Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result)

Rectum Adenocarcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

Maintainer Information

Citation Information

Maintained by Dan DiCara (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result). Broad Institute of MIT and Harvard. doi:10.7908/C16T0JQ7

- Overview

+ Introduction

- Summary

MAF used for this analysis:READ-TP.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 3
Mutations seen in COSMIC: 222
Significantly mutated genes in COSMIC territory: 10
Significantly mutated genesets: 111

Mutation Preprocessing

Read 38 MAFs of type "Broad"
Read 35 MAFs of type "Baylor-SOLiD"
Total number of mutations in input MAFs: 29413
After removing 257 invalidated mutations: 29156
After removing 200 noncoding mutations: 28956
After collapsing adjacent/redundant mutations: 21679

Mutation Filtering

Number of mutations before filtering: 21679
After removing 200 mutations outside gene set: 21479
After removing 172 mutations outside category set: 21307
After removing 2 "impossible" mutations in
gene-patient-category bins of zero coverage: 20933

- Results

+ Breakdown of Mutations by Type

type	count
De_novo_Start_InFrame	4
De_novo_Start_OutOfFrame	30
Frame_Shift_Del	151
Frame_Shift_Ins	155
In_Frame_Del	27
In_Frame_Ins	7
Missense_Mutation	14471
Nonsense_Mutation	1779
Nonstop_Mutation	6
Read-through	10
Silent	4629
Splice_Site	38
Total	21307

+ Breakdown of Mutation Rates by Category Type

category	n	N	rate	rate_per_mb	relative_rate
*CpG->T	4919	99673101	0.000049	49	5.4
*Cp(A/C/T)->mut	6673	832257993	8e-06	8	0.89
A->mut	2743	908854391	3e-06	3	0.33
*CpG->(G/A)	135	99673101	1.4e-06	1.4	0.15
indel+null	2050	1840785523	1.1e-06	1.1	0.12
double_null	157	1840785523	8.5e-08	0.085	0.0094
Total	16677	1840785523	9.1e-06	9.1	1

+ Target Coverage for Each Individual

+ Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples

+ CoMut Plot

+ Significantly Mutated Genes

Column Descriptions:

N = number of sequenced bases in this gene across the individual set
n = number of (nonsilent) mutations in this gene across the individual set
npat = number of patients (individuals) with at least one nonsilent mutation
nsite = number of unique sites having a non-silent mutation
nsil = number of silent mutations in this gene across the individual set
n1 = number of nonsilent mutations of type: *CpG->T
n2 = number of nonsilent mutations of type: *Cp(A/C/T)->mut
n3 = number of nonsilent mutations of type: A->mut
n4 = number of nonsilent mutations of type: *CpG->(G/A)
n5 = number of nonsilent mutations of type: indel+null
n6 = number of nonsilent mutations of type: double_null
p_cons = p-value for enrichment of mutations at evolutionarily most-conserved sites in gene
p_joint = p-value for clustering + conservation
p = p-value (overall)
q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 3. Number of genes displayed: 35. Click on a gene name to display its stick figure depicting the distribution of mutations and mutation types across the chosen gene (this feature may not be available for all significant genes).

