
GO:0035631 CD40 receptor complex 4/11 0.013
GO:0033256 I-kappaB/NF-kappaB complex 2/4 0.0166
GO:1902554 serine/threonine protein kinase complex 4/88 0.0239
GO:0035976 transcription factor AP-1 complex 2/5 0.033
GO:1902911 protein kinase complex 4/108 0.0413
GO:0005768 endosome 9/902 0.0422
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Term id Term Definition Enrichment Corrected pvalue
GO:0044389 ubiquitin-like protein ligase binding 9/306 0.0056
GO:0005126 cytokine receptor binding 8/287 0.0116
GO:0004905 type I interferon receptor activity 2/2 0.0162
GO:0032813 tumor necrosis factor receptor superfamily binding 4/46 0.0212
GO:0031625 ubiquitin protein ligase binding 7/288 0.0269
GO:0019903 protein phosphatase binding 5/138 0.032
GO:0003725 double-stranded RNA binding 4/74 0.0369
GO:0016772 "transferase activity, transferring phosphorus-containing groups" 12/987 0.0409
GO:0070566 adenylyltransferase activity 3/29 0.0482
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Rank Gene Symbol Definition Systemic Processes Interactions Drugs
1 CHUK conserved helix-loop-helix ubiquitous kinase 13 7 5
2 IKBKB inhibitor of nuclear factor kappa B kinase subunit beta 12 10 9
3 IKBKG inhibitor of nuclear factor kappa B kinase subunit gamma 12 10 7
4 MAP3K7 mitogen-activated protein kinase kinase kinase 7 11 9 0
5 MYD88 "MYD88, innate immune signal transduction adaptor" 11 6 0
6 TRAF6 TNF receptor associated factor 6 11 8 0
7 IKBKE inhibitor of nuclear factor kappa B kinase subunit epsilon 10 8 0
8 IRF3 interferon regulatory factor 3 10 4 0
9 TAB1 TGF-beta activated kinase 1 (MAP3K7) binding protein 1 10 5 0
10 NFKBIA NFKB inhibitor alpha 9 8 1
11 NFKB1 nuclear factor kappa B subunit 1 9 5 13
12 TLR7 toll like receptor 7 8 1 11
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Rank Cell line Perturbagen Dose(um) Duration(h) Enrichment Score Perturbed Genes
1 NPC BRD-K52911425 10.0 24 2/8 0.923 IKBKB, IKBKE
2 VCAP c3930 10.0 6 2/13 0.431 IKBKB, IKBKE
3 ASC 1391-0741 10.0 24 2/14 0.374 IKBKB, IKBKE
4 VCAP p5172 10.0 6 1/4 0.282 IKBKB
5 A375 BRD-K88008216 10.0 6 2/18 0.210 IKBKB, IKBKE
6 VCAP geldanamycin 10.0 6 2/18 0.210 IKBKB, IKBKE
7 HT29 BRD-K12168891 10.0 6 1/5 0.154 IKBKE
8 VCAP rottlerin 10.0 24 1/5 0.154 IKBKE
9 MCF7 1391-0741 10.0 6 1/5 0.154 IKBKE
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Rank Cell line Perturbagen Dose(um) Duration(h) Enrichment Score Perturbed Genes
1 VCAP mls-0391006 10.0 6 1/2 0.966 IKBKB
2 HA1E 16beta-bromoandrosterone 11.1 24 2/19 0.266 IKBKB, IKBKE
3 MCF7 crotamiton 10.0 6 1/5 0.242 NFKBIA
4 SKB BRD-K33164466 10.0 24 2/24 0.159 IKBKB, IKBKE
5 PHH cycloheximide 10.0 24 2/31 0.072 IKBKB, IKBKE
6 PC3 BRD-K32485462 10.0 6 2/32 0.063 IKBKB, IKBKE
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Rank Cell line Perturbagen Dose(um) Duration(h) Enrichment Score Perturbed Genes
1 VCAP c3930 10.0 6 2/31 0.642 IKBKB, IKBKE
2 ASC 1391-0741 10.0 24 2/36 0.472 IKBKB, IKBKE
3 NPC BRD-K52911425 10.0 24 2/38 0.415 IKBKB, IKBKE
4 PHH s1118 10.0 24 2/40 0.358 IKBKB, IKBKE
5 PC3 BRD-K32485462 10.0 6 2/45 0.245 IKBKB, IKBKE
6 A375 sb_216641_hydrochloride 10.0 6 2/48 0.208 IKBKB, IKBKE
7 VCAP BRD-K77830450_(forskolin) 10.0 24 1/12 0.208 IKBKB
8 A549 saracatinib 3.33 24 1/13 0.132 IKBKE
9 HA1E 16beta-bromoandrosterone 11.1 24 2/56 0.094 IKBKB, IKBKE
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