Mutation Analysis (MutSig v2.0)

Colon Adenocarcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

Maintainer Information

Citation Information

Maintained by Dan DiCara (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C14M92KC

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 v2.0 was used to generate the results found in this report.

Working with individual set: COAD-TP
Number of patients in set: 155

Input

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

An annotated .maf file describing the mutations called for the respective individual, and their properties.
A .wig file that contains information about the coverage of the sample.

Summary

MAF used for this analysis:COAD-TP.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 75
Mutations seen in COSMIC: 517
Significantly mutated genes in COSMIC territory: 23
Genes with clustered mutations (≤ 3 aa apart): 350
Significantly mutated genesets: 156
Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing

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

Mutation Filtering

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

Results

Breakdown of Mutations by Type

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

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

Breakdown of Mutation Rates by Category Type

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
*CpG->T	15461	235764747	0.000066	66	6.2
*Np(A/C/T)->transit	10142	3394090912	3e-06	3	0.28
*ApG->G	966	657627616	1.5e-06	1.5	0.14
transver	13028	4287483275	3e-06	3	0.29
indel+null	5396	4287483377	1.3e-06	1.3	0.12
double_null	147	4287483377	3.4e-08	0.034	0.0033
Total	45140	4287483377	0.000011	11	1

Target Coverage for Each Individual

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. Patients counts and rates file used to generate this plot: COAD-TP.patients.counts_and_rates.txt

CoMut Plot

Figure 3. Get High-res Image The matrix in the center of the figure represents individual mutations in patient samples, color-coded by type of mutation, for the significantly mutated genes. The rate of synonymous and non-synonymous mutations is displayed at the top of the matrix. The barplot on the left of the matrix shows the number of mutations in each gene. The percentages represent the fraction of tumors with at least one mutation in the specified gene. The barplot to the right of the matrix displays the q-values for the most significantly mutated genes. The purple boxplots below the matrix (only displayed if required columns are present in the provided MAF) represent the distributions of allelic fractions observed in each sample. The plot at the bottom represents the base substitution distribution of individual samples, using the same categories that were used to calculate significance.

Significantly Mutated Genes

Column Descriptions:

N = number of sequenced bases in this gene across the individual set
n = number of (nonsilent) mutations in this gene across the individual set
npat = number of patients (individuals) with at least one nonsilent mutation
nsite = number of unique sites having a non-silent mutation
nsil = number of silent mutations in this gene across the individual set
n1 = number of nonsilent mutations of type: *CpG->T
n2 = number of nonsilent mutations of type: *Np(A/C/T)->transit
n3 = number of nonsilent mutations of type: *ApG->G
n4 = number of nonsilent mutations of type: transver
n5 = number of nonsilent mutations of type: indel+null
n6 = number of nonsilent mutations of type: double_null
p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene
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: 75. 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_classic	p_cons	p_joint	p	q
1	FBXW7	F-box and WD repeat domain containing 7	400174	33	29	21	2	17	1	0	8	7	0	7.77e-15	0.12	0.00077	2.22e-16	2.57e-12
2	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	90830	15	15	7	0	2	2	0	11	0	0	6.55e-15	0.033	0.0012	3.33e-16	2.57e-12
3	APC	adenomatous polyposis coli	1314776	121	103	85	4	5	6	1	11	64	34	<1.00e-15	0.85	0	<1.00e-15	<2.57e-12
4	TP53	tumor protein p53	188069	77	75	50	1	29	11	0	11	26	0	2.00e-15	2e-07	0	<1.00e-15	<2.57e-12
5	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	109406	58	58	8	0	0	31	0	27	0	0	<1.00e-15	9e-06	0	<1.00e-15	<2.57e-12
6	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	423914	33	26	18	1	5	19	1	8	0	0	7.33e-15	0.000021	0	<1.00e-15	<2.57e-12
7	BRAF	v-raf murine sarcoma viral oncogene homolog B1	342233	21	20	3	0	0	0	0	21	0	0	3.86e-12	0.00017	0	<1.00e-15	<2.57e-12
8	SMAD4	SMAD family member 4	262233	21	18	17	0	8	7	0	2	3	1	3.11e-15	0.01	0.016	2.00e-15	4.49e-12
9	FAM123B	family with sequence similarity 123B	451470	19	19	17	1	1	2	0	2	14	0	1.14e-12	0.72	0.088	3.11e-12	6.20e-09
10	TTN	titin	12154158	203	69	199	58	61	50	3	73	10	6	1.55e-12	0.82	1	4.36e-11	7.83e-08
11	WBSCR17	Williams-Beuren syndrome chromosome region 17	278161	17	17	16	2	10	2	1	1	3	0	1.76e-09	0.63	0.1	4.16e-09	6.79e-06
12	ACVR1B	activin A receptor, type IB	235764	13	13	13	0	4	6	0	2	1	0	4.07e-08	0.0019	0.0059	5.53e-09	8.28e-06
13	TNFRSF10C	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	116831	6	6	2	0	0	0	0	6	0	0	8.37e-06	1	0.000036	6.98e-09	9.64e-06
14	SMAD2	SMAD family member 2	223461	11	10	8	1	3	0	0	4	4	0	1.92e-07	0.096	0.025	9.60e-08	0.000123
15	MAP2K4	mitogen-activated protein kinase kinase 4	171130	9	9	8	0	2	3	1	2	1	0	2.36e-06	0.0021	0.0042	1.93e-07	0.000232
16	PCBP1	poly(rC) binding protein 1	127765	4	4	2	0	0	0	2	2	0	0	0.00111	0.043	5e-05	9.87e-07	0.00111
17	FAT4	FAT tumor suppressor homolog 4 (Drosophila)	2176174	56	29	56	16	14	19	0	20	3	0	4.35e-05	0.62	0.002	1.46e-06	0.00154
18	LRP1B	low density lipoprotein-related protein 1B (deleted in tumors)	2190256	55	30	55	14	8	11	3	26	4	3	1.25e-07	0.71	0.73	1.57e-06	0.00156
19	NRXN1	neurexin 1	545096	21	17	21	8	8	1	0	10	2	0	4.27e-06	0.22	0.032	2.29e-06	0.00217
20	SDK1	sidekick homolog 1, cell adhesion molecule (chicken)	943748	27	25	25	7	18	2	0	6	1	0	2.78e-06	0.57	0.082	3.72e-06	0.00334
21	GRIA1	glutamate receptor, ionotropic, AMPA 1	431079	18	14	17	5	7	5	2	3	1	0	3.69e-06	0.98	0.065	3.90e-06	0.00334
22	SOX9	SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal)	180663	9	9	9	0	0	1	0	0	8	0	1.47e-06	0.62	0.2	4.81e-06	0.00393
23	DMD	dystrophin (muscular dystrophy, Duchenne and Becker types)	1775675	36	27	35	4	6	5	2	16	7	0	4.21e-06	0.78	0.1	6.58e-06	0.00514
24	CNTN6	contactin 6	490742	19	15	19	2	5	3	0	10	1	0	4.76e-07	0.75	1	7.40e-06	0.00554
25	GABRA5	gamma-aminobutyric acid (GABA) A receptor, alpha 5	125970	8	8	7	0	3	2	0	2	1	0	1.17e-05	0.54	0.05	9.03e-06	0.00649
26	OR2M4	olfactory receptor, family 2, subfamily M, member 4	145654	8	8	8	0	3	2	1	0	2	0	4.77e-06	0.044	0.17	1.22e-05	0.00842
27	PCDH9	protocadherin 9	573119	19	16	19	6	1	4	0	13	1	0	1.01e-06	0.78	1	1.50e-05	0.00987
28	OR6N1	olfactory receptor, family 6, subfamily N, member 1	145983	8	8	8	2	1	2	1	4	0	0	3.50e-06	0.37	0.3	1.54e-05	0.00987
29	TXNDC3	thioredoxin domain containing 3 (spermatozoa)	283045	13	10	13	2	3	1	1	3	5	0	1.69e-06	0.84	0.79	1.94e-05	0.0120
30	MGC26647	chromosome 7 open reading frame 62	117898	7	7	7	0	1	1	0	2	3	0	6.98e-06	0.82	0.21	2.14e-05	0.0128
31	FAM22F	family with sequence similarity 22, member F	194820	8	8	4	1	1	0	0	6	1	0	2.71e-05	0.4	0.07	2.69e-05	0.0156
32	ACVR2A	activin A receptor, type IIA	245516	9	8	8	1	0	1	0	3	5	0	0.000222	0.037	0.0089	2.79e-05	0.0156
33	TCF7L2	transcription factor 7-like 2 (T-cell specific, HMG-box)	281477	13	11	13	3	3	2	0	3	5	0	2.03e-05	0.51	0.11	3.07e-05	0.0167
34	AFF2	AF4/FMR2 family, member 2	612522	17	15	16	9	2	7	0	8	0	0	6.25e-06	0.45	0.38	3.32e-05	0.0175
35	CNBD1	cyclic nucleotide binding domain containing 1	124236	7	6	7	4	0	1	1	4	1	0	0.000352	0.011	0.0093	4.47e-05	0.0230

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: 23. Number of genes displayed: 10

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

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	nmuts0	nmuts3	nmuts12	npairs0	npairs3	npairs12
6113	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	58	959	1135	1136	959	1135	1136
1160	BRAF	v-raf murine sarcoma viral oncogene homolog B1	21	171	171	171	171	171	171
11991	TP53	tumor protein p53	77	102	181	290	102	181	290
602	APC	adenomatous polyposis coli	121	82	105	149	82	105	149
8703	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	33	53	81	103	53	81	103
4161	FBXW7	F-box and WD repeat domain containing 7	33	41	45	53	41	45	53
7726	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	15	26	36	36	26	36	36
10803	SMAD4	SMAD family member 4	21	10	14	24	10	14	24
4004	FAM22F	family with sequence similarity 22, member F	8	10	10	10	10	10	10
3770	ERBB3	v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian)	11	6	10	10	6	10	10

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: 156. Number of genesets displayed: 10