rank	gene	description	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p_cons	p_joint	p_cv	p	q
1	APC	adenomatous polyposis coli	576224	66	57	56	0	1	4	4	0	39	18	0.97	0	6.6e-15	0	0
2	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	48604	38	38	8	0	0	36	1	0	1	0	0.0029	0	8.1e-11	0	0
3	TP53	tumor protein p53	79667	45	45	30	1	19	6	6	2	12	0	6e-07	0	5e-15	0	0
4	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	40433	5	5	4	0	0	3	2	0	0	0	0.49	0.026	0.00034	0.00011	0.5
5	FBXW7	F-box and WD repeat domain containing 7	177744	12	9	10	0	6	2	2	0	2	0	0.08	0.079	0.00036	0.00032	1
6	SMAD2	SMAD family member 2	98964	5	5	5	0	0	3	1	0	1	0	0.37	0.02	0.0056	0.0011	1
7	ERBB2	v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)	227547	4	4	2	1	4	0	0	0	0	0	0.031	0.00013	1	0.0013	1
8	SMAD4	SMAD family member 4	115264	8	8	6	0	2	3	3	0	0	0	0.2	0.26	0.00054	0.0014	1
9	PPPDE1		38842	2	1	2	0	0	1	0	0	1	0	0.37	0.29	0.00051	0.0014	1
10	ZNF706	zinc finger protein 706	15822	1	1	1	0	0	0	0	0	1	0	NaN	NaN	0.0018	0.0018	1
11	PFDN1	prefoldin subunit 1	22914	1	1	1	0	0	0	0	0	1	0	NaN	NaN	0.0021	0.0021	1
12	ELF3	E74-like factor 3 (ets domain transcription factor, epithelial-specific )	71547	3	3	3	0	0	0	0	0	3	0	0.35	0.083	0.0027	0.0021	1
13	MARCKSL1	MARCKS-like 1	28945	2	2	1	0	0	0	0	0	2	0	0.2	0.091	0.0034	0.0028	1
14	TCF7L2	transcription factor 7-like 2 (T-cell specific, HMG-box)	119026	7	7	7	1	2	3	0	0	2	0	0.085	0.11	0.003	0.0031	1
15	KIAA1804		162266	11	9	9	0	7	3	1	0	0	0	0.051	0.05	0.0094	0.0041	1
16	PALMD	palmdelphin	114488	3	2	3	0	1	1	0	0	1	0	0.28	0.041	0.013	0.0047	1
17	DYNLRB2	dynein, light chain, roadblock-type 2	20963	1	1	1	0	0	0	0	0	1	0	NaN	NaN	0.005	0.005	1
18	NIT2	nitrilase family, member 2	58349	2	2	1	0	0	1	0	0	1	0	0.16	0.069	0.0087	0.0051	1
19	GLRX	glutaredoxin (thioltransferase)	22470	1	1	1	0	0	0	0	0	1	0	NaN	NaN	0.0056	0.0056	1
20	TLL2	tolloid-like 2	209091	3	3	2	2	2	0	1	0	0	0	0.22	0.001	0.82	0.0067	1
21	BOLA3	bolA homolog 3 (E. coli)	24127	1	1	1	0	0	0	0	0	1	0	NaN	NaN	0.0077	0.0077	1
22	KRTAP5-5	keratin associated protein 5-5	34487	2	2	1	0	0	0	0	2	0	0	0.0062	0.013	0.078	0.0081	1
23	HEBP2	heme binding protein 2	34871	1	1	1	0	0	0	0	0	1	0	NaN	NaN	0.0082	0.0082	1
24	PECAM1	platelet/endothelial cell adhesion molecule (CD31 antigen)	74138	1	1	1	0	0	1	0	0	0	0	NaN	NaN	0.0082	0.0082	1
25	IQCK	IQ motif containing K	56949	2	2	2	0	1	0	0	0	1	0	0.3	0.21	0.005	0.0084	1
26	SIP1	survival of motor neuron protein interacting protein 1	54290	2	2	2	0	0	0	0	0	2	0	0.24	0.74	0.0015	0.0087	1
27	GLT8D2	glycosyltransferase 8 domain containing 2	74554	2	2	2	1	0	1	0	0	1	0	0.64	0.23	0.0053	0.0093	1
28	FAM123B	family with sequence similarity 123B	190503	8	6	8	1	0	2	1	0	5	0	0.71	0.14	0.0085	0.0094	1
29	C6orf125	chromosome 6 open reading frame 125	25522	1	1	1	0	0	0	0	0	1	0	NaN	NaN	0.01	0.01	1
30	MAPK10	mitogen-activated protein kinase 10	99738	4	4	4	0	0	1	1	0	2	0	0.64	0.67	0.002	0.01	1
31	C6orf162	chromosome 6 open reading frame 162	20829	1	1	1	0	0	0	0	0	1	0	NaN	NaN	0.011	0.011	1
32	HSPB3	heat shock 27kDa protein 3	30908	1	1	1	0	0	0	0	0	1	0	NaN	NaN	0.011	0.011	1
33	BAG5	BCL2-associated athanogene 5	80849	4	2	3	0	2	0	0	0	2	0	0.14	0.049	0.034	0.012	1
34	FAM49B	family with sequence similarity 49, member B	70006	2	2	2	0	0	0	0	0	2	0	0.16	0.42	0.004	0.013	1
35	TRIM69	tripartite motif-containing 69	99933	2	2	2	1	0	1	0	0	1	0	0.0073	0.015	0.12	0.013	1

