Mutation Analysis (MutSig v2.0) - Colon/Rectal Adenocarcinoma (Primary solid tumor)

Mutation Analysis (MutSig v2.0)

Colon/Rectal Adenocarcinoma (Primary solid tumor)

22 February 2013 | analyses__2013_02_22

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/C1TT4P4C

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: COADREAD-TP
Number of patients in set: 224

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:COADREAD-TP.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 135
Mutations seen in COSMIC: 739
Significantly mutated genes in COSMIC territory: 29
Genes with clustered mutations (≤ 3 aa apart): 1746
Significantly mutated genesets: 146
Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing

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

Mutation Filtering

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

Results

Breakdown of Mutations by Type

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

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

Breakdown of Mutation Rates by Category Type

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	20381	335477044	0.000061	61	6
*Cp(A/C/T)->mut	21021	2775898083	7.6e-06	7.6	0.75
A->mut	12112	3017613932	4e-06	4	0.4
*CpG->(G/A)	562	335477044	1.7e-06	1.7	0.17
indel+null	7447	6128989199	1.2e-06	1.2	0.12
double_null	304	6128989199	5e-08	0.05	0.0049
Total	61827	6128989199	1e-05	10	1

Target Coverage for Each Individual

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: COADREAD-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: *Cp(A/C/T)->mut
n3 = number of nonsilent mutations of type: A->mut
n4 = number of nonsilent mutations of type: *CpG->(G/A)
n5 = number of nonsilent mutations of type: indel+null
n6 = number of nonsilent mutations of type: double_null
p_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: 135. 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	577918	45	38	28	2	23	6	5	2	9	0	5.88e-15	0.052	0.000048	0.000	0.000
2	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	618889	40	33	21	2	6	20	14	0	0	0	6.99e-15	0.00015	2e-06	0.000	0.000
3	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	131263	20	20	8	0	2	14	4	0	0	0	7.99e-15	0.16	0.000061	0.000	0.000
4	SMAD4	SMAD family member 4	377497	29	26	22	0	10	6	9	0	3	1	7.55e-15	0.0024	0.0022	6.66e-16	2.24e-12
5	APC	adenomatous polyposis coli	1891000	187	160	128	4	6	15	11	0	103	52	3.77e-15	0.98	0	<1.00e-15	<2.24e-12
6	TP53	tumor protein p53	267736	122	120	69	2	48	22	12	2	38	0	<1.00e-15	0	0	<1.00e-15	<2.24e-12
7	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	158010	96	96	11	0	0	91	4	0	1	0	2.11e-15	0.0014	0	<1.00e-15	<2.24e-12
8	BRAF	v-raf murine sarcoma viral oncogene homolog B1	493213	23	22	4	0	0	0	23	0	0	0	8.54e-12	0	0	<1.00e-15	<2.24e-12
9	FAM123B	family with sequence similarity 123B	641973	27	25	24	2	1	3	4	0	19	0	3.66e-15	0.85	0.019	2.66e-15	5.31e-12
10	TTN	titin	16863591	290	85	286	79	82	114	72	2	13	7	2.11e-13	0.97	1	6.36e-12	1.14e-08
11	SMAD2	SMAD family member 2	322425	16	15	12	1	3	5	3	0	5	0	4.63e-11	0.18	0.02	2.60e-11	4.24e-08
12	TCF7L2	transcription factor 7-like 2 (T-cell specific, HMG-box)	400503	20	18	18	4	5	5	3	0	7	0	9.40e-11	0.21	0.022	5.87e-11	8.78e-08
13	FAT4	FAT tumor suppressor homolog 4 (Drosophila)	3144726	73	39	73	21	19	30	19	1	4	0	3.76e-08	0.61	0.002	1.87e-09	2.58e-06
14	KRTAP5-5	keratin associated protein 5-5	119310	4	4	1	1	0	0	0	4	0	0	2.66e-06	0.000048	0.000048	3.05e-09	3.91e-06
