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

Colon 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/C1W37TB7

- Overview

+ Introduction

- Summary

MAF used for this analysis:COAD-TP.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 14
Mutations seen in COSMIC: 517
Significantly mutated genes in COSMIC territory: 23
Significantly mutated genesets: 156

Mutation Preprocessing

Read 102 MAFs of type "Broad"
Read 53 MAFs of type "Baylor-SOLiD"
Total number of mutations in input MAFs: 62560
After removing 1112 invalidated mutations: 61448
After removing 976 noncoding mutations: 60472
After collapsing adjacent/redundant mutations: 60470

Mutation Filtering

Number of mutations before filtering: 60470
After removing 665 mutations outside gene set: 59805
After removing 171 mutations outside category set: 59634
After removing 9 "impossible" mutations in
gene-patient-category bins of zero coverage: 58789

- Results

+ Breakdown of Mutations by Type

type	count
De_novo_Start_InFrame	16
De_novo_Start_OutOfFrame	126
Frame_Shift_Del	1137
Frame_Shift_Ins	655
In_Frame_Del	139
In_Frame_Ins	19
Missense_Mutation	39601
Nonsense_Mutation	3274
Nonstop_Mutation	30
Silent	14487
Splice_Site	148
Translation_Start_Site	2
Total	59634

+ Breakdown of Mutation Rates by Category Type

category	n	N	rate	rate_per_mb	relative_rate
*CpG->T	15461	235764747	0.000066	66	6.2
*Np(A/C/T)->transit	10142	3394090912	3e-06	3	0.28
*ApG->G	966	657627616	1.5e-06	1.5	0.14
transver	13028	4287483275	3e-06	3	0.29
indel+null	5396	4287483377	1.3e-06	1.3	0.12
double_null	147	4287483377	3.4e-08	0.034	0.0033
Total	45140	4287483377	0.000011	11	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: *Np(A/C/T)->transit
n3 = number of nonsilent mutations of type: *ApG->G
n4 = number of nonsilent mutations of type: transver
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: 14. 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	1314776	121	103	85	4	5	6	1	11	64	34	0.85	0	2.9e-15	0	0
2	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	423914	33	26	18	1	5	19	1	8	0	0	0.000021	0	1.2e-06	0	0
3	BRAF	v-raf murine sarcoma viral oncogene homolog B1	342233	21	20	3	0	0	0	0	21	0	0	0.00017	0	0.000013	0	0
4	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	109406	58	58	8	0	0	31	0	27	0	0	9e-06	0	7.1e-15	0	0
5	TP53	tumor protein p53	188069	77	75	50	1	29	11	0	11	26	0	2e-07	0	1.9e-15	0	0
6	FBXW7	F-box and WD repeat domain containing 7	400174	33	29	21	2	17	1	0	8	7	0	0.12	0.00077	1.9e-13	5.4e-15	1.6e-11
7	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	90830	15	15	7	0	2	2	0	11	0	0	0.033	0.0012	5.4e-11	2e-12	5.1e-09
8	SMAD4	SMAD family member 4	262233	21	18	17	0	8	7	0	2	3	1	0.01	0.016	1.5e-08	5.7e-09	0.000013
9	FAM123B	family with sequence similarity 123B	451470	19	19	17	1	1	2	0	2	14	0	0.72	0.088	1.1e-08	2.1e-08	0.000042
10	SOX9	SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal)	180663	9	9	9	0	0	1	0	0	8	0	0.62	0.2	5.2e-07	1.8e-06	0.0032
11	ACVR2A	activin A receptor, type IIA	245516	9	8	8	1	0	1	0	3	5	0	0.037	0.0089	0.000022	3.2e-06	0.0053
12	TNFRSF10C	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	116831	6	6	2	0	0	0	0	6	0	0	1	0.000036	0.0071	4.2e-06	0.0062
13	SMAD2	SMAD family member 2	223461	11	10	8	1	3	0	0	4	4	0	0.096	0.025	0.0001	0.000035	0.049
