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

Colon/Rectal 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/C1V122TH

- Overview

+ Introduction

- Summary

MAF used for this analysis:COADREAD-TP.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 20
Mutations seen in COSMIC: 739
Significantly mutated genes in COSMIC territory: 29
Significantly mutated genesets: 146

Mutation Preprocessing

Read 140 MAFs of type "Broad"
Read 88 MAFs of type "Baylor-SOLiD"
Total number of mutations in input MAFs: 91973
After removing 1369 invalidated mutations: 90604
After removing 1176 noncoding mutations: 89428
After collapsing adjacent/redundant mutations: 82149

Mutation Filtering

Number of mutations before filtering: 82149
After removing 855 mutations outside gene set: 81294
After removing 343 mutations outside category set: 80951
After removing 11 "impossible" mutations in
gene-patient-category bins of zero coverage: 79742

- Results

+ Breakdown of Mutations by Type

type	count
De_novo_Start_InFrame	20
De_novo_Start_OutOfFrame	156
Frame_Shift_Del	1289
Frame_Shift_Ins	810
In_Frame_Del	166
In_Frame_Ins	26
Missense_Mutation	54081
Nonsense_Mutation	5053
Nonstop_Mutation	36
Read-through	10
Silent	19116
Splice_Site	186
Translation_Start_Site	2
Total	80951