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p	q
1	HSA04310_WNT_SIGNALING_PATHWAY	Genes involved in Wnt signaling pathway	APC, APC2, AXIN1, AXIN2, BTRC, CACYBP, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CCND1, CCND2, CCND3, CER1, CHD8, CHP, CREBBP, CSNK1A1, CSNK1A1L, CSNK1E, CSNK2A1, CSNK2A2, CSNK2B, CTBP1, CTBP2, CTNNB1, CTNNBIP1, CUL1, CXXC4, DAAM1, DAAM2, DKK1, DKK2, DKK4, DVL1, DVL2, DVL3, EP300, FBXW11, FOSL1, FRAT1, FRAT2, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LEF1, LOC652788, LRP5, LRP6, MAP3K7, MAPK10, MAPK8, MAPK9, MMP7, MYC, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NKD1, NKD2, NLK, PLCB1, PLCB2, PLCB3, PLCB4, PORCN, PPARD, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRICKLE1, PRICKLE2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PSEN1, RAC1, RAC2, RAC3, RBX1, RHOA, ROCK1, ROCK2, RUVBL1, SENP2, SFRP1, SFRP2, SFRP4, SFRP5, SIAH1, SKP1, SMAD2, SMAD3, SMAD4, SOX17, TBL1X, TBL1XR1, TBL1Y, TCF7, TCF7L1, TCF7L2, TP53, VANGL1, VANGL2, WIF1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B	144	APC(121), APC2(1), AXIN1(1), AXIN2(7), BTRC(2), CACYBP(1), CAMK2A(1), CAMK2B(2), CAMK2D(2), CAMK2G(2), CCND2(1), CCND3(1), CER1(3), CHD8(4), CREBBP(21), CSNK1A1(2), CSNK1A1L(5), CSNK2A1(4), CSNK2A2(2), CSNK2B(2), CTBP1(1), CTBP2(2), CTNNB1(8), CTNNBIP1(1), CUL1(7), CXXC4(1), DAAM1(1), DAAM2(5), DKK1(3), DKK2(5), DKK4(4), DVL2(8), DVL3(2), EP300(13), FBXW11(7), FZD10(4), FZD2(2), FZD3(10), FZD4(1), FZD6(3), FZD7(3), FZD8(1), GSK3B(7), LEF1(4), LRP5(5), LRP6(10), MAP3K7(2), MAPK10(4), MAPK8(2), MAPK9(3), MMP7(3), NFAT5(5), NFATC1(1), NFATC2(3), NFATC3(4), NFATC4(4), NKD1(3), NKD2(1), NLK(1), PLCB1(8), PLCB2(3), PLCB3(3), PLCB4(9), PORCN(2), PPARD(1), PPP2CA(1), PPP2R1A(4), PPP2R1B(1), PPP2R2A(1), PPP2R2B(1), PPP2R2C(3), PPP3CA(1), PPP3CB(4), PPP3CC(3), PPP3R1(1), PPP3R2(1), PRICKLE1(8), PRICKLE2(5), PRKACB(1), PRKACG(2), PRKCA(2), PRKCG(8), PRKX(2), PSEN1(3), RHOA(4), ROCK1(8), ROCK2(2), RUVBL1(6), SENP2(2), SFRP1(2), SFRP2(1), SFRP4(3), SFRP5(1), SIAH1(1), SKP1(1), SMAD2(11), SMAD3(6), SMAD4(21), SOX17(2), TBL1X(5), TBL1XR1(6), TCF7(3), TCF7L1(3), TCF7L2(13), TP53(77), VANGL1(2), VANGL2(5), WIF1(2), WNT1(1), WNT10B(3), WNT11(3), WNT16(2), WNT2B(1), WNT3(4), WNT3A(1), WNT4(1), WNT5A(3), WNT7A(2), WNT7B(2), WNT8A(1), WNT9A(2), WNT9B(1)	35522515	631	150	557	121	207	110	8	124	147	35	<1.00e-15	<3.24e-14
2	WNT_SIGNALING	Wnt signaling genes	APC, ARHA, AXIN1, C2orf31, CCND1, CCND2, CCND3, CSNK1E, CSNK1E, LOC400927, CTNNB1, DIPA, DVL1, DVL2, DVL3, FBXW2, FOSL1, FRAT1, FZD1, FZD10, FZD2, FZD3, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LDLR, MAPK10, MAPK9, MYC, PAFAH1B1, PLAU, PPP2R5C, PPP2R5E, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCM, PRKCQ, PRKCZ, PRKD1, RAC1, RHOA, SFRP4, TCF7, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B	58	