14	ACOT4	acyl-CoA thioesterase 4	151821	3	3	2	1	0	0	0	0	2	1	0.026	0.00038	0.0077	4e-05	0.051
15	PCBP1	poly(rC) binding protein 1	127765	4	4	2	0	0	0	2	2	0	0	0.043	5e-05	0.21	0.00013	0.15
16	CRTC1	CREB regulated transcription coactivator 1	244087	5	5	3	1	1	0	0	0	4	0	0.081	0.0095	0.0017	0.0002	0.22
17	SAT1	spermidine/spermine N1-acetyltransferase 1	78557	4	4	2	0	0	0	0	1	3	0	NaN	NaN	0.00037	0.00037	0.39
18	TCF7L2	transcription factor 7-like 2 (T-cell specific, HMG-box)	281477	13	11	13	3	3	2	0	3	5	0	0.51	0.11	0.00033	0.0004	0.4
19	WBSCR17	Williams-Beuren syndrome chromosome region 17	278161	17	17	16	2	10	2	1	1	3	0	0.63	0.1	0.00043	0.00048	0.45
20	GGT1	gamma-glutamyltransferase 1	178906	3	3	1	1	0	3	0	0	0	0	0.000017	0.000052	0.84	0.00048	0.45
21	TXNDC3	thioredoxin domain containing 3 (spermatozoa)	283045	13	10	13	2	3	1	1	3	5	0	0.84	0.79	0.000061	0.00053	0.45
22	MGC26647	chromosome 7 open reading frame 62	117898	7	7	7	0	1	1	0	2	3	0	0.82	0.21	0.00035	0.00078	0.64
23	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	180955	6	4	5	1	2	0	0	1	2	1	0.0046	0.0051	0.017	0.00088	0.69
24	CASP8	caspase 8, apoptosis-related cysteine peptidase	266056	11	10	10	0	1	3	1	2	4	0	0.6	0.81	0.00013	0.0011	0.8
25	ACVR1B	activin A receptor, type IB	235764	13	13	13	0	4	6	0	2	1	0	0.0019	0.0059	0.027	0.0015	1
26	OR6A2	olfactory receptor, family 6, subfamily A, member 2	153139	2	2	2	0	1	1	0	0	0	0	0.0045	0.00039	0.42	0.0016	1
27	KLK2	kallikrein-related peptidase 2	127435	3	3	1	0	0	0	0	3	0	0	0.2	0.00044	0.42	0.0018	1
28	MAP2K4	mitogen-activated protein kinase kinase 4	171130	9	9	8	0	2	3	1	2	1	0	0.0021	0.0042	0.046	0.0019	1
29	ELF3	E74-like factor 3 (ets domain transcription factor, epithelial-specific )	167304	3	3	3	0	0	1	0	0	2	0	0.47	0.11	0.0019	0.0021	1
30	MIER3	mesoderm induction early response 1, family member 3	259908	10	10	10	0	2	2	0	2	4	0	0.64	0.64	0.00047	0.0027	1
31	SULT1C4	sulfotransferase family, cytosolic, 1C, member 4	145166	3	3	1	0	2	0	0	1	0	0	0.2	0.0014	0.26	0.0033	1
32	FAM22F	family with sequence similarity 22, member F	194820	8	8	4	1	1	0	0	6	1	0	0.4	0.07	0.0052	0.0033	1
33	TBC1D10C	TBC1 domain family, member 10C	134780	2	2	1	0	0	0	0	0	2	0	0.97	0.29	0.0013	0.0035	1
34	MUC20	mucin 20, cell surface associated	124950	2	2	1	1	0	0	0	0	2	0	0.0025	0.0036	0.12	0.0038	1
35	OR2M4	olfactory receptor, family 2, subfamily M, member 4	145654	8	8	8	0	3	2	1	0	2	0	0.044	0.17	0.0026	0.0039	1

+ COSMIC analyses

rank	gene	description	n	cos	n_cos	N_cos	cos_ev	p	q
1	APC	adenomatous polyposis coli	121	839	87	130045	1536	0	0
2	TP53	tumor protein p53	77	824	77	127720	27419	0	0
3	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	15	33	13	5115	12243	6.7e-14	1e-10
4	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	58	52	58	8060	650714	1e-13	1.2e-10
5	BRAF	v-raf murine sarcoma viral oncogene homolog B1	21	89	19	13795	273106	1.6e-13	1.3e-10
6	FBXW7	F-box and WD repeat domain containing 7	33	91	25	14105	899	1.7e-13	1.3e-10
7	SMAD4	SMAD family member 4	21	159	13	24645	51	2.6e-13	1.7e-10
8	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	33	220	30	34100	11874	3.3e-13	1.9e-10
9	ERBB3	v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian)	11	6	5	930	5	7.5e-13	3.8e-10
10	CDC27	cell division cycle 27 homolog (S. cerevisiae)	9	3	4	465	4	2.4e-11	1.1e-08

