Uterine Corpus Endometrioid Carcinoma: 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: UCEC.

Number of patients in set: 239

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): 240

Mutations seen in COSMIC: 1

Significantly mutated genes in COSMIC territory: 0

Genes with clustered mutations (&le 3 aa apart): 21

Significantly mutated genesets: 217

Significantly mutated genesets: (excluding sig. mutated genes): 50

Results

Breakdown of Mutations by Type

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

type	count
Frame_Shift_Del	2848
Frame_Shift_Ins	1040
In_Frame_Del	204
In_Frame_Ins	28
Indel	2
Missense_Mutation	112137
Nonsense_Mutation	11196
Nonstop_Mutation	160
Silent	36723
Splice_Site	2821
Total	167159

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	34661	3330542914	1e-05	10	0.53
C->(A/T)	52348	3324649891	0.000016	16	0.8
A->(C/G)	18461	3330542914	5.5e-06	5.5	0.28
C->G	6658	3324649891	2e-06	2	0.1
indel+null	16724	6655193044	2.5e-06	2.5	0.13
double_null	1584	6655193044	2.4e-07	0.24	0.012
Total	130436	6655193044	2e-05	20	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: 240. Number of genes displayed: 35

rank	gene	description	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p	q
1	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	298272	198	150	121	5	17	12	54	5	90	20	<1.00e-15	<1.73e-11
2	ARID1A	AT rich interactive domain 1A (SWI-like)	1385483	109	86	85	5	5	7	3	2	68	24	8.66e-15	7.48e-11
3	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	168973	29	29	5	0	19	0	10	0	0	0	4.03e-14	9.78e-11
4	RPL22	ribosomal protein L22	92493	15	14	5	0	0	1	0	2	10	2	4.46e-14	9.78e-11
5	TP53	tumor protein p53	313329	40	36	30	2	12	9	4	3	12	0	4.50e-14	9.78e-11
6	ARID5B	AT rich interactive domain 5B (MRF1-like)	862073	36	29	32	8	7	8	4	3	12	2	4.64e-14	9.78e-11
7	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	785593	138	110	61	2	49	31	44	8	6	0	4.93e-14	9.78e-11
8	PIK3R1	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	565235	67	52	55	2	3	6	13	3	31	11	5.05e-14	9.78e-11
9	CTNNB1	catenin (cadherin-associated protein), beta 1, 88kDa	574078	66	63	21	5	11	35	8	12	0	0	5.30e-14	9.78e-11
10	CTCF	CCCTC-binding factor (zinc finger protein)	531536	55	48	40	1	3	9	5	1	33	4	5.66e-14	9.78e-11
11	PPP2R1A	protein phosphatase 2 (formerly 2A), regulatory subunit A , alpha isoform	417772	27	24	20	3	6	15	1	3	2	0	3.19e-13	5.00e-10
12	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome)	644344	27	25	15	2	2	9	5	10	1	0	1.65e-12	2.38e-09
13	MLL4		1092469	53	35	50	8	11	18	8	2	14	0	2.61e-12	3.47e-09
14	MUC5B	mucin 5B, oligomeric mucus/gel-forming	1730599	78	46	77	35	13	45	9	3	8	0	1.03e-11	1.27e-08
15	FBXW7	F-box and WD repeat domain containing 7	617576	34	24	28	2	5	15	1	2	9	2	2.16e-11	2.49e-08
16	BCOR	BCL6 co-repressor	1215076	52	38	41	10	6	27	14	1	4	0	2.61e-11	2.82e-08
17	SPOP	speckle-type POZ protein	277479	19	18	15	0	11	1	2	2	3	0	5.06e-11	5.14e-08
18	RNF43	ring finger protein 43	567386	22	22	15	2	1	7	0	0	14	0	1.00e-10	9.60e-08
19	ZFHX3	zinc finger homeobox 3	2606295	80	45	75	11	16	33	5	2	18	6	1.30e-09	1.18e-06
20	RB1	retinoblastoma 1 (including osteosarcoma)	658206	31	25	30	4	7	7	6	1	6	4	3.39e-09	2.93e-06
21	RASA1	RAS p21 protein activator (GTPase activating protein) 1	689993	29	22	27	2	6	6	3	1	11	2	1.00e-07	0.000082
22	CCND1	cyclin D1	118783	10	10	9	1	3	3	1	1	2	0	1.66e-07	0.00013
23	PCGF3	polycomb group ring finger 3	92971	10	10	8	1	1	6	0	0	3	0	2.87e-07	0.00022
24	PXDN	peroxidasin homolog (Drosophila)	790612	43	27	41	8	9	19	3	3	7	2	3.38e-07	0.00024
25	SMTNL2	smoothelin-like 2	152004	9	9	3	2	1	1	0	0	7	0	3.44e-07	0.00024
26	ETV3	ets variant gene 3	106116	12	11	12	0	3	2	5	0	2	0	5.05e-07	0.00034
27	NFASC	neurofascin homolog (chicken)	983246	33	27	33	3	10	13	4	1	3	2	6.96e-07	0.00044
28	CSMD3	CUB and Sushi multiple domains 3	2741330	106	40	101	20	33	37	15	5	7	9	7.14e-07	0.00044
29	DCC	deleted in colorectal carcinoma	1065940	35	27	34	3	11	14	3	2	5	0	1.86e-06	0.0011
30	INPPL1	inositol polyphosphate phosphatase-like 1	794914	23	19	20	7	4	6	2	0	9	2	2.15e-06	0.0012
31	CHD3	chromodomain helicase DNA binding protein 3	1425157	39	30	35	5	10	12	7	1	9	0	2.17e-06	0.0012
32	MUC4	mucin 4, cell surface associated	1204082	43	29	42	17	9	20	5	5	4	0	3.14e-06	0.0017
33	CNTN6	contactin 6	758825	36	24	34	7	8	14	4	2	8	0	3.78e-06	0.0019
34	LRCH2	leucine-rich repeats and calponin homology (CH) domain containing 2	355871	23	19	22	2	10	6	3	0	4	0	3.83e-06	0.0019
35	BRD3	bromodomain containing 3	239000	15	14	13	7	6	3	1	0	5	0	3.94e-06	0.0019