APC(121), AXIN1(1), CCND2(1), CCND3(1), CTNNB1(8), DVL2(8), DVL3(2), FBXW2(2), FZD10(4), FZD2(2), FZD3(10), FZD6(3), FZD7(3), FZD8(1), GSK3B(7), LDLR(4), MAPK10(4), MAPK9(3), PAFAH1B1(3), PLAU(2), PPP2R5C(2), PPP2R5E(2), PRKCA(2), PRKCD(3), PRKCE(4), PRKCG(8), PRKCH(2), PRKCI(4), PRKCQ(4), PRKD1(10), RHOA(4), SFRP4(3), TCF7(3), WNT1(1), WNT10B(3), WNT11(3), WNT16(2), WNT2B(1), WNT3(4), WNT4(1), WNT5A(3), WNT7A(2), WNT7B(2)	13007053	263	129	225	48	68	34	3	45	79	34	<1.00e-15	<3.24e-14
3	HSA04110_CELL_CYCLE	Genes involved in cell cycle	ABL1, ANAPC1, ANAPC10, ANAPC11, ANAPC2, ANAPC4, ANAPC5, ANAPC7, ATM, ATR, BUB1, BUB1B, BUB3, CCNA1, CCNA2, CCNB1, CCNB2, CCNB3, CCND1, CCND2, CCND3, CCNE1, CCNE2, CCNH, CDC14A, CDC14B, CDC16, CDC2, CDC20, CDC23, CDC25A, CDC25B, CDC25C, CDC26, CDC27, CDC45L, CDC6, CDC7, CDK2, CDK4, CDK6, CDK7, CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B, CDKN2C, CDKN2D, CHEK1, CHEK2, CREBBP, CUL1, DBF4, E2F1, E2F2, E2F3, EP300, ESPL1, FZR1, GADD45A, GADD45B, GADD45G, GSK3B, hCG_1982709, HDAC1, HDAC2, LOC440917, LOC728919, MAD1L1, MAD2L1, MAD2L2, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MDM2, ORC1L, ORC2L, ORC3L, ORC4L, ORC5L, ORC6L, PCNA, PKMYT1, PLK1, PRKDC, PTTG1, PTTG2, RB1, RBL1, RBL2, RBX1, SFN, SKP1, SKP2, SMAD2, SMAD3, SMAD4, SMC1A, SMC1B, TFDP1, TGFB1, TGFB2, TGFB3, TP53, WEE1, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ	108	ABL1(4), ANAPC1(3), ANAPC10(2), ANAPC2(1), ANAPC4(1), ANAPC5(2), ANAPC7(4), ATM(27), ATR(13), BUB1(4), BUB1B(3), BUB3(2), CCNA1(4), CCNA2(3), CCNB1(2), CCNB2(2), CCNB3(4), CCND2(1), CCND3(1), CCNE1(3), CCNE2(1), CCNH(2), CDC14A(1), CDC14B(3), CDC16(3), CDC20(3), CDC23(6), CDC25A(2), CDC25B(5), CDC25C(3), CDC27(9), CDC7(2), CDK2(2), CDK4(2), CDK6(1), CDK7(1), CDKN1A(1), CDKN1B(1), CDKN2A(1), CDKN2C(1), CHEK1(1), CHEK2(1), CREBBP(21), CUL1(7), DBF4(2), E2F2(1), E2F3(1), EP300(13), ESPL1(8), GSK3B(7), HDAC1(2), HDAC2(2), MAD1L1(1), MAD2L1(1), MAD2L2(1), MCM3(1), MCM4(4), MCM5(3), MCM6(3), MCM7(2), MDM2(4), ORC1L(1), ORC3L(1), ORC4L(1), ORC5L(1), PCNA(2), PKMYT1(1), PLK1(6), PRKDC(13), PTTG1(1), RB1(4), RBL1(3), RBL2(8), SKP1(1), SKP2(1), SMAD2(11), SMAD3(6), SMAD4(21), SMC1A(10), SMC1B(4), TFDP1(4), TGFB1(1), TGFB2(5), TP53(77), WEE1(3), YWHAB(2), YWHAE(3), YWHAQ(1)	30252673	414	127	377	73	128	89	8	105	81	3	<1.00e-15	<3.24e-14
4	HSA04210_APOPTOSIS	Genes involved in apoptosis	AIFM1, AKT1, AKT2, AKT3, APAF1, ATM, BAD, BAX, BCL2, BCL2L1, BID, BIRC2, BIRC3, BIRC4, CAPN1, CAPN2, CASP10, CASP3, CASP6, CASP7, CASP8, CASP9, CFLAR, CHP, CHUK, CSF2RB, CYCS, DFFA, DFFB, ENDOG, FADD, FAS, FASLG, IKBKB, IKBKG, IL1A, IL1B, IL1R1, IL1RAP, IL3, IL3RA, IRAK1, IRAK2, IRAK3, IRAK4, MAP3K14, MYD88, NFKB1, NFKB2, NFKBIA, NGFB, NTRK1, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKACA, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, RELA, RIPK1, TNF, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFRSF1A, TNFSF10, TP53, TRADD, TRAF2	