+ 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: 156. 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	HSA04310_WNT_SIGNALING_PATHWAY	Genes involved in Wnt signaling pathway	APC, APC2, AXIN1, AXIN2, BTRC, CACYBP, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CCND1, CCND2, CCND3, CER1, CHD8, CHP, CREBBP, CSNK1A1, CSNK1A1L, CSNK1E, CSNK2A1, CSNK2A2, CSNK2B, CTBP1, CTBP2, CTNNB1, CTNNBIP1, CUL1, CXXC4, DAAM1, DAAM2, DKK1, DKK2, DKK4, DVL1, DVL2, DVL3, EP300, FBXW11, FOSL1, FRAT1, FRAT2, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LEF1, LOC652788, LRP5, LRP6, MAP3K7, MAPK10, MAPK8, MAPK9, MMP7, MYC, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NKD1, NKD2, NLK, PLCB1, PLCB2, PLCB3, PLCB4, PORCN, PPARD, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRICKLE1, PRICKLE2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PSEN1, RAC1, RAC2, RAC3, RBX1, RHOA, ROCK1, ROCK2, RUVBL1, SENP2, SFRP1, SFRP2, SFRP4, SFRP5, SIAH1, SKP1, SMAD2, SMAD3, SMAD4, SOX17, TBL1X, TBL1XR1, TBL1Y, TCF7, TCF7L1, TCF7L2, TP53, VANGL1, VANGL2, WIF1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B	144	APC(121), APC2(1), AXIN1(1), AXIN2(7), BTRC(2), CACYBP(1), CAMK2A(1), CAMK2B(2), CAMK2D(2), CAMK2G(2), CCND2(1), CCND3(1), CER1(3), CHD8(4), CREBBP(21), CSNK1A1(2), CSNK1A1L(5), CSNK2A1(4), CSNK2A2(2), CSNK2B(2), CTBP1(1), CTBP2(2), CTNNB1(8), CTNNBIP1(1), CUL1(7), CXXC4(1), DAAM1(1), DAAM2(5), DKK1(3), DKK2(5), DKK4(4), DVL2(8), DVL3(2), EP300(13), FBXW11(7), FZD10(4), FZD2(2), FZD3(10), FZD4(1), FZD6(3), FZD7(3), FZD8(1), GSK3B(7), LEF1(4), LRP5(5), LRP6(10), MAP3K7(2), MAPK10(4), MAPK8(2), MAPK9(3), MMP7(3), NFAT5(5), NFATC1(1), NFATC2(3), NFATC3(4), NFATC4(4), NKD1(3), NKD2(1), NLK(1), PLCB1(8), PLCB2(3), PLCB3(3), PLCB4(9), PORCN(2), PPARD(1), PPP2CA(1), PPP2R1A(4), PPP2R1B(1), PPP2R2A(1), PPP2R2B(1), PPP2R2C(3), PPP3CA(1), PPP3CB(4), PPP3CC(3), PPP3R1(1), PPP3R2(1), PRICKLE1(8), PRICKLE2(5), PRKACB(1), PRKACG(2), PRKCA(2), PRKCG(8), PRKX(2), PSEN1(3), RHOA(4), ROCK1(8), ROCK2(2), RUVBL1(6), SENP2(2), SFRP1(2), SFRP2(1), SFRP4(3), SFRP5(1), SIAH1(1), SKP1(1), SMAD2(11), SMAD3(6), SMAD4(21), SOX17(2), TBL1X(5), TBL1XR1(6), TCF7(3), TCF7L1(3), TCF7L2(13), TP53(77), VANGL1(2), VANGL2(5), WIF1(2), WNT1(1), WNT10B(3), WNT11(3), WNT16(2), WNT2B(1), WNT3(4), WNT3A(1), WNT4(1), WNT5A(3), WNT7A(2), WNT7B(2), WNT8A(1), WNT9A(2), WNT9B(1)	35522515	631	150	557	121	207	110	8	124	147	35	<1.00e-15	<3.24e-14