+ Breakdown of Mutation Rates by Category Type

category	n	N	rate	rate_per_mb	relative_rate
*CpG->T	20381	335477044	0.000061	61	6
*Cp(A/C/T)->mut	21021	2775898083	7.6e-06	7.6	0.75
A->mut	12112	3017613932	4e-06	4	0.4
*CpG->(G/A)	562	335477044	1.7e-06	1.7	0.17
indel+null	7447	6128989199	1.2e-06	1.2	0.12
double_null	304	6128989199	5e-08	0.05	0.0049
Total	61827	6128989199	1e-05	10	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: 20. 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	1891000	187	160	128	4	6	15	11	0	103	52	0.98	0	3.2e-15	0	0
2	FBXW7	F-box and WD repeat domain containing 7	577918	45	38	28	2	23	6	5	2	9	0	0.052	0.000048	4.1e-15	0	0
3	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	131263	20	20	8	0	2	14	4	0	0	0	0.16	0.000061	1.5e-14	0	0
4	BRAF	v-raf murine sarcoma viral oncogene homolog B1	493213	23	22	4	0	0	0	23	0	0	0	0	0	5.5e-06	0	0
5	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	158010	96	96	11	0	0	91	4	0	1	0	0.0014	0	5.6e-15	0	0
6	TP53	tumor protein p53	267736	122	120	69	2	48	22	12	2	38	0	0	0	2.7e-15	0	0
7	SMAD4	SMAD family member 4	377497	29	26	22	0	10	6	9	0	3	1	0.0024	0.0022	5.9e-14	4.9e-15	1.3e-11
8	FAM123B	family with sequence similarity 123B	641973	27	25	24	2	1	3	4	0	19	0	0.85	0.019	1.6e-12	9.7e-13	2.2e-09
9	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	618889	40	33	21	2	6	20	14	0	0	0	0.00015	2e-06	3.5e-08	2.2e-12	4.3e-09
10	SMAD2	SMAD family member 2	322425	16	15	12	1	3	5	3	0	5	0	0.18	0.02	1.2e-07	4.7e-08	0.000085
11	TCF7L2	transcription factor 7-like 2 (T-cell specific, HMG-box)	400503	20	18	18	4	5	5	3	0	7	0	0.21	0.022	2e-07	9.2e-08	0.00015
12	ACVR2A	activin A receptor, type IIA	354442	10	9	9	1	0	0	4	0	5	1	0.011	0.018	5.5e-07	2e-07	0.00029
13	SOX9	SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal)	256689	10	10	10	0	0	0	1	0	8	1	0.48	0.07	2.2e-07	2.9e-07	0.0004
14	ELF3	E74-like factor 3 (ets domain transcription factor, epithelial-specific )	238851	6	6	5	0	0	0	1	0	5	0	0.34	0.015	2e-06	5.4e-07	0.0007
15	CRTC1	CREB regulated transcription coactivator 1	348788	6	6	3	1	1	0	0	0	5	0	0.059	0.0013	0.0004	7.9e-06	0.0095
16	TNFRSF10C	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	167178	6	6	2	0	0	6	0	0	0	0	1	0.000071	0.012	0.000012	0.014
17	KRTAP5-5	keratin associated protein 5-5	119310	4	4	1	1	0	0	0	4	0	0	0.000048	0.000048	0.029	2e-05	0.021
18	KIAA1804		532518	18	15	16	0	8	7	1	0	2	0	0.017	0.0091	0.0002	0.000025	0.025
19	ACOT4	acyl-CoA thioesterase 4	215425	3	3	2	1	0	0	0	0	2	1	0.026	0.00041	0.015	0.000078	0.074
20	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	260038	10	7	8	1	3	2	1	0	3	1	0.0065	0.012	0.00067	0.0001	0.09
21	MYO1B	myosin IB	774252	15	13	14	2	1	3	4	0	5	2	0.96	0.044	0.00025	0.00014	0.12
22	PCBP1	poly(rC) binding protein 1	176357	6	6	3	0	0	0	6	0	0	0	0.0035	0.0003	0.12	0.0004	0.32
23	GGT1	gamma-glutamyltransferase 1	245492	3	3	1	1	0	3	0	0	0	0	0.000053	0.000038	0.96	0.00041	0.32
24	CDC27	cell division cycle 27 homolog (S. cerevisiae)	510134	13	10	9	6	3	1	6	0	3	0	0.97	0.079	0.00052	0.00046	0.34
25	CCDC160	coiled-coil domain containing 160	85540	9	7	9	0	0	4	0	1	3	1	0.38	0.87	0.000048	0.00046	0.34
26	ACVR1B	activin A receptor, type IB	339499	15	14	15	0	4	7	2	0	2	0	0.00093	0.0044	0.015	0.0007	0.48
27	DKK2	dickkopf homolog 2 (Xenopus laevis)	176618	6	6	5	1	6	0	0	0	0	0	0.13	0.00039	0.18	0.00076	0.5
28	FAM116A	family with sequence similarity 116, member A	387395	6	6	6	0	2	1	1	0	2	0	0.071	0.0026	0.029	0.00077	0.5
29	SAT1	spermidine/spermine N1-acetyltransferase 1	111639	4	4	2	0	0	0	1	0	3	0	NaN	NaN	0.0011	0.0011	0.7
30	B2M	beta-2-microglobulin	82419	6	5	5	0	0	1	2	0	2	1	0.49	1	0.00011	0.0011	0.7
31	HTR3B	5-hydroxytryptamine (serotonin) receptor 3B	304904	6	6	5	1	4	2	0	0	0	0	0.00022	0.0013	0.09	0.0012	0.7
32	LOXL2	lysyl oxidase-like 2	481795	10	9	10	2	7	1	1	0	1	0	0.87	0.002	0.065	0.0013	0.72
33	ZNF593	zinc finger protein 593	41786	4	4	4	0	1	1	0	0	2	0	0.66	1	0.00022	0.0021	1
34	KLK2	kallikrein-related peptidase 2	182657	3	3	1	1	0	3	0	0	0	0	0.27	0.0005	0.54	0.0025	1
35	MGC26647	chromosome 7 open reading frame 62	169881	7	7	7	0	1	2	1	0	3	0	0.79	0.21	0.0013	0.0025	1

+ COSMIC analyses

rank	gene	description	n	cos	n_cos	N_cos	cos_ev	p	q
1	APC	adenomatous polyposis coli	187	839	137	187936	2584	0	0
2	TP53	tumor protein p53	122	824	122	184576	45406	0	0
3	ERBB3	v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian)	14	6	6	1344	6	7.9e-14	1.2e-10
4	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	20	33	18	7392	17998	3.7e-13	4.1e-10
5	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	96	52	95	11648	1013913	5.5e-13	5e-10
6	BRAF	v-raf murine sarcoma viral oncogene homolog B1	23	89	20	19936	287480	8.7e-13	5.7e-10
7	FBXW7	F-box and WD repeat domain containing 7	45	91	31	20384	1228	8.9e-13	5.7e-10
8	KRTAP5-5	keratin associated protein 5-5	4	1	4	224	4	1.1e-12	6e-10
9	SMAD4	SMAD family member 4	29	159	19	35616	90	1.3e-12	6.7e-10
10	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	40	220	34	49280	13256	1.6e-12	7.2e-10