80	AIFM1(1), AKT1(2), AKT2(5), APAF1(7), ATM(27), BAD(1), BAX(1), BCL2(1), BCL2L1(1), BID(1), BIRC2(2), BIRC3(2), CAPN1(2), CAPN2(5), CASP10(2), CASP3(1), CASP6(1), CASP7(1), CASP8(11), CASP9(2), CFLAR(2), CHUK(4), CSF2RB(7), DFFA(2), DFFB(2), FASLG(1), IKBKB(2), IL1A(1), IL1R1(3), IL3(3), IRAK1(1), IRAK2(8), IRAK3(1), IRAK4(2), MAP3K14(2), MYD88(1), NFKB1(3), NFKB2(2), NTRK1(6), PIK3CA(33), PIK3CB(2), PIK3CD(2), PIK3CG(12), PIK3R1(5), PIK3R2(1), PIK3R5(1), PPP3CA(1), PPP3CB(4), PPP3CC(3), PPP3R1(1), PPP3R2(1), PRKACB(1), PRKACG(2), PRKAR1A(1), PRKAR1B(1), PRKAR2B(2), RELA(2), RIPK1(2), TNFRSF10A(3), TNFRSF10B(2), TNFRSF10C(6), TNFRSF1A(1), TNFSF10(1), TP53(77), TRADD(1), TRAF2(1)	18529387	298	127	250	48	91	71	6	74	55	1	<1.00e-15	<3.24e-14
5	ALKPATHWAY	Activin receptor-like kinase 3 (ALK3) is required during gestation for cardiac muscle development.	ACVR1, APC, ATF2, AXIN1, BMP10, BMP2, BMP4, BMP5, BMP7, BMPR1A, BMPR2, CHRD, CTNNB1, DVL1, FZD1, GATA4, GSK3B, MADH1, MADH4, MADH5, MADH6, MAP3K7, MEF2C, MYL2, NKX2-5, NOG, NPPA, NPPB, RFC1, TCF1, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TGFBR3, WNT1	32	ACVR1(3), APC(121), AXIN1(1), BMP10(2), BMP4(1), BMP5(4), BMP7(5), BMPR1A(4), BMPR2(7), CHRD(5), CTNNB1(8), GATA4(1), GSK3B(7), MAP3K7(2), MEF2C(7), MYL2(1), NKX2-5(1), NPPA(1), RFC1(10), TGFB1(1), TGFB2(5), TGFBR1(6), TGFBR2(7), TGFBR3(5), WNT1(1)	7996440	216	126	179	31	37	23	2	37	83	34	<1.00e-15	<3.24e-14
6	ST_WNT_BETA_CATENIN_PATHWAY	Beta-catenin is degraded in the absence of Wnt signaling; when extracellular Wnt binds Frizzled receptors, beta-catenin accumulates in the nucleus and may promote cell survival.	AKT1, AKT2, AKT3, ANKRD6, APC, AXIN1, AXIN2, C22orf2, CER1, CSNK1A1, CTNNB1, DACT1, DKK1, DKK2, DKK3, DKK4, DVL1, FRAT1, FSTL1, GSK3A, GSK3B, IDAX, LAMR1, LRP1, MVP, NKD1, NKD2, PIN1, PSEN1, PTPRA, SENP2, SFRP1, TSHB, WIF1	30	AKT1(2), AKT2(5), ANKRD6(5), APC(121), AXIN1(1), AXIN2(7), CER1(3), CSNK1A1(2), CTNNB1(8), DACT1(5), DKK1(3), DKK2(5), DKK3(2), DKK4(4), FSTL1(5), GSK3A(2), GSK3B(7), LRP1(14), MVP(4), NKD1(3), NKD2(1), PIN1(1), PSEN1(3), PTPRA(2), SENP2(2), SFRP1(2), WIF1(2)	8848505	221	126	184	33	52	22	4	32	77	34	<1.00e-15	<3.24e-14
7	GSK3PATHWAY	Bacterial lipopolysaccharide activates AKT to promote the survival and activation of macrophages and inhibits Gsk3-beta to promote beta-catenin accumulation in the nucleus.	AKT1, APC, AXIN1, CCND1, CD14, CTNNB1, DVL1, FZD1, GJA1, GNAI1, GSK3B, IRAK1, LBP, LEF1, LY96, MYD88, NFKB1, PDPK1, PIK3CA, PIK3R1, PPP2CA, PRKR, RELA, TIRAP, TLR4, TOLLIP, WNT1	26	AKT1(2), APC(121), AXIN1(1), CD14(1), CTNNB1(8), GJA1(3), GNAI1(3), GSK3B(7), IRAK1(1), LBP(1), LEF1(4), LY96(2), MYD88(1), NFKB1(3), PDPK1(1), PIK3CA(33), PIK3R1(5), PPP2CA(1), RELA(2), TIRAP(1), TLR4(7), TOLLIP(1), WNT1(1)	6608775	210	123	159	24	32	36	4	29	75	34	<1.00e-15	<3.24e-14
