Stomach Adenocarcinoma: Mutation Analysis (MutSig)

Maintained by Dan DiCara (Broad Institute)

Overview

Introduction

This report serves to describe the mutational landscape and properties of a given individual set, as well as rank genes and genesets according to mutational significance. MutSig v1.5 was used to generate the results found in this report.

Working with individual set: STAD.

Number of patients in set: 133

Input

The input for this pipeline is a set of individuals with the following files associated for each:

1. An annotated .maf file describing the mutations called for the respective individual, and their properties.

2. A .wig file that contains information about the coverage of the sample.

Summary

Significantly mutated genes (q ≤ 0.1): 141

Mutations seen in COSMIC: 0

Significantly mutated genes in COSMIC territory: 0

Genes with clustered mutations (&le 3 aa apart): 2

Significantly mutated genesets: 151

Significantly mutated genesets: (excluding sig. mutated genes): 41

Results

Breakdown of Mutations by Type

Table 1. Get Full Table Table representing breakdown of mutations by type.

type	count
Frame_Shift_Del	2090
Frame_Shift_Ins	308
In_Frame_Del	142
In_Frame_Ins	18
Indel	78
Missense_Mutation	35920
Nonsense_Mutation	1639
Nonstop_Mutation	41
Silent	15189
Splice_Site	881
Translation_Start_Site	23
Total	56329

Breakdown of Mutation Rates by Category Type

Table 2. Get Full Table A breakdown of mutation rates per category discovered for this individual set.

category	n	N	rate	rate_per_mb	relative_rate
A->T	9314	1972774636	4.7e-06	4.7	0.46
C->(A/T)	14586	2075005485	7e-06	7	0.69
A->(C/G)	8804	1972774636	4.5e-06	4.5	0.44
C->G	3233	2075005485	1.6e-06	1.6	0.15
indel+null	5067	4047780254	1.3e-06	1.3	0.12
double_null	136	4047780254	3.4e-08	0.034	0.0033
Total	41140	4047780254	1e-05	10	1

Target Coverage for Each Individual

The x axis represents the samples. The y axis represents the exons, one row per exon, and they are sorted by average coverage across samples. For exons with exactly the same average coverage, they are sorted next by the %GC of the exon. (The secondary sort is especially useful for the zero-coverage exons at the bottom).

Figure 1.

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

Figure 2.

Significantly Mutated Genes

Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 141. Number of genes displayed: 35

rank	gene	description	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p	q
1	TP53	tumor protein p53	170506	56	52	43	2	8	18	6	2	20	2	<1.00e-15	<1.80e-11
2	CBWD1	COBW domain containing 1	149758	18	17	3	0	1	0	1	0	16	0	3.28e-14	2.09e-10
3	ACVR2A	activin A receptor, type IIA	210938	16	15	3	0	1	0	1	0	14	0	4.10e-14	2.09e-10
4	ARID1A	AT rich interactive domain 1A (SWI-like)	783104	27	23	26	1	2	4	1	1	13	6	4.63e-14	2.09e-10
5	RPL22	ribosomal protein L22	51471	10	10	1	0	0	0	0	0	10	0	4.66e-13	1.68e-09
6	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	437171	23	21	11	3	10	3	10	0	0	0	1.13e-11	3.38e-08
7	PGM5	phosphoglucomutase 5	197505	19	16	5	0	1	2	14	0	2	0	5.24e-11	1.35e-07
8	INO80E		77938	10	9	4	0	0	2	0	0	6	2	6.65e-09	0.000015
9	CDH1	cadherin 1, type 1, E-cadherin (epithelial)	338086	12	12	12	4	1	9	0	0	2	0	8.17e-09	0.000016
10	PREX2		686147	24	18	24	6	6	8	8	0	2	0	2.97e-08	0.000053
11	SOX1	SRY (sex determining region Y)-box 1	50540	6	6	6	1	0	3	1	0	2	0	3.34e-08	0.000055
12	RNF43	ring finger protein 43	308560	14	13	7	2	1	0	2	0	11	0	4.79e-08	0.000067
13	PCDH15	protocadherin 15	990584	20	20	20	3	4	3	8	1	4	0	4.84e-08	0.000067
14	CSMD3	CUB and Sushi multiple domains 3	1525510	41	30	40	10	9	8	15	5	4	0	5.17e-08	0.000067
15	TTN	titin	14715386	212	69	209	52	36	63	73	21	15	4	7.03e-08	0.000085
16	SPRYD5	SPRY domain containing 5	121296	8	8	6	0	1	0	1	1	5	0	1.50e-07	0.00017
17	FAT4	FAT tumor suppressor homolog 4 (Drosophila)	1996862	53	34	52	10	19	15	15	4	0	0	3.33e-07	0.00035
18	CSMD1	CUB and Sushi multiple domains 1	1372028	40	27	39	14	7	11	14	5	3	0	5.43e-07	0.00054
19	SPTA1	spectrin, alpha, erythrocytic 1 (elliptocytosis 2)	993244	22	20	22	3	5	8	6	1	2	0	9.36e-07	0.00089
20	CTNND2	catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)	458052	16	15	14	5	4	5	4	1	2	0	1.07e-06	0.00096
21	DCLK1	doublecortin-like kinase 1	295925	10	10	10	3	3	3	2	1	1	0	1.14e-06	0.00098
22	GRID1	glutamate receptor, ionotropic, delta 1	400463	14	14	14	1	3	5	3	1	2	0	1.91e-06	0.0016
23	FLG	filaggrin	1610364	34	26	31	7	4	18	5	4	3	0	2.28e-06	0.0018
24	HIST1H1B	histone cluster 1, H1b	91105	7	7	7	3	1	1	3	0	2	0	3.43e-06	0.0026
25	EDNRB	endothelin receptor type B	191520	10	10	9	2	2	4	1	0	3	0	3.76e-06	0.0027
26	PXDN	peroxidasin homolog (Drosophila)	558733	18	17	17	9	6	7	3	1	1	0	3.91e-06	0.0027
27	SULF1	sulfatase 1	358036	12	12	10	2	3	2	3	0	4	0	4.65e-06	0.0031
28	TUSC3	tumor suppressor candidate 3	144970	8	8	7	0	3	2	1	2	0	0	5.85e-06	0.0038
29	PHF2	PHD finger protein 2	376523	12	12	3	3	1	0	1	0	10	0	6.67e-06	0.0041
30	ASTN2	astrotactin 2	490238	18	15	18	1	4	5	7	0	2	0	7.20e-06	0.0043
31	LRP1B	low density lipoprotein-related protein 1B (deleted in tumors)	1883812	37	29	36	10	10	6	13	2	4	2	7.74e-06	0.0045
32	DDI1	DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)	158935	9	9	9	3	3	4	2	0	0	0	9.32e-06	0.0053
33	PXDNL	peroxidasin homolog (Drosophila)-like	530803	18	16	18	4	6	9	1	1	1	0	0.000011	0.0061
34	KCNH8	potassium voltage-gated channel, subfamily H (eag-related), member 8	450604	12	12	12	3	2	0	4	4	2	0	0.000012	0.0061
35	OR4C16	olfactory receptor, family 4, subfamily C, member 16	124621	7	7	6	1	1	1	1	4	0	0	0.000012	0.0061