15	ACVR1B	activin A receptor, type IB	339499	15	14	15	0	4	7	2	0	2	0	1.57e-07	0.00093	0.0044	1.52e-08	1.82e-05
16	WBSCR17	Williams-Beuren syndrome chromosome region 17	400400	19	19	18	3	10	5	1	0	3	0	1.30e-08	0.74	0.18	4.94e-08	5.54e-05
17	PCDH9	protocadherin 9	823363	26	22	26	7	3	11	11	0	1	0	4.66e-09	0.94	1	9.41e-08	9.94e-05
18	LRP1B	low density lipoprotein-related protein 1B (deleted in tumors)	3162768	75	39	73	18	11	34	22	0	5	3	5.27e-09	0.91	1	1.06e-07	0.000105
19	TNFRSF10C	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	167178	6	6	2	0	0	6	0	0	0	0	8.51e-05	1	0.000071	1.20e-07	0.000113
20	MAP2K4	mitogen-activated protein kinase kinase 4	246117	11	11	10	1	3	4	2	0	2	0	4.09e-07	0.067	0.037	2.86e-07	0.000257
21	KIAA1804		532518	18	15	16	0	8	7	1	0	2	0	1.89e-06	0.017	0.0091	3.25e-07	0.000278
22	NRXN1	neurexin 1	761168	24	20	24	11	10	7	4	1	2	0	1.12e-06	0.23	0.031	6.25e-07	0.000510
23	KLHL4	kelch-like 4 (Drosophila)	494271	16	16	16	3	6	8	2	0	0	0	4.58e-08	0.62	0.86	7.10e-07	0.000554
24	SOX9	SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal)	256689	10	10	10	0	0	0	1	0	8	1	1.21e-06	0.48	0.07	1.46e-06	0.00109
25	PRDM9	PR domain containing 9	448274	19	16	19	4	6	7	4	0	1	1	1.41e-07	0.96	0.73	1.77e-06	0.00127
26	PCBP1	poly(rC) binding protein 1	176357	6	6	3	0	0	0	6	0	0	0	0.000416	0.0035	0.0003	2.11e-06	0.00146
27	DMD	dystrophin (muscular dystrophy, Duchenne and Becker types)	2565596	47	33	46	6	10	14	14	0	9	0	1.27e-06	0.86	0.1	2.23e-06	0.00148
28	CSMD1	CUB and Sushi multiple domains 1	1444240	45	26	44	19	9	21	9	1	3	2	2.45e-07	0.66	1	3.97e-06	0.00255
29	LIFR	leukemia inhibitory factor receptor alpha	744473	24	18	24	5	4	6	9	1	4	0	3.77e-07	0.63	0.86	5.18e-06	0.00321
30	OR6N1	olfactory receptor, family 6, subfamily N, member 1	210752	10	10	10	2	2	6	2	0	0	0	4.24e-06	0.27	0.092	6.13e-06	0.00367
31	CCDC160	coiled-coil domain containing 160	85540	9	7	9	0	0	4	0	1	3	1	6.02e-07	0.38	0.87	8.06e-06	0.00467
32	CNTN6	contactin 6	708576	22	17	22	3	5	13	2	0	2	0	6.93e-07	0.98	1	1.05e-05	0.00591
33	CPXCR1	CPX chromosome region, candidate 1	186322	10	9	10	1	2	5	2	0	1	0	1.22e-06	0.21	0.63	1.16e-05	0.00631
34	SLITRK1	SLIT and NTRK-like family, member 1	448459	17	15	16	5	6	2	6	0	3	0	2.95e-06	0.93	0.35	1.52e-05	0.00803
35	CTNNB1	catenin (cadherin-associated protein), beta 1, 88kDa	528618	12	11	12	0	3	4	3	1	1	0	3.98e-06	0.97	0.38	2.20e-05	0.0111

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: 29. Number of genes displayed: 10

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

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
6654	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	96	2294	2964	3043	2294	2964	3043
13035	TP53	tumor protein p53	122	280	459	747	280	459	747
1255	BRAF	v-raf murine sarcoma viral oncogene homolog B1	23	190	190	190	190	190	190
645	APC	adenomatous polyposis coli	187	166	221	326	166	221	326
4535	FBXW7	F-box and WD repeat domain containing 7	45	81	87	105	81	87	105
9463	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	40	74	111	136	74	111	136
8399	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	20	61	73	73	61	73	73
11751	SMAD4	SMAD family member 4	29	24	30	56	24	30	56
4110	ERBB3	v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian)	14	10	15	15	10	15	15
4362	FAM22F	family with sequence similarity 22, member F	9	10	10	10	10	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: 146. Number of genesets displayed: 10