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	cos	n_cos	N_cos	cos_ev	p	q
1	SYNE1	spectrin repeat containing, nuclear envelope 1	116	22	1	5258	1	0.098	1
2	A4GNT	alpha-1,4-N-acetylglucosaminyltransferase	6	0	0	0	0	1	1
3	AACS	acetoacetyl-CoA synthetase	9	0	0	0	0	1	1
4	ABCA9	ATP-binding cassette, sub-family A (ABC1), member 9	29	0	0	0	0	1	1
5	ABCC10	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	14	0	0	0	0	1	1
6	ABCF2	ATP-binding cassette, sub-family F (GCN20), member 2	5	0	0	0	0	1	1
7	ABHD2	abhydrolase domain containing 2	4	0	0	0	0	1	1
8	ABHD4	abhydrolase domain containing 4	11	0	0	0	0	1	1
9	ACADS	acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain	5	0	0	0	0	1	1
10	ACOT11	acyl-CoA thioesterase 11	6	0	0	0	0	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	npairs3	npairs12
1878	C3orf63	chromosome 3 open reading frame 63	25	3	3
3911	DMBT1	deleted in malignant brain tumors 1	34	1	3
2601	CDCP1	CUB domain containing protein 1	13	1	1
3932	DNAH11	dynein, axonemal, heavy chain 11	84	1	1
7129	KIAA1432	KIAA1432	16	1	1
7178	KIF20B		47	1	1
7472	LARP1	La ribonucleoprotein domain family, member 1	17	1	1
8159	MDN1	MDN1, midasin homolog (yeast)	58	1	1
9070	NLGN4X	neuroligin 4, X-linked	11	1	1
10055	PCM1	pericentriolar material 1	25	1	1