Note:

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: A->T .

n2 - number of nonsilent mutations of type: C->(A/T) .

n3 - number of nonsilent mutations of type: A->(C/G) .

n4 - number of nonsilent mutations of type: C->G .

n5 - number of nonsilent mutations of type: indel+null .

null - mutation category that includes nonsense, frameshift, splice-site mutations

p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene

p_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene

p = p-value (overall)

q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

COSMIC analyses

In this analysis, COSMIC is used as a filter to increase power by restricting the territory of each gene. Cosmic version: v48.

Table 4. Get Full Table Significantly mutated genes (COSMIC territory only). To access the database please go to: COSMIC. Number of significant genes found: 0. Number of genes displayed: 10

rank	gene	description	n	p	q
1	A4GNT	alpha-1,4-N-acetylglucosaminyltransferase	3	1	1
2	AACS	acetoacetyl-CoA synthetase	2	1	1
3	ABCA9	ATP-binding cassette, sub-family A (ABC1), member 9	8	1	1
4	ABCC10	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	3	1	1
5	ABCF2	ATP-binding cassette, sub-family F (GCN20), member 2	2	1	1
6	ABHD2	abhydrolase domain containing 2	0	1	1
7	ABHD4	abhydrolase domain containing 4	2	1	1
8	ACADS	acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain	0	1	1
9	ACOT11	acyl-CoA thioesterase 11	2	1	1
10	ACRBP	acrosin binding protein	2	1	1

Note:

n - number of (nonsilent) mutations in this gene across the individual set.

cos = number of unique mutated sites in this gene in COSMIC

n_cos = overlap between n and cos.

N_cos = number of individuals times cos.

cos_ev = total evidence: number of reports in COSMIC for mutations seen in this gene.

p = p-value for seeing the observed amount of overlap in this gene)

q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

Clustered Mutations

Table 5. Get Full Table Genes with Clustered Mutations

num	gene	desc	n	mindist	npairs3	npairs12
11845	TRANK1		14	0	1	3
9996	SCN10A	sodium channel, voltage-gated, type X, alpha subunit	7	0	1	1
4112	FER1L6	fer-1-like 6 (C. elegans)	9	3	0	1
55	ABCC9	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	20	4	0	1
6885	MGEA5	meningioma expressed antigen 5 (hyaluronidase)	6	5	0	1
10764	SORCS1	sortilin-related VPS10 domain containing receptor 1	8	5	0	1
8544	PHRF1		7	6	0	1
3785	F13A1	coagulation factor XIII, A1 polypeptide	8	11	0	1
11137	SYNE1	spectrin repeat containing, nuclear envelope 1	54	13	0	0
4564	GLDC	glycine dehydrogenase (decarboxylating)	5	25	0	0

Note:

n - number of mutations in this gene in the individual set.

mindist - distance (in aa) between closest pair of mutations in this gene

npairs3 - how many pairs of mutations are within 3 aa of each other.

npairs12 - how many pairs of mutations are within 12 aa of each other.