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p	q
1	HSA04310_WNT_SIGNALING_PATHWAY	Genes involved in Wnt signaling pathway	APC, APC2, AXIN1, AXIN2, BTRC, CACYBP, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CCND1, CCND2, CCND3, CER1, CHD8, CHP, CREBBP, CSNK1A1, CSNK1A1L, CSNK1E, CSNK2A1, CSNK2A2, CSNK2B, CTBP1, CTBP2, CTNNB1, CTNNBIP1, CUL1, CXXC4, DAAM1, DAAM2, DKK1, DKK2, DKK4, DVL1, DVL2, DVL3, EP300, FBXW11, FOSL1, FRAT1, FRAT2, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LEF1, LOC652788, LRP5, LRP6, MAP3K7, MAPK10, MAPK8, MAPK9, MMP7, MYC, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NKD1, NKD2, NLK, PLCB1, PLCB2, PLCB3, PLCB4, PORCN, PPARD, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRICKLE1, PRICKLE2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PSEN1, RAC1, RAC2, RAC3, RBX1, RHOA, ROCK1, ROCK2, RUVBL1, SENP2, SFRP1, SFRP2, SFRP4, SFRP5, SIAH1, SKP1, SMAD2, SMAD3, SMAD4, SOX17, TBL1X, TBL1XR1, TBL1Y, TCF7, TCF7L1, TCF7L2, TP53, VANGL1, VANGL2, WIF1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B	144	APC(187), APC2(1), AXIN1(2), AXIN2(9), BTRC(5), CACYBP(2), CAMK2A(1), CAMK2B(2), CAMK2D(3), CAMK2G(2), CCND2(1), CCND3(1), CER1(3), CHD8(6), CREBBP(25), CSNK1A1(2), CSNK1A1L(5), CSNK2A1(4), CSNK2A2(2), CSNK2B(2), CTBP1(1), CTBP2(2), CTNNB1(12), CTNNBIP1(1), CUL1(8), CXXC4(1), DAAM1(2), DAAM2(9), DKK1(5), DKK2(6), DKK4(7), DVL2(9), DVL3(4), EP300(15), FBXW11(8), FZD1(1), FZD10(6), FZD2(2), FZD3(13), FZD4(2), FZD6(6), FZD7(3), FZD8(1), GSK3B(8), LEF1(4), LRP5(5), LRP6(17), MAP3K7(4), MAPK10(8), MAPK8(7), MAPK9(5), MMP7(5), NFAT5(5), NFATC1(2), NFATC2(5), NFATC3(5), NFATC4(5), NKD1(3), NKD2(1), NLK(1), PLCB1(8), PLCB2(3), PLCB3(4), PLCB4(10), PORCN(2), PPARD(2), PPP2CA(1), PPP2CB(2), PPP2R1A(4), PPP2R1B(2), PPP2R2A(1), PPP2R2B(3), PPP2R2C(4), PPP3CA(3), PPP3CB(5), PPP3CC(4), PPP3R1(1), PPP3R2(1), PRICKLE1(11), PRICKLE2(6), PRKACA(1), PRKACB(1), PRKACG(3), PRKCA(4), PRKCG(10), PRKX(2), PSEN1(3), RBX1(1), RHOA(5), ROCK1(15), ROCK2(6), RUVBL1(8), SENP2(3), SFRP1(3), SFRP2(3), SFRP4(4), SFRP5(1), SIAH1(1), SKP1(1), SMAD2(16), SMAD3(9), SMAD4(29), SOX17(2), TBL1X(6), TBL1XR1(6), TBL1Y(1), TCF7(6), TCF7L1(3), TCF7L2(20), TP53(122), VANGL1(2), VANGL2(5), WIF1(2), WNT1(1), WNT10B(4), WNT11(3), WNT16(2), WNT2(1), WNT2B(3), WNT3(4), WNT3A(1), WNT4(1), WNT5A(3), WNT6(1), WNT7A(2), WNT7B(2), WNT8A(2), WNT9A(2), WNT9B(2)	50774791	894	218	758	156	275	204	133	8	221	53	<1.00e-15	<4.11e-14