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: 217. 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	SIG_CHEMOTAXIS	Genes related to chemotaxis	ACTR2, ACTR3, AKT1, AKT2, AKT3, ANGPTL2, ARHGAP1, ARHGAP4, ARHGEF11, BTK, CDC42, CFL1, CFL2, GDI1, GDI2, INPPL1, ITPR1, ITPR2, ITPR3, LIMK1, MYLK, MYLK2, P101-PI3K, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PDK1, PIK3CA, PIK3CD, PIK3CG, PIK3R1, PITX2, PPP1R13B, PTEN, RACGAP1, RHO, ROCK1, ROCK2, RPS4X, SAG, WASF1, WASL	44	ACTR2(7), ACTR3(3), AKT1(8), AKT2(4), AKT3(8), ANGPTL2(9), ARHGAP1(2), ARHGAP4(15), ARHGEF11(22), BTK(11), CDC42(5), CFL1(1), CFL2(8), GDI1(4), GDI2(3), INPPL1(23), ITPR1(31), ITPR2(38), ITPR3(23), LIMK1(7), MYLK(17), MYLK2(7), PAK1(3), PAK2(6), PAK3(14), PAK4(2), PAK6(3), PAK7(12), PDK1(7), PIK3CA(138), PIK3CD(10), PIK3CG(25), PIK3R1(67), PITX2(10), PPP1R13B(7), PTEN(198), RACGAP1(8), RHO(8), ROCK1(27), ROCK2(15), RPS4X(4), SAG(5), WASF1(3), WASL(8)	24593100	836	210	656	135	193	221	160	34	189	39	<1.00e-15	<2.46e-14
2	EIF4PATHWAY	The eIF-4F complex recognizes 5' mRNA caps, recruits RNA helicases, and maintains mRNA-ribosome bridging.	AKT1, EIF4A1, EIF4A2, EIF4E, EIF4EBP1, EIF4G1, EIF4G2, EIF4G3, FRAP1, GHR, IRS1, MAPK1, MAPK14, MAPK3, MKNK1, PABPC1, PDK2, PDPK1, PIK3CA, PIK3R1, PRKCA, PRKCB1, PTEN, RPS6KB1	22	AKT1(8), EIF4A1(4), EIF4A2(6), EIF4E(4), EIF4G1(15), EIF4G2(8), EIF4G3(26), GHR(10), IRS1(17), MAPK1(2), MAPK14(6), MAPK3(4), MKNK1(6), PABPC1(11), PDK2(5), PDPK1(3), PIK3CA(138), PIK3R1(67), PRKCA(10), PTEN(198), RPS6KB1(3)	9912525	551	208	382	44	101	111	133	26	149	31	<1.00e-15	<2.46e-14
3	IGF1MTORPATHWAY	Growth factor IGF-1 activates AKT, Gsk3-beta, and mTOR to promote muscle hypertrophy.	AKT1, EIF2B5, EIF2S1, EIF2S2, EIF2S3, EIF4E, EIF4EBP1, FRAP1, GSK3B, IGF1, IGF1R, INPPL1, PDK2, PDPK1, PIK3CA, PIK3R1, PPP2CA, PTEN, RPS6, RPS6KB1	19	AKT1(8), EIF2B5(6), EIF2S1(1), EIF2S2(5), EIF2S3(6), EIF4E(4), GSK3B(11), IGF1(3), IGF1R(13), INPPL1(23), PDK2(5), PDPK1(3), PIK3CA(138), PIK3R1(67), PPP2CA(6), PTEN(198), RPS6(6), RPS6KB1(3)	6967089	506	208	333	43	91	92	121	20	149	33	<1.00e-15	<2.46e-14
4	MTORPATHWAY	Mammalian target of rapamycin (mTOR) senses mitogenic factors and nutrients, including ATP, and induces cell proliferation.	AKT1, EIF3S10, EIF4A1, EIF4A2, EIF4B, EIF4E, EIF4EBP1, EIF4G1, EIF4G2, EIF4G3, FKBP1A, FRAP1, MKNK1, PDK2, PDPK1, PIK3CA, PIK3R1, PPP2CA, PTEN, RPS6, RPS6KB1, TSC1, TSC2	21	AKT1(8), EIF4A1(4), EIF4A2(6), EIF4B(6), EIF4E(4), EIF4G1(15), EIF4G2(8), EIF4G3(26), MKNK1(6), PDK2(5), PDPK1(3), PIK3CA(138), PIK3R1(67), PPP2CA(6), PTEN(198), RPS6(6), RPS6KB1(3), TSC1(13), TSC2(14)	9012929	536	208	366	42	96	113	124	25	147	31	<1.00e-15	<2.46e-14
5	SIG_INSULIN_RECEPTOR_PATHWAY_IN_CARDIAC_MYOCYTES	Genes related to the insulin receptor pathway	AKT1, AKT2, AKT3, BRD4, CAP1, CBL, CDC42, CDKN2A, F2RL2, FLOT1, FLOT2, FOXO1A, GRB2, GSK3A, GSK3B, IGFBP1, INPPL1, IRS1, IRS2, IRS4, LNPEP, MAPK1, MAPK3, PARD3, PARD6A, PDK1, PIK3CA, PIK3CD, PIK3R1, PPYR1, PSCD3, PTEN, PTPN1, RAF1, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KB1, SERPINB6, SFN, SHC1, SLC2A4, SORBS1, SOS1, SOS2, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ	48	AKT1(8), AKT2(4), AKT3(8), BRD4(9), CAP1(7), CBL(10), CDC42(5), CDKN2A(1), F2RL2(3), FLOT1(1), FLOT2(3), GRB2(3), GSK3A(9), GSK3B(11), IGFBP1(5), INPPL1(23), IRS1(17), IRS4(20), LNPEP(9), MAPK1(2), MAPK3(4), PARD3(27), PARD6A(1), PDK1(7), PIK3CA(138), PIK3CD(10), PIK3R1(67), PPYR1(7), PTEN(198), PTPN1(4), RAF1(7), RPS6KA1(5), RPS6KA2(16), RPS6KA3(17), RPS6KB1(3), SERPINB6(4), SHC1(11), SLC2A4(4), SORBS1(22), SOS1(21), SOS2(22), YWHAB(1), YWHAE(1), YWHAG(3), YWHAH(4), YWHAQ(3), YWHAZ(1)	20132165	766	208	583	117	159	183	167	32	188	37	<1.00e-15	<2.46e-14