8	HSA04540_GAP_JUNCTION	Genes involved in gap junction	ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ADRB1, CDC2, CSNK1D, DRD1, DRD2, EDG2, EGF, EGFR, GJA1, GJD2, GNA11, GNAI1, GNAI2, GNAI3, GNAQ, GNAS, GRB2, GRM1, GRM5, GUCY1A2, GUCY1A3, GUCY1B3, GUCY2C, GUCY2D, GUCY2F, HRAS, HTR2A, HTR2B, HTR2C, ITPR1, ITPR2, ITPR3, KRAS, LOC643224, LOC654264, MAP2K1, MAP2K2, MAP2K5, MAP3K2, MAPK1, MAPK3, MAPK7, NPR1, NPR2, NRAS, PDGFA, PDGFB, PDGFC, PDGFD, PDGFRA, PDGFRB, PLCB1, PLCB2, PLCB3, PLCB4, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKG1, PRKG2, PRKX, PRKY, RAF1, SOS1, SOS2, SRC, TJP1, TUBA1A, TUBA1B, TUBA1C, TUBA3C, TUBA3D, TUBA3E, TUBA4A, TUBA8, TUBAL3, TUBB, TUBB1, TUBB2A, TUBB2B, TUBB2C, TUBB3, TUBB4, TUBB4Q, TUBB6, TUBB8	92	ADCY1(4), ADCY2(12), ADCY3(1), ADCY4(9), ADCY5(8), ADCY6(1), ADCY7(3), ADCY8(11), ADCY9(4), ADRB1(2), CSNK1D(3), DRD1(1), DRD2(3), EGF(3), EGFR(10), GJA1(3), GNA11(1), GNAI1(3), GNAQ(3), GNAS(6), GRB2(2), GRM1(9), GRM5(8), GUCY1A2(8), GUCY1A3(12), GUCY1B3(7), GUCY2C(7), GUCY2D(4), GUCY2F(7), HTR2A(2), HTR2B(1), HTR2C(6), ITPR1(11), ITPR2(12), ITPR3(11), KRAS(58), MAP2K1(3), MAP2K5(2), MAP3K2(2), MAPK1(2), MAPK3(2), MAPK7(3), NPR1(6), NPR2(9), NRAS(15), PDGFA(1), PDGFC(2), PDGFD(3), PDGFRA(13), PDGFRB(5), PLCB1(8), PLCB2(3), PLCB3(3), PLCB4(9), PRKACB(1), PRKACG(2), PRKCA(2), PRKCG(8), PRKG1(4), PRKG2(3), PRKX(2), RAF1(4), SOS1(5), SOS2(9), SRC(3), TJP1(5), TUBA3C(9), TUBA3D(2), TUBA3E(4), TUBA4A(1), TUBA8(1), TUBAL3(3), TUBB(1), TUBB1(2), TUBB2A(1), TUBB2B(3), TUBB3(1), TUBB4(2), TUBB4Q(2), TUBB6(3), TUBB8(2)	28826153	432	123	372	142	154	105	11	133	28	1	<1.00e-15	<3.24e-14
9	ST_MYOCYTE_AD_PATHWAY	Cardiac myocytes have a variety of adrenergic receptors that induce subtype-specific signaling effects.	ADRB1, AKT1, APC, ASAH1, BF, CAMP, CAV3, DAG1, DLG4, EPHB2, GAS, GNAI1, GNAQ, HTATIP, ITPR1, ITPR2, ITPR3, KCNJ3, KCNJ5, KCNJ9, MAPK1, PITX2, PLB, PTX1, PTX3, RAC1, RHO, RYR1	23	ADRB1(2), AKT1(2), APC(121), ASAH1(3), CAV3(2), DAG1(4), DLG4(2), EPHB2(7), GNAI1(3), GNAQ(3), ITPR1(11), ITPR2(12), ITPR3(11), KCNJ3(6), KCNJ5(3), KCNJ9(2), MAPK1(2), PITX2(2), PTX3(2), RHO(2), RYR1(19)	9853585	221	123	184	49	55	22	5	33	72	34	<1.00e-15	<3.24e-14
10	WNTPATHWAY	The Wnt glycoprotein binds to membrane-bound receptors such as Frizzled to activate a number of signaling pathways, including that of beta-catenin.	APC, AXIN1, BTRC, CCND1, CREBBP, CSNK1A1, CSNK1D, CSNK2A1, CTBP1, CTNNB1, DVL1, FRAT1, FZD1, GSK3B, HDAC1, MADH4, MAP3K7, MAP3K7IP1, MYC, NLK, PPARD, PPP2CA, TCF1, TLE1, WIF1, WNT1	22	APC(121), AXIN1(1), BTRC(2), CREBBP(21), CSNK1A1(2), CSNK1D(3), CSNK2A1(4), CTBP1(1), CTNNB1(8), GSK3B(7), HDAC1(2), MAP3K7(2), NLK(1), PPARD(1), PPP2CA(1), TLE1(1), WIF1(2), WNT1(1)	6371845	181	120	145	22	26	21	2	24	74	34	<1.00e-15	<3.24e-14