2	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	58	APC(121), AXIN1(1), CCND2(1), CCND3(1), CTNNB1(8), DVL2(8), DVL3(2), FBXW2(2), FZD10(4), FZD2(2), FZD3(10), FZD6(3), FZD7(3), FZD8(1), GSK3B(7), LDLR(4), MAPK10(4), MAPK9(3), PAFAH1B1(3), PLAU(2), PPP2R5C(2), PPP2R5E(2), PRKCA(2), PRKCD(3), PRKCE(4), PRKCG(8), PRKCH(2), PRKCI(4), PRKCQ(4), PRKD1(10), RHOA(4), SFRP4(3), TCF7(3), WNT1(1), WNT10B(3), WNT11(3), WNT16(2), WNT2B(1), WNT3(4), WNT4(1), WNT5A(3), WNT7A(2), WNT7B(2)	13007053	263	129	225	48	68	34	3	45	79	34	<1.00e-15	<3.24e-14
3	HSA04110_CELL_CYCLE	Genes involved in cell cycle	ABL1, ANAPC1, ANAPC10, ANAPC11, ANAPC2, ANAPC4, ANAPC5, ANAPC7, ATM, ATR, BUB1, BUB1B, BUB3, CCNA1, CCNA2, CCNB1, CCNB2, CCNB3, CCND1, CCND2, CCND3, CCNE1, CCNE2, CCNH, CDC14A, CDC14B, CDC16, CDC2, CDC20, CDC23, CDC25A, CDC25B, CDC25C, CDC26, CDC27, CDC45L, CDC6, CDC7, CDK2, CDK4, CDK6, CDK7, CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B, CDKN2C, CDKN2D, CHEK1, CHEK2, CREBBP, CUL1, DBF4, E2F1, E2F2, E2F3, EP300, ESPL1, FZR1, GADD45A, GADD45B, GADD45G, GSK3B, hCG_1982709, HDAC1, HDAC2, LOC440917, LOC728919, MAD1L1, MAD2L1, MAD2L2, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MDM2, ORC1L, ORC2L, ORC3L, ORC4L, ORC5L, ORC6L, PCNA, PKMYT1, PLK1, PRKDC, PTTG1, PTTG2, RB1, RBL1, RBL2, RBX1, SFN, SKP1, SKP2, SMAD2, SMAD3, SMAD4, SMC1A, SMC1B, TFDP1, TGFB1, TGFB2, TGFB3, TP53, WEE1, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ	108	ABL1(4), ANAPC1(3), ANAPC10(2), ANAPC2(1), ANAPC4(1), ANAPC5(2), ANAPC7(4), ATM(27), ATR(13), BUB1(4), BUB1B(3), BUB3(2), CCNA1(4), CCNA2(3), CCNB1(2), CCNB2(2), CCNB3(4), CCND2(1), CCND3(1), CCNE1(3), CCNE2(1), CCNH(2), CDC14A(1), CDC14B(3), CDC16(3), CDC20(3), CDC23(6), CDC25A(2), CDC25B(5), CDC25C(3), CDC27(9), CDC7(2), CDK2(2), CDK4(2), CDK6(1), CDK7(1), CDKN1A(1), CDKN1B(1), CDKN2A(1), CDKN2C(1), CHEK1(1), CHEK2(1), CREBBP(21), CUL1(7), DBF4(2), E2F2(1), E2F3(1), EP300(13), ESPL1(8), GSK3B(7), HDAC1(2), HDAC2(2), MAD1L1(1), MAD2L1(1), MAD2L2(1), MCM3(1), MCM4(4), MCM5(3), MCM6(3), MCM7(2), MDM2(4), ORC1L(1), ORC3L(1), ORC4L(1), ORC5L(1), PCNA(2), PKMYT1(1), PLK1(6), PRKDC(13), PTTG1(1), RB1(4), RBL1(3), RBL2(8), SKP1(1), SKP2(1), SMAD2(11), SMAD3(6), SMAD4(21), SMC1A(10), SMC1B(4), TFDP1(4), TGFB1(1), TGFB2(5), TP53(77), WEE1(3), YWHAB(2), YWHAE(3), YWHAQ(1)	30252673	414	127	377	73	128	89	8	105	81	3	<1.00e-15	<3.24e-14