Geneset Analyses

Table 6. Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 151. 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	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(1), ATM(16), BUB1(6), BUB1B(1), BUB3(1), CCNA1(2), CCNA2(1), CCNB1(1), CCNB2(1), CCNB3(3), CCND2(1), CCND3(2), CCNE2(1), CCNH(2), CDAN1(4), CDC14A(4), CDC20(2), CDC25A(2), CDC25B(4), CDC25C(2), CDC6(2), CDC7(2), CDH1(12), CDK2(2), CDKN1A(1), CDKN2A(2), CHEK1(2), CHEK2(3), DTX4(3), E2F5(1), EP300(10), ESPL1(5), GSK3B(1), HDAC1(2), HDAC2(3), HDAC3(3), HDAC4(6), HDAC5(3), HDAC6(3), HDAC8(3), MAD1L1(4), MAD2L2(1), MCM2(9), MCM3(3), MCM4(4), MCM5(3), MCM6(1), MCM7(3), MDM2(2), MPEG1(4), ORC1L(9), ORC2L(1), ORC3L(4), ORC4L(2), ORC6L(1), PCNA(2), PLK1(4), PRKDC(18), PTPRA(4), RB1(6), RBL1(3), SKP2(2), SMAD4(5), TBC1D8(4), TGFB1(2), TP53(56), WEE1(1)	22527407	284	93	267	74	45	101	55	16	63	4	<1.00e-15	<1.44e-13
2	ARFPATHWAY	Cyclin-dependent kinase inhibitor 2A is a tumor suppressor that induces G1 arrest and can activate the p53 pathway, leading to G2/M arrest.	ABL1, CDKN2A, E2F1, MDM2, MYC, PIK3CA, PIK3R1, POLR1A, POLR1B, POLR1C, POLR1D, RAC1, RB1, TBX2, TP53, TWIST1	16	ABL1(1), CDKN2A(2), MDM2(2), PIK3CA(23), PIK3R1(5), POLR1A(7), POLR1B(2), POLR1C(2), POLR1D(1), RB1(6), TBX2(3), TP53(56)	4062884	110	76	84	17	25	30	23	3	27	2	<1.00e-15	<1.44e-13
3	APOPTOSIS_GENMAPP		APAF1, BAK1, BCL2L7P1, BAX, BCL2, BCL2L1, BID, BIRC2, BIRC3, BIRC4, CASP2, CASP3, CASP6, CASP7, CASP8, CASP9, CYCS, FADD, FAS, FASLG, GZMB, IKBKG, JUN, MAP2K4, MAP3K1, MAP3K14, MAPK10, MCL1, MDM2, MYC, NFKB1, NFKBIA, PARP1, PRF1, RELA, RIPK1, TNF, TNFRSF1A, TNFRSF1B, TNFSF10, TP53, TRADD, TRAF1, TRAF2	41	APAF1(2), BAK1(1), BID(1), BIRC2(1), BIRC3(3), CASP2(2), CASP3(1), CASP7(2), CASP8(3), CASP9(1), CYCS(1), FAS(1), JUN(2), MAP2K4(5), MAP3K1(5), MAP3K14(1), MAPK10(3), MDM2(2), NFKB1(4), PARP1(4), PRF1(1), RELA(2), TNF(1), TNFRSF1A(3), TNFSF10(2), TP53(56), TRAF2(2)	7658938	112	74	99	21	22	38	16	5	29	2	<1.00e-15	<1.44e-13
4	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	AKT1(2), EGFR(7), IGF1R(11), POLR2A(6), PPP2CA(1), RB1(6), TEP1(10), TERF1(1), TERT(3), TNKS(5), TP53(56), XRCC5(2)	5739615	110	65	96	33	22	35	21	4	26	2	<1.00e-15	<1.44e-13
5	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(1), AKT3(3), APAF1(2), ATM(16), BAD(1), BID(1), BIRC2(1), BIRC3(3), CAPN1(1), CAPN2(3), CASP10(2), CASP3(1), CASP7(2), CASP8(3), CASP9(1), CSF2RB(5), CYCS(1), DFFA(2), DFFB(2), ENDOG(1), FAS(1), IKBKB(3), IL1B(1), IL1R1(2), IL1RAP(3), IL3(1), IRAK1(4), IRAK2(4), IRAK3(2), IRAK4(1), MAP3K14(1), MYD88(2), NFKB1(4), NFKB2(2), NTRK1(3), PIK3CA(23), PIK3CB(4), PIK3CD(6), PIK3CG(9), PIK3R1(5), PIK3R2(3), PIK3R3(1), PIK3R5(4), PPP3CA(2), PPP3CB(1), PPP3R2(1), PRKACA(1), PRKACB(2), PRKACG(2), PRKAR1A(2), PRKAR2A(1), PRKAR2B(5), RELA(2), TNF(1), TNFRSF10A(2), TNFRSF10B(1), TNFRSF10C(1), TNFRSF10D(2), TNFRSF1A(3), TNFSF10(2), TP53(56), TRAF2(2)	16869188	233	92	206	53	54	79	46	12	38	4	1.78e-15	1.44e-13