Table 7. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 0. 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	EOSINOPHILSPATHWAY	Recruitment of eosinophils in the inflammatory response observed in asthma occurs via the chemoattractant eotaxin binding to the CCR3 receptor.	CCL11, CCL5, CCR3, CSF2, HLA-DRA, HLA-DRB1, IL3, IL5	8	CCR3(3), HLA-DRA(4), HLA-DRB1(1), IL3(3)	661548	11	11	10	2	5	1	0	3	0	2	0.0017	0.48
2	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	232	ADCYAP1R1(1), ADORA1(5), ADORA2A(3), ADORA2B(1), ADORA3(3), ADRA1A(5), ADRA1B(4), ADRA2A(3), ADRB1(2), ADRB3(1), AGTR1(3), AGTR2(4), AVPR1A(3), AVPR1B(3), AVPR2(6), BDKRB2(2), BRS3(1), C3AR1(2), C5AR1(2), CALCR(3), CALCRL(5), CCKAR(1), CCKBR(3), CGA(1), CHRM1(3), CHRM2(8), CHRM3(4), CHRM5(1), CNR1(3), CRHR1(1), CRHR2(4), CTSG(2), CYSLTR1(3), CYSLTR2(3), DRD1(1), DRD2(3), DRD3(3), DRD5(2), EDNRA(4), EDNRB(7), F2(2), F2RL2(2), FPR1(2), FSHB(1), FSHR(6), GABBR1(4), GABBR2(3), GABRA1(2), GABRA2(6), GABRA3(4), GABRA4(6), GABRA6(4), GABRB1(6), GABRB2(4), GABRB3(5), GABRE(5), GABRG1(7), GABRG2(8), GABRG3(5), GABRP(2), GABRQ(7), GABRR1(2), GABRR2(3), GALR1(1), GH1(1), GH2(1), GHR(6), GHRHR(2), GHSR(5), GLP1R(2), GLP2R(3), GLRA1(2), GLRA2(2), GLRA3(7), GLRB(6), GNRHR(4), GPR156(6), GPR50(5), GPR63(2), GPR83(1), GRIA2(10), GRIA3(5), GRIA4(12), GRID1(15), GRID2(10), GRIK1(5), GRIK2(10), GRIK4(11), GRIK5(5), GRIN1(1), GRIN2A(15), GRIN2B(8), GRIN2C(2), GRIN2D(3), GRIN3A(3), GRM1(9), GRM2(3), GRM3(5), GRM4(7), GRM5(8), GRM6(9), GRM7(8), GRM8(7), GRPR(3), GZMA(2), HCRTR1(1), HCRTR2(1), HRH1(1), HRH2(4), HRH4(2), HTR1A(3), HTR1B(3), HTR1D(2), HTR1E(5), HTR1F(2), HTR2A(2), HTR2B(1), HTR2C(6), HTR4(2), HTR5A(2), HTR7(6), LEP(1), LEPR(5), LHB(1), LHCGR(4), MAS1(1), MC2R(2), MC3R(1), MC4R(3), MC5R(4), MCHR1(6), MCHR2(2), MLNR(3), MTNR1B(3), NMUR1(4), NMUR2(6), NPBWR1(3), NPFFR2(3), NPY1R(4), NPY2R(5), NPY5R(1), NR3C1(3), NTSR1(1), NTSR2(4), OPRD1(1), OPRK1(5), OPRM1(1), OXTR(2), P2RX1(1), P2RX2(1), P2RX3(2), P2RX4(2), P2RX5(1), P2RX7(2), P2RY1(3), P2RY10(6), P2RY13(2), P2RY14(4), P2RY2(2), P2RY4(6), PARD3(5), PPYR1(1), PRL(2), PRLR(2), PRSS1(3), PRSS2(1), PRSS3(4), PTAFR(1), PTGER2(1), PTGER3(6), PTGFR(6), PTGIR(1), PTH2R(6), RXFP1(2), RXFP2(8), SCTR(3), SSTR1(4), SSTR2(2), SSTR4(2), TAAR1(3), TAAR2(2), TAAR5(5), TAAR6(2), TAAR8(1), TAAR9(1), TACR1(2), TACR2(1), TACR3(4), THRA(2), THRB(4), TRHR(6), TRPV1(3), TSHR(6), VIPR1(3), VIPR2(3)	48166910	709	118	706	266	272	154	15	210	58	0	0.0022	0.48
3	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	13	AXIN1(1), CREBBP(21), CTNNB1(8), EP300(13), GSK3B(7), HDAC1(2), LDB1(3), LEF1(4), PITX2(2), TRRAP(17), WNT1(1)	6009423	79	46	78	21	33	25	1	8	12	0	0.0028	0.48
4	PELP1PATHWAY	Pelp1 acts downstream of activated estrogen receptor to promote cell proliferation and is overexpressed in many breast tumors.	CREBBP, EP300, ESR1, MAPK1, MAPK3, PELP1, SRC	7	CREBBP(21), EP300(13), ESR1(12), MAPK1(2), MAPK3(2), PELP1(2), SRC(3)	3251889	55	34	55	13	18	20	1	9	7	0	0.0032	0.48
5	CTLA4PATHWAY	T cell activation requires interaction with an antigen-MHC-I complex on an antigen-presenting cell (APC), as well as CD28 interaction with the APC's CD80 or 86.	CD28, CD3D, CD3E, CD3G, CD3Z, CD80, CD86, CTLA4, GRB2, HLA-DRA, HLA-DRB1, ICOS, ICOSL, IL2, ITK, LCK, PIK3CA, PIK3R1, PTPN11, TRA@, TRB@	16	CD28(1), CD3D(1), CD3G(2), CTLA4(1), GRB2(2), HLA-DRA(4), HLA-DRB1(1), ICOS(1), IL2(3), ITK(8), LCK(2), PIK3R1(5), PTPN11(2)	2385350	33	23	32	7	7	9	2	8	5	2	0.0044	0.48