+ COSMIC analyses

rank	gene	description	n	cos	n_cos	N_cos	cos_ev	p	q
1	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	38	52	37	3588	363199	1.6e-13	7.2e-10
2	TP53	tumor protein p53	45	824	45	56856	17987	1.6e-12	2.4e-09
3	APC	adenomatous polyposis coli	66	839	50	57891	1048	1.6e-12	2.4e-09
4	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	5	33	5	2277	5755	3.1e-11	3.5e-08
5	FBXW7	F-box and WD repeat domain containing 7	12	91	6	6279	329	4.5e-11	4.1e-08
6	SMAD4	SMAD family member 4	8	159	6	10971	39	1.2e-09	9.2e-07
7	KRTAP5-5	keratin associated protein 5-5	2	1	2	69	2	1.9e-07	0.00012
8	ERBB2	v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)	4	42	3	2898	6	3e-06	0.0017
9	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	7	220	4	15180	1382	0.000013	0.0067
10	LRP1B	low density lipoprotein-related protein 1B (deleted in tumors)	20	18	2	1242	2	0.000063	0.028

+ Geneset Analyses

Table 5. Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 111. Number of genesets displayed: 10

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p	q
1	WNT_SIGNALING	Wnt signaling genes	APC, ARHA, AXIN1, C2orf31, CCND1, CCND2, CCND3, CSNK1E, CSNK1E, LOC400927, CTNNB1, DIPA, DVL1, DVL2, DVL3, FBXW2, FOSL1, FRAT1, FZD1, FZD10, FZD2, FZD3, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LDLR, MAPK10, MAPK9, MYC, PAFAH1B1, PLAU, PPP2R5C, PPP2R5E, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCM, PRKCQ, PRKCZ, PRKD1, RAC1, RHOA, SFRP4, TCF7, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B	57	APC(66), AXIN1(1), CTNNB1(4), DVL2(1), DVL3(2), FBXW2(1), FZD1(1), FZD10(2), FZD3(3), FZD6(3), GSK3B(1), LDLR(1), MAPK10(4), MAPK9(2), PLAU(1), PPP2R5C(1), PRKCA(2), PRKCE(2), PRKCG(2), PRKCH(1), PRKCQ(1), PRKD1(5), RHOA(1), SFRP4(1), TCF7(3), WNT10B(1), WNT2(1), WNT2B(2), WNT6(1)	5514820	117	58	107	13	15	27	8	0	49	18	<1.00e-15	<8.25e-14
2	TELPATHWAY	Telomerase is a ribonucleotide protein that adds telomeric repeats to the 3' ends of chromosomes.	AKT1, BCL2, EGFR, G22P1, HSPCA, IGF1R, KRAS2, MYC, POLR2A, PPP2CA, PRKCA, RB1, TEP1, TERF1, TERT, TNKS, TP53, XRCC5	15	EGFR(1), IGF1R(1), PRKCA(2), RB1(3), TERF1(1), TP53(45), XRCC5(2)	2767314	55	48	40	6	22	9	9	2	13	0	<1.00e-15	<8.25e-14