6	CHEMICALPATHWAY	DNA damage promotes Bid cleavage, which stimulates mitochondrial cytochrome c release and consequent caspase activation, resulting in apoptosis.	ADPRT, AKT1, APAF1, ATM, BAD, BAX, BCL2, BCL2L1, BID, CASP3, CASP6, CASP7, CASP9, CYCS, EIF2S1, PRKCA, PRKCB1, PTK2, PXN, STAT1, TLN1, TP53	20	AKT1(2), APAF1(2), ATM(16), BAD(1), BID(1), CASP3(1), CASP7(2), CASP9(1), CYCS(1), EIF2S1(1), PTK2(5), PXN(2), STAT1(3), TLN1(9), TP53(56)	5572700	103	67	89	15	21	32	19	3	24	4	1.78e-15	1.44e-13
7	TERTPATHWAY	hTERC, the RNA subunit of telomerase, and hTERT, the catalytic protein subunit, are required for telomerase activity and are overexpressed in many cancers.	HDAC1, MAX, MYC, SP1, SP3, TP53, WT1, ZNF42	7	HDAC1(2), SP1(2), SP3(2), TP53(56), WT1(1)	1415785	63	54	50	9	10	19	9	2	21	2	2.33e-15	1.44e-13
8	ST_JNK_MAPK_PATHWAY	JNKs are MAP kinases regulated by several levels of kinases (MAPKK, MAPKKK) and phosphorylate transcription factors and regulatory proteins.	AKT1, ATF2, CDC42, DLD, DUSP10, DUSP4, DUSP8, GAB1, GADD45A, GCK, IL1R1, JUN, MAP2K4, MAP2K5, MAP2K7, MAP3K1, MAP3K10, MAP3K11, MAP3K12, MAP3K13, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K7, MAP3K7IP1, MAP3K7IP2, MAP3K9, MAPK10, MAPK7, MAPK8, MAPK9, MYEF2, NFATC3, NR2C2, PAPPA, SHC1, TP53, TRAF6, ZAK	38	AKT1(2), CDC42(1), DLD(2), DUSP10(2), DUSP8(1), GCK(2), IL1R1(2), JUN(2), MAP2K4(5), MAP2K5(1), MAP2K7(8), MAP3K1(5), MAP3K10(5), MAP3K11(3), MAP3K12(3), MAP3K13(2), MAP3K2(2), MAP3K3(1), MAP3K4(5), MAP3K7(7), MAP3K9(3), MAPK10(3), MAPK7(8), MAPK8(4), MAPK9(1), MYEF2(3), NFATC3(3), NR2C2(3), PAPPA(12), SHC1(3), TP53(56), TRAF6(3), ZAK(2)	10285023	165	76	152	37	29	65	22	9	38	2	2.44e-15	1.44e-13
9	ATRBRCAPATHWAY	BRCA1 and 2 block cell cycle progression in response to DNA damage and promote double-stranded break repair; mutations induce breast cancer susceptibility.	ATM, ATR, BRCA1, BRCA2, CHEK1, CHEK2, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, HUS1, MRE11A, NBS1, RAD1, RAD17, RAD50, RAD51, RAD9A, TP53, TREX1	21	ATM(16), ATR(5), BRCA1(6), BRCA2(14), CHEK1(2), CHEK2(3), FANCC(2), FANCD2(6), FANCF(1), FANCG(3), HUS1(1), MRE11A(2), RAD1(1), RAD50(6), RAD51(1), RAD9A(1), TP53(56)	8856603	126	72	112	16	21	36	31	4	30	4	2.66e-15	1.44e-13
10	G2PATHWAY	Activated Cdc2-cyclin B kinase regulates the G2/M transition; DNA damage stimulates the DNA-PK/ATM/ATR kinases, which inactivate Cdc2.	ATM, ATR, BRCA1, CCNB1, CDC2, CDC25A, CDC25B, CDC25C, CDC34, CDKN1A, CDKN2D, CHEK1, CHEK2, EP300, GADD45A, MDM2, MYT1, PLK, PRKDC, RPS6KA1, TP53, WEE1, YWHAH, YWHAQ	22	ATM(16), ATR(5), BRCA1(6), CCNB1(1), CDC25A(2), CDC25B(4), CDC25C(2), CDC34(1), CDKN1A(1), CDKN2D(1), CHEK1(2), CHEK2(3), EP300(10), MDM2(2), PRKDC(18), RPS6KA1(2), TP53(56), WEE1(1), YWHAQ(2)	8663886	135	76	121	19	20	43	26	4	38	4	3.22e-15	1.44e-13