6	METPATHWAY	The hepatocyte growth factor receptor c-Met stimulates proliferation and alters cell motility and adhesion on binding the ligand HGF.	ACTA1, CRK, CRKL, DOCK1, ELK1, FOS, GAB1, GRB2, GRF2, HGF, HRAS, ITGA1, ITGB1, JUN, MAP2K1, MAP2K2, MAP4K1, MAPK1, MAPK3, MAPK8, MET, PAK1, PIK3CA, PIK3R1, PTEN, PTK2, PTK2B, PTPN11, PXN, RAF1, RAP1A, RAP1B, RASA1, SOS1, SRC, STAT3	34	ACTA1(4), CRK(1), CRKL(5), DOCK1(32), ELK1(2), FOS(6), GAB1(10), GRB2(3), HGF(15), ITGA1(20), ITGB1(12), JUN(1), MAP2K1(2), MAP4K1(13), MAPK1(2), MAPK3(4), MAPK8(7), MET(10), PAK1(3), PIK3CA(138), PIK3R1(67), PTEN(198), PTK2(11), PTK2B(16), PTPN11(8), PXN(6), RAF1(7), RAP1A(3), RAP1B(2), RASA1(29), SOS1(21), SRC(2), STAT3(12)	15458520	672	205	498	85	136	158	146	27	170	35	<1.00e-15	<2.46e-14
7	PTENPATHWAY	PTEN suppresses AKT-induced cell proliferation and antagonizes the action of PI3K.	AKT1, BCAR1, CDKN1B, FOXO3A, GRB2, ILK, ITGB1, MAPK1, MAPK3, PDK2, PDPK1, PIK3CA, PIK3R1, PTEN, PTK2, SHC1, SOS1, TNFSF6	15	AKT1(8), CDKN1B(5), GRB2(3), ILK(8), ITGB1(12), MAPK1(2), MAPK3(4), PDK2(5), PDPK1(3), PIK3CA(138), PIK3R1(67), PTEN(198), PTK2(11), SHC1(11), SOS1(21)	6356683	496	203	321	30	86	92	124	20	141	33	<1.00e-15	<2.46e-14
8	ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY	The phosphoinositide-3 kinase pathway produces the lipid second messenger PIP3 and regulates cell growth, survival, and movement.	A1BG, AKT1, AKT2, AKT3, BAD, BTK, CDKN2A, CSL4, DAF, DAPP1, FOXO1A, GRB2, GSK3A, GSK3B, IARS, IGFBP1, INPP5D, P14, PDK1, PIK3CA, PPP1R13B, PSCD3, PTEN, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KB1, SFN, SHC1, SOS1, SOS2, TEC, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ	33	A1BG(3), AKT1(8), AKT2(4), AKT3(8), BAD(2), BTK(11), CDKN2A(1), DAPP1(7), GRB2(3), GSK3A(9), GSK3B(11), IARS(13), IGFBP1(5), INPP5D(14), PDK1(7), PIK3CA(138), PPP1R13B(7), PTEN(198), RPS6KA1(5), RPS6KA2(16), RPS6KA3(17), RPS6KB1(3), SHC1(11), SOS1(21), SOS2(22), TEC(5), YWHAB(1), YWHAE(1), YWHAG(3), YWHAH(4), YWHAQ(3), YWHAZ(1)	12586696	562	201	396	60	115	137	132	22	132	24	<1.00e-15	<2.46e-14
9	SA_PTEN_PATHWAY	PTEN is a tumor suppressor that dephosphorylates the lipid messenger phosphatidylinositol triphosphate.	AKT1, AKT2, AKT3, BPNT1, GRB2, ILK, MAPK1, MAPK3, PDK1, PIK3CA, PIK3CD, PIP3-E, PTEN, PTK2B, RBL2, SHC1, SOS1	16	AKT1(8), AKT2(4), AKT3(8), BPNT1(1), GRB2(3), ILK(8), MAPK1(2), MAPK3(4), PDK1(7), PIK3CA(138), PIK3CD(10), PTEN(198), PTK2B(16), RBL2(21), SHC1(11), SOS1(21)	6977366	460	198	293	36	98	93	112	20	112	25	<1.00e-15	<2.46e-14
10	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	79	AIFM1(12), AKT1(8), AKT2(4), AKT3(8), APAF1(19), ATM(54), BAD(2), BAX(4), BCL2L1(3), BID(3), BIRC2(13), BIRC3(3), CAPN1(4), CAPN2(6), CASP10(10), CASP3(4), CASP6(4), CASP7(4), CASP8(21), CASP9(3), CFLAR(7), CHUK(11), CSF2RB(11), CYCS(3), DFFA(1), DFFB(3), FADD(1), FAS(7), FASLG(6), IKBKB(15), IL1A(1), IL1B(2), IL1R1(5), IL1RAP(2), IL3RA(11), IRAK1(5), IRAK2(7), IRAK3(13), IRAK4(6), MAP3K14(12), MYD88(1), NFKB1(12), NFKB2(10), NFKBIA(3), NTRK1(11), PIK3CA(138), PIK3CB(19), PIK3CD(10), PIK3CG(25), PIK3R1(67), PIK3R2(4), PIK3R3(8), PIK3R5(8), PPP3CA(4), PPP3CB(7), PPP3CC(6), PPP3R1(2), PPP3R2(1), PRKACA(4), PRKACB(2), PRKACG(6), PRKAR1A(4), PRKAR1B(8), PRKAR2A(4), PRKAR2B(5), RELA(6), RIPK1(8), TNF(1), TNFRSF10A(3), TNFRSF10B(5), TNFRSF10C(3), TNFRSF10D(10), TNFRSF1A(6), TNFSF10(1), TP53(40), TRAF2(5)	28018448	775	186	659	164	177	260	136	44	141	17	<1.00e-15	<2.46e-14