3	HSA04810_REGULATION_OF_ACTIN_CYTOSKELETON	Genes involved in regulation of actin cytoskeleton	ABI2, ACTN1, ACTN2, ACTN3, ACTN4, APC, APC2, ARAF, ARHGEF1, ARHGEF12, ARHGEF4, ARHGEF6, ARHGEF7, ARPC1A, ARPC1B, ARPC2, ARPC3, ARPC4, ARPC5, ARPC5L, BAIAP2, BCAR1, BDKRB1, BDKRB2, BRAF, C3orf10, CD14, CDC42, CFL1, CFL2, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CRK, CRKL, CSK, CYFIP1, CYFIP2, DIAPH1, DIAPH2, DIAPH3, DOCK1, EGF, EGFR, EZR, F2, F2R, FGD1, FGD3, FGF1, FGF10, FGF11, FGF12, FGF13, FGF14, FGF16, FGF17, FGF18, FGF19, FGF2, FGF20, FGF21, FGF22, FGF23, FGF3, FGF4, FGF5, FGF6, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, FGFR4, FN1, GIT1, GNA12, GNA13, GNG12, GRLF1, GSN, HRAS, INS, IQGAP1, IQGAP2, IQGAP3, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAD, ITGAE, ITGAL, ITGAM, ITGAV, ITGAX, ITGB1, ITGB2, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, KRAS, LIMK1, LIMK2, LOC200025, LOC645126, LOC653888, MAP2K1, MAP2K2, MAPK1, MAPK3, MLCK, MOS, MRAS, MRCL3, MRLC2, MSN, MYH10, MYH14, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLK, MYLK2, MYLPF, NCKAP1, NCKAP1L, NRAS, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PDGFA, PDGFB, PDGFRA, PDGFRB, PFN1, PFN2, PFN3, PFN4, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIP4K2A, PIP4K2B, PIP4K2C, PIP5K1A, PIP5K1B, PIP5K1C, PIP5K3, PPP1CA, PPP1CB, PPP1CC, PPP1R12A, PPP1R12B, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, RDX, RHOA, ROCK1, ROCK2, RRAS, RRAS2, SCIN, SLC9A1, SOS1, SOS2, SSH1, SSH2, SSH3, TIAM1, TIAM2, TMSB4X, TMSB4Y, TMSL3, VAV1, VAV2, VAV3, VCL, WAS, WASF1, WASF2, WASL	203	ABI2(1), ACTN1(2), ACTN2(1), ACTN3(1), ACTN4(1), APC(66), ARHGEF1(1), ARHGEF12(2), ARHGEF4(1), ARHGEF6(3), ARPC2(1), ARPC5L(1), BAIAP2(1), BDKRB2(1), BRAF(2), CDC42(1), CHRM2(3), CHRM4(1), CHRM5(1), CSK(2), CYFIP1(1), CYFIP2(1), DIAPH2(3), DIAPH3(2), DOCK1(2), EGFR(1), F2(1), FGD1(2), FGD3(1), FGF11(1), FGF12(1), FGF13(1), FGF19(1), FGF20(1), FGF5(2), FGFR1(1), FGFR2(5), FN1(4), GIT1(1), GRLF1(5), IQGAP1(3), IQGAP2(3), ITGA10(4), ITGA11(2), ITGA2(1), ITGA2B(2), ITGA4(5), ITGA6(1), ITGA8(3), ITGA9(2), ITGAD(1), ITGAE(2), ITGAL(3), ITGAM(3), ITGAV(4), ITGAX(2), ITGB2(1), ITGB3(2), ITGB4(1), ITGB5(1), ITGB8(1), KRAS(38), LIMK1(1), LIMK2(1), MAP2K1(1), MAP2K2(1), MAPK3(1), MOS(1), MSN(3), MYH10(2), MYH14(3), MYH9(3), MYL9(2), MYLK(3), MYLK2(1), NCKAP1(1), NCKAP1L(4), NRAS(5), PAK1(1), PAK2(1), PAK3(2), PAK7(3), PDGFRA(4), PDGFRB(1), PIK3CA(7), PIK3CD(1), PIK3CG(2), PIK3R1(5), PIK3R3(4), PIP5K1B(1), PIP5K1C(1), PPP1CB(1), PPP1CC(1), PPP1R12A(1), PPP1R12B(4), RAF1(2), RDX(1), RHOA(1), ROCK1(7), ROCK2(4), RRAS2(1), SCIN(1), SLC9A1(2), SOS1(2), SOS2(2), SSH1(2), SSH3(1), TIAM1(5), TIAM2(2), VAV1(2), VAV2(2), VAV3(2), VCL(1), WASF1(2), WASL(2)	26346557	332	66	291	70	74	124	38	4	72	20	1.11e-15	8.25e-14