Table 7. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 41. 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	CALCIUM_REGULATION_IN_CARDIAC_CELLS		ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ADRA1A, ADRA1B, ADRA1D, ADRB1, ADRB2, ADRB3, ANXA6, ARRB1, ARRB2, ATP1A4, ATP1B1, ATP1B2, ATP1B3, ATP2A2, ATP2A3, ATP2B1, ATP2B2, ATP2B3, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1S, CACNB1, CACNB3, CALM1, CALM2, CALM3, CALR, CAMK1, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CAMK4, CASQ1, CASQ2, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, FXYD2, GJA1, GJA12, GJA4, GJA5, GJB1, GJB2, GJB3, GJB4, GJB5, GJB6, GNA11, GNAI2, GNAI3, GNAO1, GNAQ, GNAZ, GNB1, GNB2, GNB3, GNB4, GNB5, GNG12, GNG13, GNG2, GNG3, GNG4, GNG5, GNG7, GNGT1, GRK4, GRK5, GRK6, ITPR1, ITPR2, ITPR3, KCNB1, KCNJ3, KCNJ5, MGC11266, MYCBP, NME7, PEA15, PKIA, PKIB, PKIG, PLCB3, PLN, PRKACA, PRKACB, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCQ, PRKCZ, PRKD1, RGS1, RGS10, RGS11, RGS14, RGS16, RGS17, RGS18, RGS19, RGS2, RGS20, RGS3, RGS4, RGS5, RGS6, RGS7, RGS9, RYR1, RYR2, RYR3, SARA1, SFN, SLC8A1, SLC8A3, USP5, YWHAB, YWHAH, YWHAQ, YWHAQ, MIB1	139	ADCY1(9), ADCY2(5), ADCY3(2), ADCY4(4), ADCY5(7), ADCY6(5), ADCY7(8), ADCY8(8), ADCY9(4), ADRA1A(4), ADRA1B(2), ADRA1D(1), ADRB1(2), ADRB2(2), ADRB3(1), ANXA6(2), ARRB1(3), ARRB2(2), ATP1A4(5), ATP1B3(1), ATP2A2(4), ATP2A3(3), ATP2B1(8), ATP2B2(7), ATP2B3(7), CACNA1A(9), CACNA1B(1), CACNA1C(17), CACNA1D(12), CACNA1E(16), CACNA1S(9), CACNB1(1), CALM1(1), CALM2(2), CALM3(1), CALR(4), CAMK1(1), CAMK2A(1), CAMK2B(2), CAMK2G(3), CAMK4(2), CASQ1(2), CASQ2(1), CHRM1(1), CHRM2(6), CHRM3(4), CHRM4(1), CHRM5(3), GJA1(7), GJA4(4), GJB3(2), GJB6(2), GNA11(1), GNAI2(3), GNAI3(3), GNAQ(1), GNAZ(5), GNB1(1), GNB2(3), GNB3(1), GNB4(3), GNG12(1), GNG7(2), GNGT1(2), GRK4(1), GRK5(1), ITPR1(13), ITPR2(12), ITPR3(10), KCNB1(3), KCNJ3(3), MIB1(1), NME7(1), PLCB3(6), PRKACA(1), PRKACB(2), PRKAR1A(2), PRKAR2A(1), PRKAR2B(5), PRKCD(2), PRKCE(3), PRKCG(4), PRKCH(2), PRKCQ(1), PRKD1(5), RGS10(2), RGS11(1), RGS14(1), RGS16(2), RGS17(1), RGS18(3), RGS2(1), RGS20(2), RGS3(7), RGS5(1), RGS6(6), RGS7(1), RGS9(2), RYR1(24), RYR2(31), RYR3(27), SLC8A1(3), SLC8A3(5), USP5(3), YWHAQ(2)	38763648	451	94	446	177	124	148	91	35	53	0	8.8e-13	5.4e-10
2	HSA04020_CALCIUM_SIGNALING_PATHWAY	Genes involved in calcium signaling pathway	ADCY1, ADCY2, ADCY3, ADCY4, ADCY7, ADCY8, ADCY9, ADORA2A, ADORA2B, ADRA1A, ADRA1B, ADRA1D, ADRB1, ADRB2, ADRB3, AGTR1, ATP2A1, ATP2A2, ATP2A3, ATP2B1, ATP2B2, ATP2B3, ATP2B4, AVPR1A, AVPR1B, BDKRB1, BDKRB2, BST1, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1F, CACNA1G, CACNA1H, CACNA1I, CACNA1S, CALM1, CALM2, CALM3, CALML3, CALML6, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CAMK4, CCKAR, CCKBR, CD38, CHP, CHRM1, CHRM2, CHRM3, CHRM5, CHRNA7, CYSLTR1, CYSLTR2, DRD1, EDNRA, EDNRB, EGFR, ERBB2, ERBB3, ERBB4, F2R, GNA11, GNA14, GNA15, GNAL, GNAQ, GNAS, GRIN1, GRIN2A, GRIN2C, GRIN2D, GRM1, GRM5, GRPR, HRH1, HRH2, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, ITPKA, ITPKB, ITPR1, ITPR2, ITPR3, LHCGR, LTB4R2, MLCK, MYLK, MYLK2, NOS1, NOS2A, NOS3, NTSR1, OXTR, P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX7, P2RXL1, PDE1A, PDE1B, PDE1C, PDGFRA, PDGFRB, PHKA1, PHKA2, PHKB, PHKG1, PHKG2, PLCB1, PLCB2, PLCB3, PLCB4, PLCD1, PLCD3, PLCD4, PLCE1, PLCG1, PLCG2, PLCZ1, PLN, PPID, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PTAFR, PTGER1, PTGER3, PTGFR, PTK2B, RYR1, RYR2, RYR3, SLC25A4, SLC25A5, SLC25A6, SLC8A1, SLC8A2, SLC8A3, SPHK1, SPHK2, TACR1, TACR2, TACR3, TBXA2R, TNNC1, TNNC2, TRHR, TRPC1, VDAC1, VDAC2, VDAC3	166	