2	HSA04810_REGULATION_OF_ACTIN_CYTOSKELETON	Genes involved in regulation of actin cytoskeleton	ABI2, ACTN1, ACTN2, ACTN3, ACTN4, APC, APC2, ARAF, ARHGEF1, ARHGEF12, ARHGEF4, ARHGEF6, ARHGEF7, ARPC1A, ARPC1B, ARPC2, ARPC3, ARPC4, ARPC5, ARPC5L, BAIAP2, BCAR1, BDKRB1, BDKRB2, BRAF, C3orf10, CD14, CDC42, CFL1, CFL2, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CRK, CRKL, CSK, CYFIP1, CYFIP2, DIAPH1, DIAPH2, DIAPH3, DOCK1, EGF, EGFR, EZR, F2, F2R, FGD1, FGD3, FGF1, FGF10, FGF11, FGF12, FGF13, FGF14, FGF16, FGF17, FGF18, FGF19, FGF2, FGF20, FGF21, FGF22, FGF23, FGF3, FGF4, FGF5, FGF6, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, FGFR4, FN1, GIT1, GNA12, GNA13, GNG12, GRLF1, GSN, HRAS, INS, IQGAP1, IQGAP2, IQGAP3, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAD, ITGAE, ITGAL, ITGAM, ITGAV, ITGAX, ITGB1, ITGB2, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, KRAS, LIMK1, LIMK2, LOC200025, LOC645126, LOC653888, MAP2K1, MAP2K2, MAPK1, MAPK3, MLCK, MOS, MRAS, MRCL3, MRLC2, MSN, MYH10, MYH14, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLK, MYLK2, MYLPF, NCKAP1, NCKAP1L, NRAS, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PDGFA, PDGFB, PDGFRA, PDGFRB, PFN1, PFN2, PFN3, PFN4, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIP4K2A, PIP4K2B, PIP4K2C, PIP5K1A, PIP5K1B, PIP5K1C, PIP5K3, PPP1CA, PPP1CB, PPP1CC, PPP1R12A, PPP1R12B, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, RDX, RHOA, ROCK1, ROCK2, RRAS, RRAS2, SCIN, SLC9A1, SOS1, SOS2, SSH1, SSH2, SSH3, TIAM1, TIAM2, TMSB4X, TMSB4Y, TMSL3, VAV1, VAV2, VAV3, VCL, WAS, WASF1, WASF2, WASL	203	ABI2(1), ACTN1(5), ACTN2(8), ACTN3(3), ACTN4(3), APC(187), APC2(1), ARAF(3), ARHGEF1(5), ARHGEF12(9), ARHGEF4(4), ARHGEF6(10), ARHGEF7(8), ARPC1A(5), ARPC1B(2), ARPC2(2), ARPC5(1), ARPC5L(2), BAIAP2(1), BDKRB2(3), BRAF(23), CD14(1), CDC42(1), CFL1(1), CHRM1(3), CHRM2(11), CHRM3(4), CHRM4(1), CHRM5(2), CRKL(2), CSK(3), CYFIP1(6), CYFIP2(5), DIAPH1(1), DIAPH2(12), DIAPH3(5), DOCK1(7), EGF(3), EGFR(11), EZR(2), F2(3), FGD1(8), FGD3(2), FGF1(2), FGF11(3), FGF12(3), FGF13(3), FGF14(5), FGF17(1), FGF19(1), FGF20(2), FGF21(1), FGF23(1), FGF3(1), FGF5(4), FGF6(3), FGF7(1), FGF8(1), FGF9(1), FGFR1(4), FGFR2(6), FGFR3(2), FGFR4(2), FN1(21), GIT1(3), GNA12(2), GNA13(2), GRLF1(12), IQGAP1(13), IQGAP2(12), IQGAP3(11), ITGA1(3), ITGA10(7), ITGA11(4), ITGA2(6), ITGA2B(4), ITGA3(4), ITGA4(8), ITGA5(7), ITGA6(4), ITGA7(6), ITGA8(8), ITGA9(6), ITGAD(8), ITGAE(7), ITGAL(8), ITGAM(8), ITGAV(5), ITGAX(6), ITGB1(6), ITGB2(5), ITGB3(9), ITGB4(3), ITGB5(6), ITGB6(6), ITGB7(4), ITGB8(5), KRAS(96), LIMK1(5), LIMK2(5), MAP2K1(4), MAP2K2(1), MAPK1(2), MAPK3(3), MOS(3), MRAS(1), MSN(6), MYH10(10), MYH14(12), MYH9(12), MYL2(1), MYL7(1), MYL9(2), MYLK(14), MYLK2(3), NCKAP1(9), NCKAP1L(11), NRAS(20), PAK1(5), PAK2(3), PAK3(5), PAK6(1), PAK7(7), PDGFA(1), PDGFRA(17), PDGFRB(6), PFN2(1), PFN4(1), PIK3CA(40), PIK3CB(2), PIK3CD(3), PIK3CG(14), PIK3R1(10), PIK3R2(1), PIK3R3(4), PIK3R5(1), PIP4K2A(2), PIP4K2B(2), PIP4K2C(3), PIP5K1A(3), PIP5K1B(2), PIP5K1C(4), PPP1CB(2), PPP1CC(2), PPP1R12A(3), PPP1R12B(9), PTK2(5), RAF1(6), RDX(3), RHOA(5), ROCK1(15), ROCK2(6), RRAS2(2), SCIN(3), SLC9A1(4), SOS1(7), SOS2(11), SSH1(6), SSH2(4), SSH3(1), TIAM1(17), TIAM2(16), TMSL3(1), VAV1(13), VAV2(4), VAV3(12), VCL(2), WAS(1), WASF1(3), WASF2(2), WASL(7)	87387370	1187	216	982	278	334	392	203	8	194	56	<1.00e-15	<4.11e-14
3	ST_ADRENERGIC	Adrenergic receptors respond to epinephrine and norepinephrine signaling.	AKT1, APC, AR, ASAH1, BF, BRAF, CAMP, CCL13, CCL15, CCL16, DAG1, EGFR, GAS, GNA11, GNA15, GNAI1, GNAQ, ITPKA, ITPKB, ITPR1, ITPR2, ITPR3, KCNJ3, KCNJ5, KCNJ9, MAPK1, MAPK10, MAPK14, PHKA2, PIK3CA, PIK3CD, PIK3R1, PITX2, PTX1, PTX3, RAF1, SRC	34	AKT1(2), APC(187), AR(6), ASAH1(3), BRAF(23), CCL13(1), CCL15(1), DAG1(5), EGFR(11), GNA11(1), GNA15(3), GNAI1(4), GNAQ(4), ITPKB(4), ITPR1(19), ITPR2(18), ITPR3(12), KCNJ3(6), KCNJ5(4), KCNJ9(3), MAPK1(2), MAPK10(8), MAPK14(3), PHKA2(6), PIK3CA(40), PIK3CD(3), PIK3R1(10), PITX2(2), PTX3(2), RAF1(6), SRC(3)	16590615	402	191	303	61	77	74	76	0	120	55	<1.00e-15	<4.11e-14
4	ST_WNT_BETA_CATENIN_PATHWAY	Beta-catenin is degraded in the absence of Wnt signaling; when extracellular Wnt binds Frizzled receptors, beta-catenin accumulates in the nucleus and may promote cell survival.	AKT1, AKT2, AKT3, ANKRD6, APC, AXIN1, AXIN2, C22orf2, CER1, CSNK1A1, CTNNB1, DACT1, DKK1, DKK2, DKK3, DKK4, DVL1, FRAT1, FSTL1, GSK3A, GSK3B, IDAX, LAMR1, LRP1, MVP, NKD1, NKD2, PIN1, PSEN1, PTPRA, SENP2, SFRP1, TSHB, WIF1	30	AKT1(2), AKT2(6), AKT3(1), ANKRD6(5), APC(187), AXIN1(2), AXIN2(9), CER1(3), CSNK1A1(2), CTNNB1(12), DACT1(6), DKK1(5), DKK2(6), DKK3(2), DKK4(7), FSTL1(6), GSK3A(2), GSK3B(8), LRP1(17), MVP(4), NKD1(3), NKD2(1), PIN1(1), PSEN1(3), PTPRA(2), SENP2(3), SFRP1(3), TSHB(1), WIF1(2)	12642186	311	185	249	37	60	43	39	1	116	52	<1.00e-15	<4.11e-14
5	GSK3PATHWAY	Bacterial lipopolysaccharide activates AKT to promote the survival and activation of macrophages and inhibits Gsk3-beta to promote beta-catenin accumulation in the nucleus.	AKT1, APC, AXIN1, CCND1, CD14, CTNNB1, DVL1, FZD1, GJA1, GNAI1, GSK3B, IRAK1, LBP, LEF1, LY96, MYD88, NFKB1, PDPK1, PIK3CA, PIK3R1, PPP2CA, PRKR, RELA, TIRAP, TLR4, TOLLIP, WNT1	26	AKT1(2), APC(187), AXIN1(2), CD14(1), CTNNB1(12), FZD1(1), GJA1(7), GNAI1(4), GSK3B(8), IRAK1(1), LBP(1), LEF1(4), LY96(2), MYD88(2), NFKB1(6), PDPK1(1), PIK3CA(40), PIK3R1(10), PPP2CA(1), RELA(2), TIRAP(1), TLR4(10), TOLLIP(1), WNT1(1)	9451888	307	183	228	28	44	50	43	1	115	54	<1.00e-15	<4.11e-14