Table 7. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 50. 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	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	162	ADCY1(17), ADCY2(17), ADCY3(8), ADCY4(8), ADCY7(6), ADCY8(16), ADCY9(25), ADORA2A(5), ADORA2B(2), ADRA1A(11), ADRA1B(7), ADRB1(2), ADRB2(8), ATP2A1(16), ATP2A2(9), ATP2A3(12), ATP2B1(17), ATP2B2(12), ATP2B3(21), ATP2B4(18), AVPR1A(8), AVPR1B(3), BDKRB1(5), BDKRB2(9), BST1(5), CACNA1A(19), CACNA1B(1), CACNA1C(30), CACNA1D(34), CACNA1E(47), CACNA1F(36), CACNA1G(20), CACNA1I(13), CACNA1S(33), CALM2(3), CALM3(1), CALML6(4), CAMK2A(8), CAMK2B(2), CAMK2D(7), CAMK2G(8), CAMK4(5), CCKAR(12), CCKBR(7), CD38(7), CHRM1(6), CHRM2(9), CHRM3(9), CHRM5(13), CHRNA7(6), CYSLTR1(5), CYSLTR2(6), DRD1(6), EDNRA(6), EDNRB(2), EGFR(20), ERBB2(6), ERBB3(16), ERBB4(29), F2R(8), GNA11(3), GNA14(5), GNA15(1), GNAL(6), GNAS(25), GRIN1(5), GRIN2A(25), GRIN2C(6), GRIN2D(8), GRM1(22), GRM5(22), GRPR(4), HRH1(9), HRH2(3), HTR2A(15), HTR2B(2), HTR4(7), HTR5A(9), HTR6(4), HTR7(4), ITPKB(6), ITPR1(31), ITPR2(38), ITPR3(23), LHCGR(16), LTB4R2(3), MYLK(17), MYLK2(7), NOS1(21), NOS3(11), NTSR1(4), OXTR(4), P2RX1(9), P2RX3(9), P2RX4(2), P2RX5(8), P2RX7(3), PDE1A(12), PDE1B(9), PDE1C(14), PDGFRA(29), PDGFRB(12), PHKA1(17), PHKA2(15), PHKB(14), PHKG1(6), PHKG2(3), PLCB1(6), PLCB2(9), PLCB3(9), PLCB4(20), PLCD1(5), PLCD3(7), PLCD4(13), PLCE1(36), PLCG1(12), PLCG2(27), PLCZ1(16), PLN(1), PPID(6), PPP3CA(4), PPP3CB(7), PPP3CC(6), PPP3R1(2), PPP3R2(1), PRKACA(4), PRKACB(2), PRKACG(6), PRKCA(10), PRKCG(10), PRKX(4), PTAFR(6), PTGER3(9), PTGFR(10), PTK2B(16), RYR1(80), RYR2(111), RYR3(87), SLC25A4(3), SLC25A5(4), SLC25A6(6), SLC8A1(20), SLC8A2(6), SLC8A3(14), SPHK1(2), SPHK2(1), TACR1(6), TACR2(4), TACR3(9), TNNC1(2), TNNC2(4), TRHR(5), TRPC1(15), VDAC1(2), VDAC3(4)	91603920	1888	150	1836	659	546	777	260	92	190	23	3.2e-15	2e-12
2	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	133	ADCY1(17), ADCY2(17), ADCY3(8), ADCY4(8), ADCY5(11), ADCY6(16), ADCY7(6), ADCY8(16), ADCY9(25), ADRA1A(11), ADRA1B(7), ADRB1(2), ADRB2(8), ANXA6(10), ARRB1(7), ARRB2(3), ATP1A4(24), ATP1B1(3), ATP1B2(7), ATP1B3(4), ATP2A2(9), ATP2A3(12), ATP2B1(17), ATP2B2(12), ATP2B3(21), CACNA1A(19), CACNA1B(1), CACNA1C(30), CACNA1D(34), CACNA1E(47), CACNA1S(33), CACNB1(9), CACNB3(6), CALM2(3), CALM3(1), CALR(4), CAMK1(9), CAMK2A(8), CAMK2B(2), CAMK2D(7), CAMK2G(8), CAMK4(5), CASQ1(7), CASQ2(8), CHRM1(6), CHRM2(9), CHRM3(9), CHRM4(9), CHRM5(13), GJA1(6), GJA4(2), GJB1(1), GJB2(3), GJB3(2), GJB4(5), GJB5(3), GJB6(4), GNA11(3), GNAI2(7), GNAI3(3), GNAO1(5), GNAZ(7), GNB1(3), GNB2(5), GNB3(4), GNB4(3), GNB5(3), GNG12(2), GNG13(2), GNG2(2), GNG3(3), GRK4(14), GRK5(10), GRK6(3), ITPR1(31), ITPR2(38), ITPR3(23), KCNB1(17), KCNJ3(15), KCNJ5(6), MIB1(8), MYCBP(1), NME7(4), PEA15(2), PKIG(2), PLCB3(9), PLN(1), PRKACA(4), PRKACB(2), PRKAR1A(4), PRKAR2A(4), PRKAR2B(5), PRKCA(10), PRKCD(7), PRKCE(11), PRKCG(10), PRKCH(9), PRKCQ(13), PRKCZ(4), PRKD1(8), RGS1(6), RGS10(3), RGS14(5), RGS16(3), RGS17(5), RGS18(2), RGS2(3), RGS20(5), RGS3(15), RGS4(6), RGS5(4), RGS6(7), RGS7(9), RGS9(19), RYR1(80), RYR2(111), RYR3(87), SLC8A1(20), SLC8A3(14), USP5(13), YWHAB(1), YWHAH(4), YWHAQ(3)	65550530	1346	138	1309	463	395	564	151	72	145	19	3.4e-11	1e-08
3	HSA04080_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION	Genes involved in neuroactive ligand-receptor interaction	ADCYAP1R1, ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA2A, ADRA2B, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BRS3, C3AR1, C5AR1, CALCR, CALCRL, CCKAR, CCKBR, CGA, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CNR1, CNR2, CRHR1, CRHR2, CTSG, CYSLTR1, CYSLTR2, DRD1, DRD2, DRD3, DRD4, DRD5, EDG1, EDG2, EDG3, EDG4, EDG5, EDG6, EDG7, EDG8, EDNRA, EDNRB, F2, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHB, FSHR, GABBR1, GABBR2, GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GABRB1, GABRB2, GABRB3, GABRD, GABRE, GABRG1, GABRG2, GABRG3, GABRP, GABRQ, GABRR1, GABRR2, GALR1, GALR2, GALR3, GCGR, GH1, GH2, GHR, GHRHR, GHSR, GIPR, GLP1R, GLP2R, GLRA1, GLRA2, GLRA3, GLRB, GNRHR, GPR156, GPR23, GPR35, GPR50, GPR63, GPR83, GRIA1, GRIA2, GRIA3, GRIA4, GRID1, GRID2, GRIK1, GRIK2, GRIK3, GRIK4, GRIK5, GRIN1, GRIN2A, GRIN2B, GRIN2C, GRIN2D, GRIN3A, GRIN3B, GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, GRM8, GRPR, GZMA, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HRH4, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, KISS1R, LEP, LEPR, LHB, LHCGR, LTB4R, LTB4R2, MAS1, MC1R, MC2R, MC3R, MC4R, MC5R, MCHR1, MCHR2, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPBWR1, NPBWR2, NPFFR1, NPFFR2, NPY1R, NPY2R, NPY5R, NR3C1, NTSR1, NTSR2, OPRD1, OPRK1, OPRL1, OPRM1, OXTR, P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX7, P2RXL1, P2RY1, P2RY10, P2RY11, P2RY13, P2RY14, P2RY2, P2RY4, P2RY5, P2RY6, P2RY8, PARD3, PPYR1, PRL, PRLHR, PRLR, PRSS1, PRSS2, PRSS3, PTAFR, PTGDR, PTGER1, PTGER2, PTGER3, PTGER4, PTGFR, PTGIR, PTH2R, PTHR1, RXFP1, RXFP2, SCTR, SSTR1, SSTR2, SSTR3, SSTR4, SSTR5, TAAR1, TAAR2, TAAR5, TAAR6, TAAR8, TAAR9, TACR1, TACR2, TACR3, TBXA2R, THRA, THRB, TRHR, TRPV1, TSHB, TSHR, TSPO, UTS2R, VIPR1, VIPR2	214	ADCYAP1R1(7), ADORA1(6), ADORA2A(5), ADORA2B(2), ADORA3(5), ADRA1A(11), ADRA1B(7), ADRA2B(5), ADRB1(2), ADRB2(8), AGTR2(8), AVPR1A(8), AVPR1B(3), AVPR2(5), BDKRB1(5), BDKRB2(9), BRS3(13), C3AR1(7), C5AR1(5), CALCR(5), CALCRL(9), CCKAR(12), CCKBR(7), CGA(1), CHRM1(6), CHRM2(9), CHRM3(9), CHRM4(9), CHRM5(13), CNR1(8), CNR2(3), CRHR1(2), CRHR2(2), CTSG(3), CYSLTR1(5), CYSLTR2(6), DRD1(6), DRD2(10), DRD3(5), DRD5(11), EDNRA(6), EDNRB(2), F2(9), F2R(8), F2RL1(3), F2RL2(3), FPR1(4), FSHR(17), GABBR1(17), GABBR2(14), GABRA1(10), GABRA2(12), GABRA3(15), GABRA4(17), GABRA5(8), GABRA6(8), GABRB1(8), GABRB2(16), GABRB3(15), GABRE(7), GABRG1(8), GABRG2(19), GABRG3(14), GABRP(5), GABRQ(7), GABRR1(5), GABRR2(2), GALR1(2), GALR3(3), GH1(6), GH2(5), GHR(10), GHRHR(2), GHSR(7), GIPR(4), GLP1R(8), GLP2R(17), GLRA1(9), GLRA2(6), GLRA3(11), GLRB(8), GNRHR(4), GPR156(6), GPR50(8), GPR63(5), GPR83(5), GRIA1(12), GRIA2(25), GRIA4(23), GRID1(16), GRID2(13), GRIK1(16), GRIK2(15), GRIK3(17), GRIK4(8), GRIK5(19), GRIN1(5), GRIN2A(25), GRIN2B(23), GRIN2C(6), GRIN2D(8), GRIN3A(15), GRM1(22), GRM2(7), GRM3(20), GRM4(16), GRM5(22), GRM7(15), GRM8(24), GRPR(4), GZMA(6), HCRTR1(1), HCRTR2(8), HRH1(9), HRH2(3), HRH4(4), HTR1A(13), HTR1B(6), HTR1D(6), HTR1E(6), HTR2A(15), HTR2B(2), HTR4(7), HTR5A(9), HTR6(4), HTR7(4), LEP(2), LEPR(15), LHB(3), LHCGR(16), LTB4R(3), LTB4R2(3), MAS1(2), MC2R(2), MC3R(8), MC4R(7), MC5R(12), MCHR1(7), MCHR2(1), MLNR(3), MTNR1A(6), MTNR1B(4), NMBR(4), NMUR1(8), NMUR2(7), NPBWR1(2), NPFFR1(2), NPFFR2(12), NPY1R(6), NPY2R(4), NPY5R(10), NR3C1(13), NTSR1(4), NTSR2(2), OPRD1(2), OPRK1(9), OPRM1(11), OXTR(4), P2RX1(9), P2RX3(9), P2RX4(2), P2RX5(8), P2RX7(3), P2RY1(2), P2RY10(6), P2RY11(7), P2RY13(3), P2RY14(5), P2RY2(6), P2RY4(7), P2RY6(3), PARD3(27), PPYR1(7), PRL(6), PRLHR(2), PRLR(6), PRSS1(7), PRSS3(2), PTAFR(6), PTGDR(6), PTGER2(5), PTGER3(9), PTGER4(8), PTGFR(10), PTGIR(3), PTH2R(7), RXFP1(16), RXFP2(17), SCTR(4), SSTR2(3), SSTR3(6), TAAR1(6), TAAR2(5), TAAR5(8), TAAR6(5), TAAR8(3), TAAR9(8), TACR1(6), TACR2(4), TACR3(9), THRA(5), THRB(4), TRHR(5), TRPV1(6), TSHB(3), TSHR(12), VIPR1(3)	71058285	1639	145	1582	539	480	673	258	73	153	2	4.3e-10	8.8e-08
4	HSA04010_MAPK_SIGNALING_PATHWAY	Genes involved in MAPK signaling pathway	ACVR1B, ACVR1C, AKT1, AKT2, AKT3, ARRB1, ARRB2, ATF2, ATF4, BDNF, BRAF, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1F, CACNA1G, CACNA1H, CACNA1I, CACNA1S, CACNA2D1, CACNA2D2, CACNA2D3, CACNA2D4, CACNB1, CACNB2, CACNB3, CACNB4, CACNG1, CACNG2, CACNG3, CACNG4, CACNG5, CACNG6, CACNG7, CACNG8, CASP3, CD14, CDC25B, CDC42, CHP, CHUK, CRK, CRKL, DAXX, DDIT3, DUSP1, DUSP10, DUSP14, DUSP16, DUSP2, DUSP3, DUSP4, DUSP5, DUSP6, DUSP7, DUSP8, DUSP9, ECSIT, EGF, EGFR, ELK1, ELK4, EVI1, FAS, FASLG, 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, FLNA, FLNB, FLNC, FOS, GADD45A, GADD45B, GADD45G, GNA12, GNG12, GRB2, HRAS, IKBKB, IKBKG, IL1A, IL1B, IL1R1, IL1R2, JUN, JUND, KRAS, LOC653852, MAP2K1, MAP2K1IP1, MAP2K2, MAP2K3, MAP2K4, MAP2K5, MAP2K6, MAP2K7, MAP3K1, MAP3K10, MAP3K12, MAP3K13, MAP3K14, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K6, MAP3K7, MAP3K7IP1, MAP3K7IP2, MAP3K8, MAP4K1, MAP4K2, MAP4K3, MAP4K4, MAPK1, MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPK7, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MAPKAPK2, MAPKAPK3, MAPKAPK5, MAPT, MAX, MEF2C, MKNK1, MKNK2, MOS, MRAS, MYC, NF1, NFATC2, NFATC4, NFKB1, NFKB2, NGFB, NLK, NR4A1, NRAS, NTF3, NTF5, NTRK1, NTRK2, PAK1, PAK2, PDGFA, PDGFB, PDGFRA, PDGFRB, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PPM1A, PPM1B, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PPP5C, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PTPN5, PTPN7, PTPRR, RAC1, RAC2, RAC3, RAF1, RAP1A, RAP1B, RAPGEF2, RASA1, RASA2, RASGRF1, RASGRF2, RASGRP1, RASGRP2, RASGRP3, RASGRP4, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KA4, RPS6KA5, RPS6KA6, RRAS, RRAS2, SOS1, SOS2, SRF, STK3, STK4, STMN1, TAOK1, TAOK2, TAOK3, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TNF, TNFRSF1A, TP53, TRAF2, TRAF6, ZAK	