ADCY1(9), ADCY2(5), ADCY3(2), ADCY4(4), ADCY7(8), ADCY8(8), ADCY9(4), ADORA2B(1), ADRA1A(4), ADRA1B(2), ADRA1D(1), ADRB1(2), ADRB2(2), ADRB3(1), AGTR1(1), ATP2A1(3), ATP2A2(4), ATP2A3(3), ATP2B1(8), ATP2B2(7), ATP2B3(7), ATP2B4(1), AVPR1A(5), AVPR1B(1), BDKRB1(1), BDKRB2(2), CACNA1A(9), CACNA1B(1), CACNA1C(17), CACNA1D(12), CACNA1E(16), CACNA1F(2), CACNA1G(10), CACNA1H(10), CACNA1I(7), CACNA1S(9), CALM1(1), CALM2(2), CALM3(1), CAMK2A(1), CAMK2B(2), CAMK2G(3), CAMK4(2), CCKAR(2), CCKBR(3), CD38(2), CHRM1(1), CHRM2(6), CHRM3(4), CHRM5(3), CHRNA7(1), CYSLTR1(2), DRD1(2), EDNRA(2), EGFR(7), ERBB2(4), ERBB3(12), ERBB4(12), F2R(2), GNA11(1), GNA14(1), GNA15(2), GNAQ(1), GNAS(12), GRIN1(3), GRIN2A(7), GRIN2C(2), GRIN2D(1), GRM1(11), GRM5(11), GRPR(3), HRH1(3), HRH2(2), HTR2A(1), HTR2B(4), HTR2C(2), HTR4(3), HTR5A(2), HTR7(3), ITPKA(1), ITPKB(4), ITPR1(13), ITPR2(12), ITPR3(10), LHCGR(5), LTB4R2(2), MYLK(7), MYLK2(2), NOS1(15), NOS3(2), NTSR1(1), OXTR(3), P2RX3(1), P2RX4(1), P2RX5(2), PDE1A(2), PDE1B(1), PDE1C(2), PDGFRA(2), PDGFRB(5), PHKA1(4), PHKA2(4), PHKB(3), PHKG1(2), PHKG2(2), PLCB1(8), PLCB2(3), PLCB3(6), PLCB4(6), PLCD3(5), PLCE1(7), PLCG1(9), PLCG2(5), PLCZ1(2), PPID(1), PPP3CA(2), PPP3CB(1), PPP3R2(1), PRKACA(1), PRKACB(2), PRKACG(2), PRKCG(4), PRKX(1), PTAFR(2), PTGER3(2), PTGFR(3), PTK2B(8), RYR1(24), RYR2(31), RYR3(27), SLC25A4(1), SLC25A5(2), SLC8A1(3), SLC8A2(3), SLC8A3(5), SPHK1(4), TACR1(2), TACR2(1), TACR3(4), TNNC1(2), TNNC2(1), TRHR(5), TRPC1(2), VDAC1(1)	55532421	648	97	638	230	179	225	126	50	64	4	2.9e-09	9e-07
3	SMOOTH_MUSCLE_CONTRACTION		ACTA1, ACTA2, ACTC, ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ADM, ADMR, ARRB1, ARRB2, ATF1, ATF2, ATF3, ATF4, ATF5, ATP2A2, ATP2A3, CACNB3, CALCA, CALM1, CALM2, CALM3, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CMKOR1, CNN1, CNN2, CORIN, CREB3, CREBL1, CREBL1, TNXB, CRH, CRHR1, DGKZ, EDG2, ETS2, FOS, GABPA, GABPB2, GBA2, GJA1, GNAQ, GNB1, GNB2, GNB3, GNB4, GNB5, GNG12, GNG13, GNG2, GNG3, GNG4, GNG5, GNG7, GNGT1, GRK4, GRK5, GRK6, GSTO1, GUCA2A, GUCA2B, GUCY1A3, HEAB, IGFBP1, IGFBP2, IGFBP3, IGFBP4, IGFBP6, IL1B, IL6, ITPR1, ITPR2, ITPR3, JUN, LGR7, LGR8, MAFF, MGC11266, MYL2, MYL4, MYLK2, NFKB1, NOS1, NOS3, OXT, OXTR, PDE4B, PDE4D, PKIA, PKIB, PKIG, PLCB3, PLCD1, PLCG1, PLCG2, PRKACA, PRKACB, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCH, PRKCQ, PRKCZ, PRKD1, RAMP1, RAMP2, RAMP3, RCP9, RGS1, RGS10, RGS11, RGS14, RGS16, RGS17, RGS18, RGS19, RGS2, RGS20, RGS3, RGS4, RGS5, RGS6, RGS7, RGS9, RLN1, RYR1, RYR2, RYR3, SARA1, SFN, SLC8A1, SP1, USP5, YWHAB, YWHAH, YWHAQ, YWHAQ, MIB1	138	ACTA1(1), ACTA2(5), ADCY1(9), ADCY2(5), ADCY3(2), ADCY4(4), ADCY5(7), ADCY6(5), ADCY7(8), ADCY8(8), ADCY9(4), ARRB1(3), ARRB2(2), ATF5(3), ATP2A2(4), ATP2A3(3), CALCA(1), CALM1(1), CALM2(2), CALM3(1), CAMK2A(1), CAMK2B(2), CAMK2G(3), CNN1(1), CORIN(4), CREB3(3), CRHR1(1), DGKZ(1), ETS2(1), GABPA(1), GABPB2(1), GBA2(2), GJA1(7), GNAQ(1), GNB1(1), GNB2(3), GNB3(1), GNB4(3), GNG12(1), GNG7(2), GNGT1(2), GRK4(1), GRK5(1), GUCA2A(1), GUCY1A3(7), IGFBP1(2), IGFBP2(1), IGFBP3(4), IL1B(1), IL6(1), ITPR1(13), ITPR2(12), ITPR3(10), JUN(2), MIB1(1), MYL2(1), MYL4(1), MYLK2(2), NFKB1(4), NOS1(15), NOS3(2), OXT(2), OXTR(3), PDE4B(4), PLCB3(6), PLCG1(9), PLCG2(5), PRKACA(1), PRKACB(2), PRKAR1A(2), PRKAR2A(1), PRKAR2B(5), PRKCD(2), PRKCE(3), PRKCH(2), PRKCQ(1), PRKD1(5), RAMP2(1), RAMP3(3), RGS10(2), RGS11(1), RGS14(1), RGS16(2), RGS17(1), RGS18(3), RGS2(1), RGS20(2), RGS3(7), RGS5(1), RGS6(6), RGS7(1), RGS9(2), RYR1(24), RYR2(31), RYR3(27), SLC8A1(3), SP1(2), TNXB(20), USP5(3), YWHAQ(2)	35609952	401	88	397	159	121	126	78	34	42	0	5.5e-08	0.000011
4	HSA04510_FOCAL_ADHESION	Genes involved in focal adhesion	ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, ARHGAP5, BAD, BCAR1, BCL2, BIRC2, BIRC3, BIRC4, BRAF, CAPN2, CAV1, CAV2, CAV3, CCND1, CCND2, CCND3, CDC42, CHAD, COL11A1, COL11A2, COL1A1, COL1A2, COL2A1, COL3A1, COL4A1, COL4A2, COL4A4, COL4A6, COL5A1, COL5A2, COL5A3, COL6A1, COL6A2, COL6A3, COL6A6, COMP, CRK, CRKL, CTNNB1, DIAPH1, DOCK1, EGF, EGFR, ELK1, ERBB2, FARP2, FIGF, FLNA, FLNB, FLNC, FLT1, FN1, FYN, GRB2, GRLF1, GSK3B, HGF, HRAS, IBSP, IGF1, IGF1R, ILK, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAV, ITGB1, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, JUN, KDR, LAMA1, LAMA2, LAMA3, LAMA4, LAMA5, LAMB1, LAMB2, LAMB3, LAMB4, LAMC1, LAMC2, LAMC3, LOC653852, MAP2K1, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MET, MLCK, MRCL3, MRLC2, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLK, MYLK2, MYLPF, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PARVA, PARVB, PARVG, PDGFA, PDGFB, PDGFC, PDGFD, PDGFRA, PDGFRB, PDPK1, PGF, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIP5K1C, PPP1CA, PPP1CB, PPP1CC, PPP1R12A, PRKCA, PRKCB1, PRKCG, PTEN, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, RAP1A, RAP1B, RAPGEF1, RELN, RHOA, ROCK1, ROCK2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SPP1, SRC, THBS1, THBS2, THBS3, THBS4, TLN1, TLN2, TNC, TNN, TNR, TNXB, VASP, VAV1, VAV2, VAV3, VCL, VEGFA, VEGFB, VEGFC, VTN, VWF, ZYX	191	ACTB(3), ACTN1(2), ACTN2(11), ACTN3(1), ACTN4(1), AKT1(2), AKT2(1), AKT3(3), ARHGAP5(6), BAD(1), BCAR1(3), BIRC2(1), BIRC3(3), BRAF(5), CAPN2(3), CAV1(2), CCND2(1), CCND3(2), CDC42(1), CHAD(3), COL11A1(12), COL11A2(5), COL1A1(6), COL1A2(13), COL2A1(7), COL3A1(6), COL4A1(5), COL4A2(4), COL4A4(4), COL4A6(5), COL5A1(7), COL5A2(4), COL5A3(5), COL6A3(15), COL6A6(15), COMP(1), CRK(1), CTNNB1(8), DIAPH1(3), DOCK1(10), EGF(4), EGFR(7), ELK1(2), ERBB2(4), FARP2(2), FLNA(5), FLNB(3), FLNC(18), FLT1(5), FN1(15), FYN(3), GRB2(1), GRLF1(8), GSK3B(1), HGF(7), IBSP(1), IGF1(2), IGF1R(11), ITGA1(4), ITGA10(4), ITGA11(5), ITGA2(3), ITGA2B(5), ITGA3(6), ITGA4(7), ITGA5(4), ITGA6(2), ITGA7(5), ITGA8(3), ITGA9(6), ITGAV(2), ITGB1(2), ITGB3(5), ITGB4(10), ITGB5(2), ITGB7(2), ITGB8(6), JUN(2), KDR(7), LAMA1(14), LAMA2(11), LAMA3(8), LAMA4(7), LAMA5(13), LAMB1(5), LAMB2(10), LAMB3(11), LAMB4(6), LAMC1(5), LAMC2(6), LAMC3(9), MAP2K1(3), MAPK1(2), MAPK10(3), MAPK3(1), MAPK8(4), MAPK9(1), MET(3), MYL2(1), MYLK(7), MYLK2(2), PAK1(2), PAK2(3), PAK3(1), PAK4(2), PAK6(3), PAK7(2), PARVA(1), PARVB(3), PARVG(2), PDGFA(1), PDGFB(3), PDGFC(2), PDGFD(3), PDGFRA(2), PDGFRB(5), PDPK1(1), PIK3CB(4), PIK3CD(6), PIK3CG(9), PIK3R1(5), PIK3R2(3), PIK3R3(1), PIK3R5(4), PIP5K1C(5), PPP1CA(2), PPP1CB(1), PPP1CC(2), PPP1R12A(1), PRKCG(4), PTEN(5), PTK2(5), PXN(2), RAC2(1), RAF1(6), RAP1A(1), RAP1B(2), RAPGEF1(6), RELN(15), RHOA(4), ROCK1(5), ROCK2(2), SHC1(3), SHC2(2), SHC3(3), SHC4(1), SOS1(3), SOS2(4), THBS1(5), THBS2(6), THBS3(2), THBS4(2), TLN1(9), TLN2(11), TNC(11), TNN(10), TNR(9), TNXB(20), VASP(2), VAV1(2), VAV2(5), VAV3(6), VCL(2), VEGFC(3), VTN(4), VWF(8), ZYX(2)	75526843	786	106	779	351	220	270	137	64	93	2	9.9e-07	0.00015
5	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	200	ABI2(3), ACTN1(2), ACTN2(11), ACTN3(1), ACTN4(1), APC(18), APC2(4), ARAF(6), ARHGEF1(1), ARHGEF12(5), ARHGEF4(4), ARHGEF6(8), ARHGEF7(7), ARPC1A(1), ARPC1B(1), ARPC4(1), BCAR1(3), BDKRB1(1), BDKRB2(2), BRAF(5), CD14(1), CDC42(1), CFL1(1), CHRM1(1), CHRM2(6), CHRM3(4), CHRM4(1), CHRM5(3), CRK(1), CSK(2), CYFIP1(2), CYFIP2(8), DIAPH1(3), DIAPH2(3), DIAPH3(10), DOCK1(10), EGF(4), EGFR(7), F2(4), F2R(2), FGD1(4), FGD3(5), FGF1(2), FGF10(4), FGF11(1), FGF12(3), FGF13(3), FGF14(3), FGF17(2), FGF18(2), FGF2(1), FGF20(1), FGF23(1), FGF5(1), FGF6(3), FGF7(1), FGF9(4), FGFR1(6), FGFR2(5), FGFR3(1), FGFR4(5), FN1(15), GIT1(2), GNA12(1), GNG12(1), GRLF1(8), GSN(4), IQGAP1(3), IQGAP2(5), IQGAP3(5), ITGA1(4), ITGA10(4), ITGA11(5), ITGA2(3), ITGA2B(5), ITGA3(6), ITGA4(7), ITGA5(4), ITGA6(2), ITGA7(5), ITGA8(3), ITGA9(6), ITGAD(3), ITGAE(4), ITGAL(6), ITGAM(4), ITGAV(2), ITGAX(5), ITGB1(2), ITGB2(5), ITGB3(5), ITGB4(10), ITGB5(2), ITGB7(2), ITGB8(6), LIMK1(2), LIMK2(3), MAP2K1(3), MAP2K2(1), MAPK1(2), MAPK3(1), MOS(3), MSN(3), MYH10(13), MYH14(8), MYH9(13), MYL2(1), MYLK(7), MYLK2(2), NCKAP1(4), NCKAP1L(7), PAK1(2), PAK2(3), PAK3(1), PAK4(2), PAK6(3), PAK7(2), PDGFA(1), PDGFB(3), PDGFRA(2), PDGFRB(5), PFN2(2), PIK3CB(4), PIK3CD(6), PIK3CG(9), PIK3R1(5), PIK3R2(3), PIK3R3(1), PIK3R5(4), PIP4K2A(3), PIP4K2B(2), PIP4K2C(1), PIP5K1A(2), PIP5K1C(5), PPP1CA(2), PPP1CB(1), PPP1CC(2), PPP1R12A(1), PPP1R12B(2), PTK2(5), PXN(2), RAC2(1), RAF1(6), RDX(1), RHOA(4), ROCK1(5), ROCK2(2), RRAS(1), RRAS2(1), SCIN(2), SLC9A1(4), SOS1(3), SOS2(4), SSH1(4), SSH2(10), SSH3(2), TIAM1(11), TIAM2(15), TMSL3(1), VAV1(2), VAV2(5), VAV3(6), VCL(2), WASF1(3), WASF2(2), WASL(1)	56277620	628	103	620	240	165	213	120	44	84	2	2.6e-06	0.00032