4	ALKPATHWAY	Activin receptor-like kinase 3 (ALK3) is required during gestation for cardiac muscle development.	ACVR1, APC, ATF2, AXIN1, BMP10, BMP2, BMP4, BMP5, BMP7, BMPR1A, BMPR2, CHRD, CTNNB1, DVL1, FZD1, GATA4, GSK3B, MADH1, MADH4, MADH5, MADH6, MAP3K7, MEF2C, MYL2, NKX2-5, NOG, NPPA, NPPB, RFC1, TCF1, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TGFBR3, WNT1	31	ACVR1(1), APC(66), ATF2(1), AXIN1(1), BMP10(1), BMP2(1), BMP4(1), BMP5(1), BMP7(1), BMPR2(3), CTNNB1(4), FZD1(1), GSK3B(1), MAP3K7(2), MEF2C(2), NPPB(1), RFC1(4), TGFB2(4), TGFBR1(3), TGFBR3(3)	3414527	102	59	92	3	13	19	9	0	43	18	1.11e-15	8.25e-14
5	HSA04664_FC_EPSILON_RI_SIGNALING_PATHWAY	Genes involved in Fc epsilon RI signaling pathway	AKT1, AKT2, AKT3, BTK, CSF2, FCER1A, FCER1G, FYN, GAB2, GRB2, HRAS, IL13, IL3, IL4, IL5, INPP5D, KRAS, LAT, LCP2, LYN, MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K6, MAP2K7, MAPK1, MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPK8, MAPK9, MS4A2, NRAS, PDK1, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PLCG1, PLCG2, PRKCA, PRKCB1, PRKCD, PRKCE, RAC1, RAC2, RAC3, RAF1, SOS1, SOS2, SYK, TNF, VAV1, VAV2, VAV3	74	AKT2(1), AKT3(1), BTK(1), FCER1A(1), FYN(1), GRB2(1), INPP5D(2), KRAS(38), LAT(1), LCP2(1), MAP2K1(1), MAP2K2(1), MAP2K3(4), MAP2K4(2), MAP2K6(1), MAPK10(4), MAPK13(1), MAPK3(1), MAPK8(5), MAPK9(2), MS4A2(2), NRAS(5), PDK1(2), PIK3CA(7), PIK3CD(1), PIK3CG(2), PIK3R1(5), PIK3R3(4), PLA2G4A(3), PLA2G6(2), PLCG2(4), PRKCA(2), PRKCE(2), RAF1(2), SOS1(2), SOS2(2), SYK(3), VAV1(2), VAV2(2), VAV3(2)	6895491	126	49	95	19	28	63	16	2	15	2	1.11e-15	8.25e-14
6	ST_WNT_BETA_CATENIN_PATHWAY	Beta-catenin is degraded in the absence of Wnt signaling; when extracellular Wnt binds Frizzled receptors, beta-catenin accumulates in the nucleus and may promote cell survival.	AKT1, AKT2, AKT3, ANKRD6, APC, AXIN1, AXIN2, C22orf2, CER1, CSNK1A1, CTNNB1, DACT1, DKK1, DKK2, DKK3, DKK4, DVL1, FRAT1, FSTL1, GSK3A, GSK3B, IDAX, LAMR1, LRP1, MVP, NKD1, NKD2, PIN1, PSEN1, PTPRA, SENP2, SFRP1, TSHB, WIF1	29	AKT2(1), AKT3(1), APC(66), AXIN1(1), AXIN2(2), CTNNB1(4), DACT1(1), DKK1(2), DKK2(1), DKK4(3), FSTL1(1), GSK3B(1), LRP1(3), SENP2(1), SFRP1(1), TSHB(1)	3759900	90	59	80	4	8	14	11	0	39	18	1.33e-15	8.25e-14