+ 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: 146. 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(187), APC2(1), AXIN1(2), AXIN2(9), BTRC(5), CACYBP(2), CAMK2A(1), CAMK2B(2), CAMK2D(3), CAMK2G(2), CCND2(1), CCND3(1), CER1(3), CHD8(6), CREBBP(25), CSNK1A1(2), CSNK1A1L(5), CSNK2A1(4), CSNK2A2(2), CSNK2B(2), CTBP1(1), CTBP2(2), CTNNB1(12), CTNNBIP1(1), CUL1(8), CXXC4(1), DAAM1(2), DAAM2(9), DKK1(5), DKK2(6), DKK4(7), DVL2(9), DVL3(4), EP300(15), FBXW11(8), FZD1(1), FZD10(6), FZD2(2), FZD3(13), FZD4(2), FZD6(6), FZD7(3), FZD8(1), GSK3B(8), LEF1(4), LRP5(5), LRP6(17), MAP3K7(4), MAPK10(8), MAPK8(7), MAPK9(5), MMP7(5), NFAT5(5), NFATC1(2), NFATC2(5), NFATC3(5), NFATC4(5), NKD1(3), NKD2(1), NLK(1), PLCB1(8), PLCB2(3), PLCB3(4), PLCB4(10), PORCN(2), PPARD(2), PPP2CA(1), PPP2CB(2), PPP2R1A(4), PPP2R1B(2), PPP2R2A(1), PPP2R2B(3), PPP2R2C(4), PPP3CA(3), PPP3CB(5), PPP3CC(4), PPP3R1(1), PPP3R2(1), PRICKLE1(11), PRICKLE2(6), PRKACA(1), PRKACB(1), PRKACG(3), PRKCA(4), PRKCG(10), PRKX(2), PSEN1(3), RBX1(1), RHOA(5), ROCK1(15), ROCK2(6), RUVBL1(8), SENP2(3), SFRP1(3), SFRP2(3), SFRP4(4), SFRP5(1), SIAH1(1), SKP1(1), SMAD2(16), SMAD3(9), SMAD4(29), SOX17(2), TBL1X(6), TBL1XR1(6), TBL1Y(1), TCF7(6), TCF7L1(3), TCF7L2(20), TP53(122), VANGL1(2), VANGL2(5), WIF1(2), WNT1(1), WNT10B(4), WNT11(3), WNT16(2), WNT2(1), WNT2B(3), WNT3(4), WNT3A(1), WNT4(1), WNT5A(3), WNT6(1), WNT7A(2), WNT7B(2), WNT8A(2), WNT9A(2), WNT9B(2)	50774791	894	218	758	156	275	204	133	8	221	53	<1.00e-15	<4.11e-14
2	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(5), ACTN2(8), ACTN3(3), ACTN4(3), APC(187), APC2(1), ARAF(3), ARHGEF1(5), ARHGEF12(9), ARHGEF4(4), ARHGEF6(10), ARHGEF7(8), ARPC1A(5), ARPC1B(2), ARPC2(2), ARPC5(1), ARPC5L(2), BAIAP2(1), BDKRB2(3), BRAF(23), CD14(1), CDC42(1), CFL1(1), CHRM1(3), CHRM2(11), CHRM3(4), CHRM4(1), CHRM5(2), CRKL(2), CSK(3), CYFIP1(6), CYFIP2(5), DIAPH1(1), DIAPH2(12), DIAPH3(5), DOCK1(7), EGF(3), EGFR(11), EZR(2), F2(3), FGD1(8), FGD3(2), FGF1(2), FGF11(3), FGF12(3), FGF13(3), FGF14(5), FGF17(1), FGF19(1), FGF20(2), FGF21(1), FGF23(1), FGF3(1), FGF5(4), FGF6(3), FGF7(1), FGF8(1), FGF9(1), FGFR1(4), FGFR2(6), FGFR3(2), FGFR4(2), FN1(21), GIT1(3), GNA12(2), GNA13(2), GRLF1(12), IQGAP1(13), IQGAP2(12), IQGAP3(11), ITGA1(3), ITGA10(7), ITGA11(4), ITGA2(6), ITGA2B(4), ITGA3(4), ITGA4(8), ITGA5(7), ITGA6(4), ITGA7(6), ITGA8(8), ITGA9(6), ITGAD(8), ITGAE(7), ITGAL(8), ITGAM(8), ITGAV(5), ITGAX(6), ITGB1(6), ITGB2(5), ITGB3(9), ITGB4(3), ITGB5(6), ITGB6(6), ITGB7(4), ITGB8(5), KRAS(96), LIMK1(5), LIMK2(5), MAP2K1(4), MAP2K2(1), MAPK1(2), MAPK3(3), MOS(3), MRAS(1), MSN(6), MYH10(10), MYH14(12), MYH9(12), MYL2(1), MYL7(1), MYL9(2), MYLK(14), MYLK2(3), NCKAP1(9), NCKAP1L(11), NRAS(20), PAK1(5), PAK2(3), PAK3(5), PAK6(1), PAK7(7), PDGFA(1), PDGFRA(17), PDGFRB(6), PFN2(1), PFN4(1), PIK3CA(40), PIK3CB(2), PIK3CD(3), PIK3CG(14), PIK3R1(10), PIK3R2(1), PIK3R3(4), PIK3R5(1), PIP4K2A(2), PIP4K2B(2), PIP4K2C(3), PIP5K1A(3), PIP5K1B(2), PIP5K1C(4), PPP1CB(2), PPP1CC(2), PPP1R12A(3), PPP1R12B(9), PTK2(5), RAF1(6), RDX(3), RHOA(5), ROCK1(15), ROCK2(6), RRAS2(2), SCIN(3), SLC9A1(4), SOS1(7), SOS2(11), SSH1(6), SSH2(4), SSH3(1), TIAM1(17), TIAM2(16), TMSL3(1), VAV1(13), VAV2(4), VAV3(12), VCL(2), WAS(1), WASF1(3), WASF2(2), WASL(7)	87387370	1187	216	982	278	334	392	203	8	194	56	<1.00e-15	<4.11e-14
3	ST_ADRENERGIC	Adrenergic receptors respond to epinephrine and norepinephrine signaling.	AKT1, APC, AR, ASAH1, BF, BRAF, CAMP, CCL13, CCL15, CCL16, DAG1, EGFR, GAS, GNA11, GNA15, GNAI1, GNAQ, ITPKA, ITPKB, ITPR1, ITPR2, ITPR3, KCNJ3, KCNJ5, KCNJ9, MAPK1, MAPK10, MAPK14, PHKA2, PIK3CA, PIK3CD, PIK3R1, PITX2, PTX1, PTX3, RAF1, SRC	34	AKT1(2), APC(187), AR(6), ASAH1(3), BRAF(23), CCL13(1), CCL15(1), DAG1(5), EGFR(11), GNA11(1), GNA15(3), GNAI1(4), GNAQ(4), ITPKB(4), ITPR1(19), ITPR2(18), ITPR3(12), KCNJ3(6), KCNJ5(4), KCNJ9(3), MAPK1(2), MAPK10(8), MAPK14(3), PHKA2(6), PIK3CA(40), PIK3CD(3), PIK3R1(10), PITX2(2), PTX3(2), RAF1(6), SRC(3)	16590615	402	191	303	61	77	74	76	0	120	55	<1.00e-15	<4.11e-14
4	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(6), AKT3(1), ANKRD6(5), APC(187), AXIN1(2), AXIN2(9), CER1(3), CSNK1A1(2), CTNNB1(12), DACT1(6), DKK1(5), DKK2(6), DKK3(2), DKK4(7), FSTL1(6), GSK3A(2), GSK3B(8), LRP1(17), MVP(4), NKD1(3), NKD2(1), PIN1(1), PSEN1(3), PTPRA(2), SENP2(3), SFRP1(3), TSHB(1), WIF1(2)	12642186	311	185	249	37	60	43	39	1	116	52	<1.00e-15	<4.11e-14
5	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(187), AXIN1(2), CD14(1), CTNNB1(12), FZD1(1), GJA1(7), GNAI1(4), GSK3B(8), IRAK1(1), LBP(1), LEF1(4), LY96(2), MYD88(2), NFKB1(6), PDPK1(1), PIK3CA(40), PIK3R1(10), PPP2CA(1), RELA(2), TIRAP(1), TLR4(10), TOLLIP(1), WNT1(1)	9451888	307	183	228	28	44	50	43	1	115	54	<1.00e-15	<4.11e-14