4	HSA04210_APOPTOSIS	Genes involved in apoptosis	AIFM1, AKT1, AKT2, AKT3, APAF1, ATM, BAD, BAX, BCL2, BCL2L1, BID, BIRC2, BIRC3, BIRC4, CAPN1, CAPN2, CASP10, CASP3, CASP6, CASP7, CASP8, CASP9, CFLAR, CHP, CHUK, CSF2RB, CYCS, DFFA, DFFB, ENDOG, FADD, FAS, FASLG, IKBKB, IKBKG, IL1A, IL1B, IL1R1, IL1RAP, IL3, IL3RA, IRAK1, IRAK2, IRAK3, IRAK4, MAP3K14, MYD88, NFKB1, NFKB2, NFKBIA, NGFB, NTRK1, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKACA, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, RELA, RIPK1, TNF, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFRSF1A, TNFSF10, TP53, TRADD, TRAF2	80	AIFM1(1), AKT1(2), AKT2(5), APAF1(7), ATM(27), BAD(1), BAX(1), BCL2(1), BCL2L1(1), BID(1), BIRC2(2), BIRC3(2), CAPN1(2), CAPN2(5), CASP10(2), CASP3(1), CASP6(1), CASP7(1), CASP8(11), CASP9(2), CFLAR(2), CHUK(4), CSF2RB(7), DFFA(2), DFFB(2), FASLG(1), IKBKB(2), IL1A(1), IL1R1(3), IL3(3), IRAK1(1), IRAK2(8), IRAK3(1), IRAK4(2), MAP3K14(2), MYD88(1), NFKB1(3), NFKB2(2), NTRK1(6), PIK3CA(33), PIK3CB(2), PIK3CD(2), PIK3CG(12), PIK3R1(5), PIK3R2(1), PIK3R5(1), PPP3CA(1), PPP3CB(4), PPP3CC(3), PPP3R1(1), PPP3R2(1), PRKACB(1), PRKACG(2), PRKAR1A(1), PRKAR1B(1), PRKAR2B(2), RELA(2), RIPK1(2), TNFRSF10A(3), TNFRSF10B(2), TNFRSF10C(6), TNFRSF1A(1), TNFSF10(1), TP53(77), TRADD(1), TRAF2(1)	18529387	298	127	250	48	91	71	6	74	55	1	<1.00e-15	<3.24e-14
5	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	32	ACVR1(3), APC(121), AXIN1(1), BMP10(2), BMP4(1), BMP5(4), BMP7(5), BMPR1A(4), BMPR2(7), CHRD(5), CTNNB1(8), GATA4(1), GSK3B(7), MAP3K7(2), MEF2C(7), MYL2(1), NKX2-5(1), NPPA(1), RFC1(10), TGFB1(1), TGFB2(5), TGFBR1(6), TGFBR2(7), TGFBR3(5), WNT1(1)	7996440	216	126	179	31	37	23	2	37	83	34	<1.00e-15	<3.24e-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	30	AKT1(2), AKT2(5), ANKRD6(5), APC(121), AXIN1(1), AXIN2(7), CER1(3), CSNK1A1(2), CTNNB1(8), DACT1(5), DKK1(3), DKK2(5), DKK3(2), DKK4(4), FSTL1(5), GSK3A(2), GSK3B(7), LRP1(14), MVP(4), NKD1(3), NKD2(1), PIN1(1), PSEN1(3), PTPRA(2), SENP2(2), SFRP1(2), WIF1(2)	8848505	221	126	184	33	52	22	4	32	77	34	<1.00e-15	<3.24e-14
7	GSK3PATHWAY	Bacterial lipopolysaccharide activates AKT to promote the survival and activation of macrophages and inhibits Gsk3-beta to promote beta-catenin accumulation in the nucleus.	AKT1, APC, AXIN1, CCND1, CD14, CTNNB1, DVL1, FZD1, GJA1, GNAI1, GSK3B, IRAK1, LBP, LEF1, LY96, MYD88, NFKB1, PDPK1, PIK3CA, PIK3R1, PPP2CA, PRKR, RELA, TIRAP, TLR4, TOLLIP, WNT1	26	AKT1(2), APC(121), AXIN1(1), CD14(1), CTNNB1(8), GJA1(3), GNAI1(3), GSK3B(7), IRAK1(1), LBP(1), LEF1(4), LY96(2), MYD88(1), NFKB1(3), PDPK1(1), PIK3CA(33), PIK3R1(5), PPP2CA(1), RELA(2), TIRAP(1), TLR4(7), TOLLIP(1), WNT1(1)	6608775	210	123	159	24	32	36	4	29	75	34	<1.00e-15	<3.24e-14