7	HSA04370_VEGF_SIGNALING_PATHWAY	Genes involved in VEGF signaling pathway	AKT1, AKT2, AKT3, BAD, CASP9, CDC42, CHP, HRAS, KDR, KRAS, MAP2K1, MAP2K2, MAPK1, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPKAPK2, MAPKAPK3, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NOS3, NRAS, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PLCG1, PLCG2, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKCA, PRKCB1, PRKCG, PTGS2, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, SH2D2A, SHC2, SPHK1, SPHK2, SRC, VEGFA	69	AKT2(1), AKT3(1), CDC42(1), KDR(2), KRAS(38), MAP2K1(1), MAP2K2(1), MAPK13(1), MAPK3(1), NFATC1(1), NFATC2(2), NFATC3(1), NFATC4(1), NRAS(5), PIK3CA(7), PIK3CD(1), PIK3CG(2), PIK3R1(5), PIK3R3(4), PLA2G4A(3), PLA2G6(2), PLCG2(4), PPP3CA(2), PPP3CB(1), PPP3CC(1), PRKCA(2), PRKCG(2), PTGS2(1), RAF1(2), SH2D2A(1), SHC2(1), SPHK1(1)	6915053	99	50	68	19	27	50	10	0	10	2	1.44e-15	8.25e-14
8	TIDPATHWAY	On ligand binding, interferon gamma receptors stimulate JAK2 kinase to phosphorylate STAT transcription factors, which promote expression of interferon responsive genes.	DNAJA3, HSPA1A, IFNG, IFNGR1, IFNGR2, IKBKB, JAK2, LIN7A, NFKB1, NFKBIA, RB1, RELA, TIP-1, TNF, TNFRSF1A, TNFRSF1B, TP53, USH1C, WT1	17	DNAJA3(1), IFNGR1(1), IFNGR2(1), IKBKB(2), JAK2(3), NFKB1(3), RB1(3), TP53(45), USH1C(3), WT1(2)	1809425	64	48	49	6	25	14	7	2	15	1	1.55e-15	8.25e-14
9	TGFBPATHWAY	The TGF-beta receptor responds to ligand binding by activating the SMAD family of transcriptional regulations, commonly blocking cell growth.	APC, CDH1, CREBBP, EP300, MADH2, MADH3, MADH4, MADH7, MADHIP, MAP2K1, MAP3K7, MAP3K7IP1, MAPK3, SKIL, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2	13	APC(66), CDH1(1), CREBBP(4), EP300(2), MAP2K1(1), MAP3K7(2), MAPK3(1), SKIL(1), TGFB2(4), TGFBR1(3)	2554178	85	57	75	4	5	10	8	0	44	18	1.78e-15	8.25e-14
10	ST_FAS_SIGNALING_PATHWAY	The Fas receptor induces apoptosis and NF-kB activation when bound to Fas ligand.	ADPRT, ALG2, BAK1, BAX, BFAR, BIRC4, BTK, CAD, CASP10, CASP3, CASP8, CASP8AP2, CD7, CDK2AP1, CSNK1A1, DAXX, DEDD, DEDD2, DFFA, DIABLO, EGFR, EPHB2, FADD, FAF1, FAIM2, FREQ, HRB, HSPB1, IL1A, IL8, MAP2K4, MAP2K7, MAP3K1, MAP3K5, MAPK1, MAPK10, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MCP, MET, NFAT5, NFKB1, NFKB2, NFKBIA, NFKBIB, NFKBIE, NFKBIL1, NFKBIL2, NR0B2, PFN1, PFN2, PTPN13, RALBP1, RIPK1, ROCK1, SMPD1, TNFRSF6, TNFRSF6B, TP53, TPX2, TRAF2, TUFM, VIL2	59	BTK(1), CAD(1), CASP3(1), CASP8AP2(6), DAXX(1), DEDD(1), DFFA(1), EGFR(1), EPHB2(1), IL8(1), MAP2K4(2), MAP3K1(2), MAP3K5(1), MAPK10(4), MAPK8(5), MAPK8IP3(1), MAPK9(2), MET(1), NFKB1(3), NFKB2(2), PTPN13(9), RALBP1(2), ROCK1(7), TP53(45), TPX2(1)	6826271	102	50	87	17	34	28	17	3	20	0	2.00e-15	8.25e-14

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