6	PITX2PATHWAY	The bicoid-related transcription factor Pitx2 is activated by Wnt binding to the Frizzled receptor and induces tissue-specific cell proliferation.	APC, AXIN1, CREBBP, CTNNB1, DVL1, EP300, FZD1, GSK3B, HDAC1, HTATIP, LDB1, LEF1, PITX2, PPARBP, TRRAP, WNT1	14	APC(187), AXIN1(2), CREBBP(25), CTNNB1(12), EP300(15), FZD1(1), GSK3B(8), HDAC1(2), LDB1(5), LEF1(4), PITX2(2), TRRAP(21), WNT1(1)	10494881	285	180	225	29	46	36	32	2	117	52	<1.00e-15	<4.11e-14
7	CELL_CYCLE_KEGG		ABL1, ASK, ATM, BUB1, BUB1B, BUB3, CCNA1, CCNA2, CCNB1, CCNB2, CCNB3, CCND2, CCND3, CCNE1, CCNE2, CCNH, CDAN1, CDC14A, CDC14B, CDC14B, CDC14C, CDC2, CDC20, CDC25A, CDC25B, CDC25C, CDC45L, CDC6, CDC7, CDH1, CDK2, CDK4, CDKN1A, CDKN2A, CHEK1, CHEK2, DTX4, E2F1, E2F2, E2F3, E2F4, E2F5, E2F6, EP300, ESPL1, FLJ14001, GADD45A, GSK3B, HDAC1, HDAC2, HDAC3, HDAC4, HDAC5, HDAC6, HDAC7A, HDAC8, MAD1L1, MAD2L1, MAD2L2, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MDM2, MPEG1, MPL, ORC1L, ORC2L, ORC3L, ORC4L, ORC5L, ORC6L, PCNA, PLK1, PRKDC, PTPRA, PTTG1, PTTG2, PTTG3, RB1, RBL1, SKP2, SMAD4, SMC1L1, TBC1D8, TFDP1, TGFB1, TP53, WEE1	82	ABL1(4), ATM(37), BUB1(6), BUB1B(6), BUB3(2), CCNA1(6), CCNA2(3), CCNB1(2), CCNB2(2), CCNB3(7), CCND2(1), CCND3(1), CCNE1(3), CCNE2(2), CCNH(2), CDAN1(3), CDC14A(4), CDC14B(4), CDC20(3), CDC25A(2), CDC25B(5), CDC25C(4), CDC6(1), CDC7(3), CDH1(5), CDK2(2), CDK4(3), CDKN1A(1), CDKN2A(1), CHEK1(1), CHEK2(1), DTX4(3), E2F2(1), E2F3(2), E2F4(1), E2F5(2), EP300(15), ESPL1(8), GSK3B(8), HDAC1(2), HDAC2(2), HDAC3(2), HDAC4(5), HDAC5(2), HDAC6(6), MAD1L1(2), MAD2L1(1), MAD2L2(1), MCM3(3), MCM4(4), MCM5(6), MCM6(4), MCM7(3), MDM2(4), MPEG1(4), MPL(2), ORC1L(1), ORC3L(1), ORC4L(1), ORC5L(1), PCNA(3), PLK1(8), PRKDC(18), PTPRA(2), PTTG1(1), RB1(7), RBL1(5), SKP2(1), SMAD4(29), TBC1D8(5), TFDP1(4), TGFB1(1), TP53(122), WEE1(3)	34828727	433	178	369	75	131	122	88	8	80	4	<1.00e-15	<4.11e-14
8	HSA04012_ERBB_SIGNALING_PATHWAY	Genes involved in ErbB signaling pathway	ABL1, ABL2, AKT1, AKT2, AKT3, ARAF, AREG, BAD, BRAF, BTC, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CBL, CBLB, CBLC, CDKN1A, CDKN1B, CRK, CRKL, EGF, EGFR, EIF4EBP1, ELK1, ERBB2, ERBB3, ERBB4, EREG, FRAP1, GAB1, GRB2, GSK3B, HBEGF, HRAS, JUN, KRAS, MAP2K1, MAP2K2, MAP2K4, MAP2K7, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MYC, NCK1, NCK2, NRAS, NRG1, NRG2, NRG3, NRG4, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLCG1, PLCG2, PRKCA, PRKCB1, PRKCG, PTK2, RAF1, RPS6KB1, RPS6KB2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SRC, STAT5A, STAT5B, TGFA	