6	GPCRDB_CLASS_A_RHODOPSIN_LIKE		ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA1D, ADRA2A, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BLR1, BRS3, C3AR1, C5R1, CCBP2, CCKAR, CCKBR, CCR1, CCR10, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CCRL1, CCRL2, CHML, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CMKLR1, CMKOR1, CNR1, CNR2, CX3CR1, CXCR3, CXCR4, DRD1, DRD2, DRD3, DRD4, DRD5, EDNRA, EDNRB, ELA3A, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHR, GALR1, GALR2, GALR3, GALT, GHSR, GNB2L1, GPR10, GPR147, GPR17, GPR173, GPR174, GPR23, GPR24, GPR27, GPR3, GPR30, GPR35, GPR37, GPR37L1, GPR4, GPR44, GPR50, GPR6, GPR63, GPR74, GPR77, GPR83, GPR85, GPR87, GPR92, GRPR, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, HTR7, LOC93164, IL8RA, IL8RB, LHCGR, LTB4R, MAS1, MC1R, MC3R, MC4R, MC5R, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPY1R, NPY2R, NPY5R, NPY6R, NTSR1, NTSR2, OPN1SW, OPN3, OPRD1, OPRK1, OPRL1, OPRM1, OR10A5, OR11A1, OR12D3, OR1C1, OR1F1, OR1Q1, OR2H1, OR5V1, OR5V1, OR12D3, OR7A5, OR7C1, OR8B8, OXTR, P2RY1, P2RY10, P2RY11, P2RY12, P2RY13, P2RY14, P2RY2, P2RY5, P2RY6, PPYR1, PTAFR, PTGDR, PTGER1, PTGER2, PTGER4, PTGFR, PTGIR, Rgr, RGR, RHO, RRH, SSTR1, SSTR2, SSTR3, SSTR4, SUCNR1, TBXA2R, TRHR	162	ADORA1(5), ADORA2A(3), ADORA2B(1), ADORA3(3), ADRA1A(5), ADRA1B(4), ADRA1D(2), ADRA2A(3), ADRB1(2), ADRB3(1), AGTR1(3), AGTR2(4), AVPR1A(3), AVPR1B(3), AVPR2(6), BDKRB2(2), BRS3(1), C3AR1(2), CCBP2(5), CCKAR(1), CCKBR(3), CCR1(5), CCR3(3), CCR5(1), CCR6(2), CCR7(1), CCR8(4), CCR9(4), CCRL1(2), CHML(4), CHRM1(3), CHRM2(8), CHRM3(4), CHRM5(1), CMKLR1(2), CNR1(3), CX3CR1(1), CXCR4(3), DRD1(1), DRD2(3), DRD3(3), DRD5(2), EDNRA(4), EDNRB(7), F2RL2(2), FPR1(2), FSHR(6), GALR1(1), GALT(2), GHSR(5), GPR17(1), GPR173(2), GPR174(2), GPR37(6), GPR37L1(3), GPR4(1), GPR50(5), GPR6(5), GPR63(2), GPR77(1), GPR83(1), GPR85(1), GPR87(4), GRPR(3), HCRTR1(1), HCRTR2(1), HRH1(1), HRH2(4), HTR1A(3), HTR1B(3), HTR1D(2), HTR1E(5), HTR1F(2), HTR2A(2), HTR2B(1), HTR2C(6), HTR4(2), HTR5A(2), HTR7(6), LHCGR(4), MAS1(1), MC3R(1), MC4R(3), MC5R(4), MLNR(3), MTNR1B(3), NMUR1(4), NMUR2(6), NPY1R(4), NPY2R(5), NPY5R(1), NTSR1(1), NTSR2(4), OPN1SW(3), OPN3(1), OPRD1(1), OPRK1(5), OPRM1(1), OR12D3(1), OR1C1(1), OR1F1(2), OR2H1(3), OR5V1(2), OR7A5(3), OR8B8(2), OXTR(2), P2RY1(3), P2RY10(6), P2RY12(3), P2RY13(2), P2RY14(4), P2RY2(2), PPYR1(1), PTAFR(1), PTGER2(1), PTGFR(6), PTGIR(1), RGR(2), RHO(2), RRH(2), SSTR1(4), SSTR2(2), SSTR4(2), TRHR(6)	26305643	350	94	351	123	144	85	5	90	26	0	0.0059	0.48
7	GABAPATHWAY	Gamma-aminobutyric acid (GABA) is an inhibitory neurotransmitter whose receptor is regulated by Plic-1, gephyrin, and GABARAP, which promote receptor clustering.	DNM1, GABARAP, GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GPHN, NSF, SRC, UBQLN1	11	DNM1(8), GABRA1(2), GABRA2(6), GABRA3(4), GABRA4(6), GABRA6(4), GPHN(11), NSF(1), SRC(3), UBQLN1(2)	2538782	47	27	45	20	13	9	1	17	7	0	0.0068	0.48
8	1_AND_2_METHYLNAPHTHALENE_DEGRADATION		ADH1A, ADH1A, ADH1B, ADH1C, ADH1B, ADH1C, ADH4, ADH6, ADH7, ADHFE1	7	ADH1B(2), ADH1C(3), ADH4(1), ADH6(5), ADH7(2), ADHFE1(6)	1229065	19	16	19	5	3	4	1	11	0	0	0.0074	0.48
9	FLUMAZENILPATHWAY	Flumazenil is a benzodiazepine receptor antagonist that may induce protective preconditioning in ischemic cardiomyocytes.	GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GPX1, PRKCE, SOD1	8	GABRA1(2), GABRA2(6), GABRA3(4), GABRA4(6), GABRA6(4), GPX1(1), PRKCE(4)	1520965	27	19	27	5	9	5	0	10	3	0	0.0075	0.48
10	CCR3PATHWAY	CCR3 is a G-protein coupled receptor that recruits eosinophils to inflammation sites via chemokine ligands.	ARHA, CCL11, CCR3, CFL1, GNAQ, GNAS, GNB1, GNGT1, HRAS, LIMK1, MAP2K1, MAPK1, MAPK3, MYL2, NOX1, PIK3C2G, PLCB1, PPP1R12B, PRKCA, PRKCB1, PTK2, RAF1, ROCK2	21	CCR3(3), CFL1(1), GNAQ(3), GNAS(6), GNB1(1), LIMK1(4), MAP2K1(3), MAPK1(2), MAPK3(2), MYL2(1), NOX1(1), PIK3C2G(7), PLCB1(8), PPP1R12B(5), PRKCA(2), PTK2(5), RAF1(4), ROCK2(2)	5505383	60	39	58	11	24	8	2	17	9	0	0.0078	0.48

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)

Made with Nozzle