6	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(18), AXIN1(8), BMP10(2), BMP2(2), BMP4(5), BMP5(5), BMP7(2), BMPR1A(1), BMPR2(9), CHRD(1), CTNNB1(8), DVL1(3), FZD1(7), GATA4(2), GSK3B(1), MAP3K7(7), MEF2C(1), MYL2(1), NKX2-5(2), NPPB(1), RFC1(1), TGFB1(2), TGFB2(4), TGFB3(3), TGFBR1(1), TGFBR2(4), TGFBR3(1), WNT1(3)	7311941	108	49	104	36	30	27	24	5	16	6	8.4e-06	0.00086
7	HSA04730_LONG_TERM_DEPRESSION	Genes involved in long-term depression	ARAF, BRAF, C7orf16, CACNA1A, CRH, CRHR1, GNA11, GNA12, GNA13, GNAI1, GNAI2, GNAI3, GNAO1, GNAQ, GNAS, GNAZ, GRIA1, GRIA2, GRIA3, GRID2, GRM1, GRM5, GUCY1A2, GUCY1A3, GUCY1B3, GUCY2C, GUCY2D, GUCY2F, HRAS, IGF1, IGF1R, ITPR1, ITPR2, ITPR3, KRAS, LYN, MAP2K1, MAP2K2, MAPK1, MAPK3, NOS1, NOS2A, NOS3, NPR1, NPR2, NRAS, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PLCB1, PLCB2, PLCB3, PLCB4, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PRKCA, PRKCB1, PRKCG, PRKG1, PRKG2, RAF1, RYR1	73	ARAF(6), BRAF(5), CACNA1A(9), CRHR1(1), GNA11(1), GNA12(1), GNAI1(1), GNAI2(3), GNAI3(3), GNAQ(1), GNAS(12), GNAZ(5), GRIA1(6), GRIA2(8), GRIA3(5), GRID2(7), GRM1(11), GRM5(11), GUCY1A2(3), GUCY1A3(7), GUCY1B3(4), GUCY2C(1), GUCY2D(5), GUCY2F(5), IGF1(2), IGF1R(11), ITPR1(13), ITPR2(12), ITPR3(10), LYN(2), MAP2K1(3), MAP2K2(1), MAPK1(2), MAPK3(1), NOS1(15), NOS3(2), NPR1(6), NPR2(2), PLA2G10(1), PLA2G12A(1), PLA2G12B(2), PLA2G2D(1), PLA2G3(5), PLA2G4A(3), PLA2G6(3), PLCB1(8), PLCB2(3), PLCB3(6), PLCB4(6), PPP2CA(1), PPP2R1A(3), PPP2R1B(3), PPP2R2A(1), PPP2R2B(2), PPP2R2C(2), PRKCG(4), PRKG1(4), PRKG2(6), RAF1(6), RYR1(24)	22546825	298	75	296	97	65	127	61	20	25	0	0.000015	0.0013
8	NO1PATHWAY	Shear stress in endothelial cells increases cytoplasmic calcium, which activates nitric oxide synthase III to release NO, which in turn regulates cardiac contractions.	ACTA1, AKT1, BDK, BDKRB2, CALM1, CALM2, CALM3, CAV1, CHRM1, CHRNA1, FLT1, FLT4, HSPCA, KDR, NOS3, PDE2A, PDE3A, PDE3B, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKG1, PRKG2, RYR2, SLC7A1, SYT1, TNNI1, VEGF	28	ACTA1(1), AKT1(2), BDKRB2(2), CALM1(1), CALM2(2), CALM3(1), CAV1(2), CHRM1(1), CHRNA1(3), FLT1(5), FLT4(6), KDR(7), NOS3(2), PDE2A(6), PDE3A(3), PDE3B(9), PRKACB(2), PRKACG(2), PRKAR1A(2), PRKAR2A(1), PRKAR2B(5), PRKG1(4), PRKG2(6), RYR2(31), SLC7A1(1)	8335775	107	59	107	37	30	36	27	11	3	0	0.000016	0.0013
9	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	24	AKT1(2), APC(18), AXIN1(8), CD14(1), CTNNB1(8), DVL1(3), FZD1(7), GJA1(7), GNAI1(1), GSK3B(1), IRAK1(4), LEF1(3), LY96(1), MYD88(2), NFKB1(4), PDPK1(1), PIK3R1(5), PPP2CA(1), RELA(2), TIRAP(1), TOLLIP(1), WNT1(3)	5370673	84	45	82	27	19	25	16	4	16	4	2e-05	0.0014
10	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(18), AXIN1(8), CREBBP(11), CTNNB1(8), DVL1(3), EP300(10), FZD1(7), GSK3B(1), HDAC1(2), LDB1(4), LEF1(3), PITX2(2), TRRAP(19), WNT1(3)	6582968	99	49	97	41	34	27	11	4	19	4	0.000023	0.0014

Methods & Data

Methods

In brief, we tabulate the number of mutations and the number of covered bases for each gene. The counts are broken down by mutation context category: four context categories that are discovered by MutSig, and one for indel and 'null' mutations, which include indels, nonsense mutations, splice-site mutations, and non-stop (read-through) mutations. For each gene, we calculate the probability of seeing the observed constellation of mutations, i.e. the product P1 x P2 x ... x Pm, or a more extreme one, given the background mutation rates calculated across the dataset.[1]

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 � 615 (2011)