225	ACVR1B(6), ACVR1C(7), AKT1(8), AKT2(4), AKT3(8), ARRB1(7), ARRB2(3), ATF2(6), ATF4(4), BDNF(8), BRAF(12), CACNA1A(19), CACNA1B(1), CACNA1C(30), CACNA1D(34), CACNA1E(47), CACNA1F(36), CACNA1G(20), CACNA1I(13), CACNA1S(33), CACNA2D1(14), CACNA2D2(9), CACNA2D3(20), CACNA2D4(18), CACNB1(9), CACNB2(11), CACNB3(6), CACNB4(14), CACNG2(3), CACNG3(9), CACNG4(6), CACNG5(4), CACNG6(6), CACNG7(10), CASP3(4), CD14(2), CDC25B(3), CDC42(5), CHUK(11), CRK(1), CRKL(5), DAXX(11), DDIT3(1), DUSP1(2), DUSP10(7), DUSP14(3), DUSP16(13), DUSP2(4), DUSP3(2), DUSP4(1), DUSP5(5), DUSP6(1), DUSP7(4), DUSP9(8), ECSIT(5), EGF(24), EGFR(20), ELK1(2), ELK4(3), FAS(7), FASLG(6), FGF1(1), FGF10(1), FGF11(2), FGF12(4), FGF13(6), FGF14(3), FGF16(1), FGF17(1), FGF18(2), FGF21(3), FGF23(6), FGF5(8), FGF6(2), FGF7(6), FGF8(2), FGF9(2), FGFR1(10), FGFR4(11), FLNA(31), FLNB(38), FLNC(34), FOS(6), GNA12(10), GNG12(2), GRB2(3), IKBKB(15), IL1A(1), IL1B(2), IL1R1(5), IL1R2(7), JUN(1), MAP2K1(2), MAP2K3(8), MAP2K4(6), MAP2K5(2), MAP2K6(9), MAP3K10(7), MAP3K12(8), MAP3K13(13), MAP3K14(12), MAP3K2(8), MAP3K3(9), MAP3K4(23), MAP3K5(21), MAP3K6(7), MAP3K7(8), MAP3K8(12), MAP4K1(13), MAP4K2(6), MAP4K3(21), MAP4K4(14), MAPK1(2), MAPK10(9), MAPK13(2), MAPK14(6), MAPK3(4), MAPK7(17), MAPK8(7), MAPK8IP1(5), MAPK9(7), MAPKAPK2(6), MAPKAPK3(4), MAPKAPK5(6), MAPT(11), MAX(8), MEF2C(11), MKNK1(6), MKNK2(4), MOS(8), MRAS(3), MYC(7), NF1(40), NFATC2(15), NFATC4(8), NFKB1(12), NFKB2(10), NLK(5), NR4A1(4), NTF3(6), NTRK1(11), NTRK2(15), PAK1(3), PAK2(6), PDGFB(4), PDGFRA(29), PDGFRB(12), PLA2G10(1), PLA2G12A(1), PLA2G12B(3), PLA2G1B(1), PLA2G2D(2), PLA2G2E(3), PLA2G2F(3), PLA2G3(5), PLA2G4A(11), PLA2G5(2), PLA2G6(6), PPM1A(7), PPM1B(6), PPP3CA(4), PPP3CB(7), PPP3CC(6), PPP3R1(2), PPP3R2(1), PPP5C(7), PRKACA(4), PRKACB(2), PRKACG(6), PRKCA(10), PRKCG(10), PRKX(4), PTPN5(5), PTPN7(5), PTPRR(18), RAC2(2), RAF1(7), RAP1A(3), RAP1B(2), RAPGEF2(38), RASA2(8), RASGRF1(13), RASGRF2(17), RASGRP1(8), RASGRP2(5), RASGRP3(8), RASGRP4(7), RPS6KA1(5), RPS6KA2(16), RPS6KA3(17), RPS6KA4(5), RPS6KA5(7), RPS6KA6(15), RRAS(1), RRAS2(5), SOS1(21), SOS2(22), SRF(3), STK3(9), STK4(6), STMN1(6), TAOK1(10), TAOK2(10), TAOK3(4), TGFB1(4), TGFB2(6), TGFB3(9), TGFBR1(8), TGFBR2(6), TNF(1), TNFRSF1A(6), TRAF2(5), TRAF6(4), ZAK(12)	92476270	1836	141	1785	566	501	733	230	111	239	22	1.1e-08	1.8e-06
5	HSA04530_TIGHT_JUNCTION	Genes involved in tight junction	ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, AMOTL1, ASH1L, CASK, CDC42, CDK4, CGN, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CRB3, CSDA, CSNK2A1, CSNK2A2, CSNK2B, CTNNA1, CTNNA2, CTNNA3, CTNNB1, CTTN, EPB41, EPB41L1, EPB41L2, EPB41L3, EXOC3, EXOC4, F11R, GNAI1, GNAI2, GNAI3, HCLS1, HRAS, IGSF5, INADL, JAM2, JAM3, KRAS, LLGL1, LLGL2, MAGI1, MAGI2, MAGI3, MLLT4, MPDZ, MPP5, MRAS, MRCL3, MRLC2, MYH1, MYH10, MYH11, MYH13, MYH14, MYH15, MYH2, MYH3, MYH4, MYH6, MYH7, MYH7B, MYH8, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLPF, NRAS, OCLN, PARD3, PARD6A, PARD6B, PARD6G, PPM1J, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP2R3A, PPP2R3B, PPP2R4, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCQ, PRKCZ, PTEN, RAB13, RAB3B, RHOA, RRAS, RRAS2, SPTAN1, SRC, SYMPK, TJAP1, TJP1, TJP2, TJP3, VAPA, YES1, ZAK	121	ACTB(5), ACTN1(13), ACTN2(9), ACTN3(10), ACTN4(11), AKT1(8), AKT2(4), AKT3(8), AMOTL1(14), ASH1L(40), CASK(20), CDC42(5), CDK4(4), CGN(15), CLDN1(2), CLDN10(9), CLDN11(1), CLDN15(4), CLDN16(6), CLDN17(2), CLDN18(4), CLDN19(2), CLDN2(4), CLDN20(4), CLDN22(3), CLDN6(1), CLDN7(1), CLDN8(5), CLDN9(2), CRB3(1), CSDA(6), CSNK2A1(9), CSNK2A2(5), CTNNA1(18), CTNNA2(13), CTNNA3(13), CTTN(8), EPB41(11), EPB41L1(11), EPB41L2(13), EPB41L3(18), EXOC3(12), EXOC4(4), F11R(2), GNAI1(4), GNAI2(7), GNAI3(3), HCLS1(8), IGSF5(9), INADL(17), JAM2(9), JAM3(3), LLGL1(14), LLGL2(5), MAGI1(32), MAGI2(26), MAGI3(17), MLLT4(32), MPDZ(22), MPP5(5), MRAS(3), MYH1(44), MYH10(29), MYH11(39), MYH13(27), MYH14(22), MYH15(22), MYH2(37), MYH3(30), MYH4(36), MYH6(23), MYH7(28), MYH7B(15), MYH8(35), MYH9(26), MYL2(1), MYL5(3), MYL7(4), MYL9(3), MYLPF(2), OCLN(5), PARD3(27), PARD6A(1), PARD6B(3), PPM1J(3), PPP2CA(6), PPP2CB(2), PPP2R1B(9), PPP2R2A(15), PPP2R2B(12), PPP2R2C(3), PPP2R3A(13), PPP2R4(7), PRKCA(10), PRKCD(7), PRKCE(11), PRKCG(10), PRKCH(9), PRKCI(8), PRKCQ(13), PRKCZ(4), RAB13(3), RAB3B(1), RHOA(4), RRAS(1), RRAS2(5), SPTAN1(29), SRC(2), SYMPK(20), TJAP1(8), TJP1(33), TJP2(16), TJP3(6), VAPA(5), YES1(5), ZAK(12)	64754182	1330	139	1292	409	366	531	194	61	161	17	3.6e-08	4.4e-06