8	HSA04540_GAP_JUNCTION	Genes involved in gap junction	ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ADRB1, CDC2, CSNK1D, DRD1, DRD2, EDG2, EGF, EGFR, GJA1, GJD2, GNA11, GNAI1, GNAI2, GNAI3, GNAQ, GNAS, GRB2, GRM1, GRM5, GUCY1A2, GUCY1A3, GUCY1B3, GUCY2C, GUCY2D, GUCY2F, HRAS, HTR2A, HTR2B, HTR2C, ITPR1, ITPR2, ITPR3, KRAS, LOC643224, LOC654264, MAP2K1, MAP2K2, MAP2K5, MAP3K2, MAPK1, MAPK3, MAPK7, NPR1, NPR2, NRAS, PDGFA, PDGFB, PDGFC, PDGFD, PDGFRA, PDGFRB, PLCB1, PLCB2, PLCB3, PLCB4, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKG1, PRKG2, PRKX, PRKY, RAF1, SOS1, SOS2, SRC, TJP1, TUBA1A, TUBA1B, TUBA1C, TUBA3C, TUBA3D, TUBA3E, TUBA4A, TUBA8, TUBAL3, TUBB, TUBB1, TUBB2A, TUBB2B, TUBB2C, TUBB3, TUBB4, TUBB4Q, TUBB6, TUBB8	92	ADCY1(4), ADCY2(12), ADCY3(1), ADCY4(9), ADCY5(8), ADCY6(1), ADCY7(3), ADCY8(11), ADCY9(4), ADRB1(2), CSNK1D(3), DRD1(1), DRD2(3), EGF(3), EGFR(10), GJA1(3), GNA11(1), GNAI1(3), GNAQ(3), GNAS(6), GRB2(2), GRM1(9), GRM5(8), GUCY1A2(8), GUCY1A3(12), GUCY1B3(7), GUCY2C(7), GUCY2D(4), GUCY2F(7), HTR2A(2), HTR2B(1), HTR2C(6), ITPR1(11), ITPR2(12), ITPR3(11), KRAS(58), MAP2K1(3), MAP2K5(2), MAP3K2(2), MAPK1(2), MAPK3(2), MAPK7(3), NPR1(6), NPR2(9), NRAS(15), PDGFA(1), PDGFC(2), PDGFD(3), PDGFRA(13), PDGFRB(5), PLCB1(8), PLCB2(3), PLCB3(3), PLCB4(9), PRKACB(1), PRKACG(2), PRKCA(2), PRKCG(8), PRKG1(4), PRKG2(3), PRKX(2), RAF1(4), SOS1(5), SOS2(9), SRC(3), TJP1(5), TUBA3C(9), TUBA3D(2), TUBA3E(4), TUBA4A(1), TUBA8(1), TUBAL3(3), TUBB(1), TUBB1(2), TUBB2A(1), TUBB2B(3), TUBB3(1), TUBB4(2), TUBB4Q(2), TUBB6(3), TUBB8(2)	28826153	432	123	372	142	154	105	11	133	28	1	<1.00e-15	<3.24e-14
9	ST_MYOCYTE_AD_PATHWAY	Cardiac myocytes have a variety of adrenergic receptors that induce subtype-specific signaling effects.	ADRB1, AKT1, APC, ASAH1, BF, CAMP, CAV3, DAG1, DLG4, EPHB2, GAS, GNAI1, GNAQ, HTATIP, ITPR1, ITPR2, ITPR3, KCNJ3, KCNJ5, KCNJ9, MAPK1, PITX2, PLB, PTX1, PTX3, RAC1, RHO, RYR1	23	ADRB1(2), AKT1(2), APC(121), ASAH1(3), CAV3(2), DAG1(4), DLG4(2), EPHB2(7), GNAI1(3), GNAQ(3), ITPR1(11), ITPR2(12), ITPR3(11), KCNJ3(6), KCNJ5(3), KCNJ9(2), MAPK1(2), PITX2(2), PTX3(2), RHO(2), RYR1(19)	9853585	221	123	184	49	55	22	5	33	72	34	<1.00e-15	<3.24e-14
10	WNTPATHWAY	The Wnt glycoprotein binds to membrane-bound receptors such as Frizzled to activate a number of signaling pathways, including that of beta-catenin.	APC, AXIN1, BTRC, CCND1, CREBBP, CSNK1A1, CSNK1D, CSNK2A1, CTBP1, CTNNB1, DVL1, FRAT1, FZD1, GSK3B, HDAC1, MADH4, MAP3K7, MAP3K7IP1, MYC, NLK, PPARD, PPP2CA, TCF1, TLE1, WIF1, WNT1	22	APC(121), AXIN1(1), BTRC(2), CREBBP(21), CSNK1A1(2), CSNK1D(3), CSNK2A1(4), CTBP1(1), CTNNB1(8), GSK3B(7), HDAC1(2), MAP3K7(2), NLK(1), PPARD(1), PPP2CA(1), TLE1(1), WIF1(2), WNT1(1)	6371845	181	120	145	22	26	21	2	24	74	34	<1.00e-15	<3.24e-14

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