85	ABL1(4), ABL2(7), AKT1(2), AKT2(6), AKT3(1), ARAF(3), BAD(1), BRAF(23), BTC(2), CAMK2A(1), CAMK2B(2), CAMK2D(3), CAMK2G(2), CBL(5), CBLB(8), CDKN1A(1), CDKN1B(3), CRKL(2), EGF(3), EGFR(11), ERBB2(10), ERBB3(14), ERBB4(21), EREG(1), GAB1(6), GRB2(3), GSK3B(8), HBEGF(1), KRAS(96), MAP2K1(4), MAP2K2(1), MAP2K4(11), MAPK1(2), MAPK10(8), MAPK3(3), MAPK8(7), MAPK9(5), NCK1(1), NRAS(20), NRG1(15), NRG2(6), NRG3(7), NRG4(1), PAK1(5), PAK2(3), PAK3(5), PAK6(1), PAK7(7), PIK3CA(40), PIK3CB(2), PIK3CD(3), PIK3CG(14), PIK3R1(10), PIK3R2(1), PIK3R3(4), PIK3R5(1), PLCG1(4), PLCG2(13), PRKCA(4), PRKCG(10), PTK2(5), RAF1(6), RPS6KB1(3), RPS6KB2(2), SHC1(3), SHC2(1), SHC3(1), SHC4(5), SOS1(7), SOS2(11), SRC(3), STAT5B(3)	33296728	518	175	369	98	118	227	115	5	51	2	<1.00e-15	<4.11e-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(187), CDH1(5), CREBBP(25), EP300(15), MAP2K1(4), MAP3K7(4), MAPK3(3), SKIL(1), TGFB1(1), TGFB2(9), TGFBR1(9), TGFBR2(7)	8403558	270	175	210	25	34	35	30	1	118	52	<1.00e-15	<4.11e-14
10	HSA04662_B_CELL_RECEPTOR_SIGNALING_PATHWAY	Genes involved in B cell receptor signaling pathway	AKT1, AKT2, AKT3, BCL10, BLNK, BTK, CARD11, CD19, CD22, CD72, CD79A, CD79B, CD81, CHP, CHUK, CR2, FCGR2B, FOS, GSK3B, HRAS, IFITM1, IKBKB, IKBKG, INPP5D, JUN, KRAS, LILRB3, LYN, MALT1, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NFKB1, NFKB2, NFKBIA, NFKBIB, NFKBIE, NRAS, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLCG2, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKCB1, PTPN6, RAC1, RAC2, RAC3, RASGRP3, SYK, VAV1, VAV2, VAV3	62	AKT1(2), AKT2(6), AKT3(1), BCL10(3), BLNK(1), BTK(7), CARD11(9), CD19(3), CD22(10), CD72(4), CD79A(3), CD79B(1), CHUK(6), CR2(11), FOS(1), GSK3B(8), IFITM1(1), IKBKB(4), INPP5D(4), KRAS(96), LILRB3(2), LYN(4), MALT1(7), NFAT5(5), NFATC1(2), NFATC2(5), NFATC3(5), NFATC4(5), NFKB1(6), NFKB2(4), NFKBIB(1), NFKBIE(2), NRAS(20), PIK3CA(40), PIK3CB(2), PIK3CD(3), PIK3CG(14), PIK3R1(10), PIK3R2(1), PIK3R3(4), PIK3R5(1), PLCG2(13), PPP3CA(3), PPP3CB(5), PPP3CC(4), PPP3R1(1), PPP3R2(1), PTPN6(4), RASGRP3(7), SYK(3), VAV1(13), VAV2(4), VAV3(12)	23448894	394	157	272	64	111	195	57	1	28	2	<1.00e-15	<4.11e-14

+ Methods & Data

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