6	HSA04910_INSULIN_SIGNALING_PATHWAY	Genes involved in insulin signaling pathway	ACACA, ACACB, AKT1, AKT2, AKT3, ARAF, BAD, BRAF, CALM1, CALM2, CALM3, CALML3, CALML6, CBL, CBLB, CBLC, CRK, CRKL, EIF4EBP1, ELK1, EXOC7, FASN, FBP1, FBP2, FLOT1, FLOT2, FOXO1, FRAP1, G6PC, G6PC2, GCK, GRB2, GSK3B, GYS1, GYS2, HRAS, IKBKB, INPP5D, INS, INSR, IRS1, IRS2, IRS4, KIAA1303, KRAS, LIPE, MAP2K1, MAP2K2, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MKNK1, MKNK2, NRAS, PCK1, PCK2, PDE3A, PDE3B, PDPK1, PFKL, PFKM, PFKP, PHKA1, PHKA2, PHKB, PHKG1, PHKG2, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PKLR, PKM2, PPARGC1A, PPP1CA, PPP1CB, PPP1CC, PPP1R3A, PPP1R3B, PPP1R3C, PPP1R3D, PRKAA1, PRKAA2, PRKAB1, PRKAB2, PRKACA, PRKACB, PRKACG, PRKAG1, PRKAG2, PRKAG3, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKCI, PRKCZ, PRKX, PRKY, PTPN1, PTPRF, PYGB, PYGL, PYGM, RAF1, RAPGEF1, RHEB, RHOQ, RPS6, RPS6KB1, RPS6KB2, SH2B2, SHC1, SHC2, SHC3, SHC4, SKIP, SLC2A4, SOCS1, SOCS2, SOCS3, SOCS4, SORBS1, SOS1, SOS2, SREBF1, TRIP10, TSC1, TSC2	118	ACACA(27), ACACB(31), AKT1(8), AKT2(4), AKT3(8), ARAF(8), BAD(2), BRAF(12), CALM2(3), CALM3(1), CALML6(4), CBL(10), CBLB(15), CBLC(5), CRK(1), CRKL(5), ELK1(2), EXOC7(8), FBP1(4), FLOT1(1), FLOT2(3), FOXO1(11), G6PC(6), G6PC2(9), GCK(5), GRB2(3), GSK3B(11), GYS1(12), GYS2(19), IKBKB(15), INPP5D(14), INSR(18), IRS1(17), IRS4(20), LIPE(7), MAP2K1(2), MAPK1(2), MAPK10(9), MAPK3(4), MAPK8(7), MAPK9(7), MKNK1(6), MKNK2(4), PCK1(15), PCK2(7), PDE3A(17), PDE3B(15), PDPK1(3), PFKM(7), PFKP(11), PHKA1(17), PHKA2(15), PHKB(14), PHKG1(6), PHKG2(3), PIK3CB(19), PIK3CD(10), PIK3CG(25), PIK3R2(4), PIK3R3(8), PIK3R5(8), PKLR(10), PKM2(5), PPARGC1A(13), PPP1CA(6), PPP1CB(7), PPP1CC(2), PPP1R3A(23), PPP1R3B(3), PPP1R3C(3), PRKAA1(6), PRKAA2(9), PRKAB1(7), PRKAB2(2), PRKACA(4), PRKACB(2), PRKACG(6), PRKAG1(2), PRKAG2(4), PRKAG3(6), PRKAR1A(4), PRKAR2A(4), PRKAR2B(5), PRKCI(8), PRKCZ(4), PRKX(4), PTPN1(4), PTPRF(34), PYGB(10), PYGL(9), PYGM(10), RAF1(7), RAPGEF1(18), RHEB(2), RHOQ(1), RPS6(6), RPS6KB1(3), RPS6KB2(6), SH2B2(2), SHC1(11), SHC3(9), SHC4(7), SLC2A4(4), SOCS2(7), SOCS4(4), SORBS1(22), SOS1(21), SOS2(22), SREBF1(6), TRIP10(6), TSC1(13), TSC2(14)	49120714	981	128	952	281	250	412	126	43	138	12	4.8e-06	0.0005
7	ERK5PATHWAY	Signaling between a tissue and its innervating axon stimulates retrograde transport via Trk receptors, which activate Erk5, which induces transcription of anti-apoptotic factors.	AKT1, CREB1, GRB2, HRAS, MAPK1, MAPK3, MAPK7, MEF2A, MEF2B, MEF2C, MEF2D, NTRK1, PIK3CA, PIK3R1, PLCG1, RPS6KA1, SHC1	15	AKT1(8), CREB1(5), GRB2(3), MAPK1(2), MAPK3(4), MAPK7(17), MEF2A(5), MEF2B(3), MEF2C(11), MEF2D(7), NTRK1(11), PLCG1(12), RPS6KA1(5), SHC1(11)	5187495	104	52	96	30	23	51	9	5	16	0	6.6e-06	0.00058
8	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	17	AXIN1(8), BTRC(13), CREBBP(37), CSNK1A1(5), CSNK2A1(9), FZD1(2), GSK3B(11), HDAC1(4), MAP3K7(8), MYC(7), NLK(5), PPARD(6), PPP2CA(6), TLE1(12), WIF1(5), WNT1(1)	6567242	139	59	136	28	43	56	17	3	18	2	0.000018	0.0014
9	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	10	AXIN1(8), CREBBP(37), EP300(29), FZD1(2), GSK3B(11), HDAC1(4), LDB1(3), LEF1(9), TRRAP(72), WNT1(1)	8072942	176	62	170	33	49	68	23	6	28	2	0.000028	0.0019
10	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	12	CDH1(15), CREBBP(37), EP300(29), MAP2K1(2), MAP3K7(8), MAPK3(4), SKIL(13), TGFB1(4), TGFB2(6), TGFB3(9), TGFBR1(8), TGFBR2(6)	6902081	141	57	136	37	35	58	20	6	22	0	0.000054	0.0032

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]

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This is an experimental feature. Location of data archives could not be determined.

References

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