6	PITX2PATHWAY	The bicoid-related transcription factor Pitx2 is activated by Wnt binding to the Frizzled receptor and induces tissue-specific cell proliferation.	APC, AXIN1, CREBBP, CTNNB1, DVL1, EP300, FZD1, GSK3B, HDAC1, HTATIP, LDB1, LEF1, PITX2, PPARBP, TRRAP, WNT1	14	APC(187), AXIN1(2), CREBBP(25), CTNNB1(12), EP300(15), FZD1(1), GSK3B(8), HDAC1(2), LDB1(5), LEF1(4), PITX2(2), TRRAP(21), WNT1(1)	10494881	285	180	225	29	46	36	32	2	117	52	<1.00e-15	<4.11e-14
7	CELL_CYCLE_KEGG		ABL1, ASK, ATM, BUB1, BUB1B, BUB3, CCNA1, CCNA2, CCNB1, CCNB2, CCNB3, CCND2, CCND3, CCNE1, CCNE2, CCNH, CDAN1, CDC14A, CDC14B, CDC14B, CDC14C, CDC2, CDC20, CDC25A, CDC25B, CDC25C, CDC45L, CDC6, CDC7, CDH1, CDK2, CDK4, CDKN1A, CDKN2A, CHEK1, CHEK2, DTX4, E2F1, E2F2, E2F3, E2F4, E2F5, E2F6, EP300, ESPL1, FLJ14001, GADD45A, GSK3B, HDAC1, HDAC2, HDAC3, HDAC4, HDAC5, HDAC6, HDAC7A, HDAC8, MAD1L1, MAD2L1, MAD2L2, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MDM2, MPEG1, MPL, ORC1L, ORC2L, ORC3L, ORC4L, ORC5L, ORC6L, PCNA, PLK1, PRKDC, PTPRA, PTTG1, PTTG2, PTTG3, RB1, RBL1, SKP2, SMAD4, SMC1L1, TBC1D8, TFDP1, TGFB1, TP53, WEE1	82	ABL1(4), ATM(37), BUB1(6), BUB1B(6), BUB3(2), CCNA1(6), CCNA2(3), CCNB1(2), CCNB2(2), CCNB3(7), CCND2(1), CCND3(1), CCNE1(3), CCNE2(2), CCNH(2), CDAN1(3), CDC14A(4), CDC14B(4), CDC20(3), CDC25A(2), CDC25B(5), CDC25C(4), CDC6(1), CDC7(3), CDH1(5), CDK2(2), CDK4(3), CDKN1A(1), CDKN2A(1), CHEK1(1), CHEK2(1), DTX4(3), E2F2(1), E2F3(2), E2F4(1), E2F5(2), EP300(15), ESPL1(8), GSK3B(8), HDAC1(2), HDAC2(2), HDAC3(2), HDAC4(5), HDAC5(2), HDAC6(6), MAD1L1(2), MAD2L1(1), MAD2L2(1), MCM3(3), MCM4(4), MCM5(6), MCM6(4), MCM7(3), MDM2(4), MPEG1(4), MPL(2), ORC1L(1), ORC3L(1), ORC4L(1), ORC5L(1), PCNA(3), PLK1(8), PRKDC(18), PTPRA(2), PTTG1(1), RB1(7), RBL1(5), SKP2(1), SMAD4(29), TBC1D8(5), TFDP1(4), TGFB1(1), TP53(122), WEE1(3)	34828727	433	178	369	75	131	122	88	8	80	4	<1.00e-15	<4.11e-14
8	HSA04012_ERBB_SIGNALING_PATHWAY	Genes involved in ErbB signaling pathway	ABL1, ABL2, AKT1, AKT2, AKT3, ARAF, AREG, BAD, BRAF, BTC, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CBL, CBLB, CBLC, CDKN1A, CDKN1B, CRK, CRKL, EGF, EGFR, EIF4EBP1, ELK1, ERBB2, ERBB3, ERBB4, EREG, FRAP1, GAB1, GRB2, GSK3B, HBEGF, HRAS, JUN, KRAS, MAP2K1, MAP2K2, MAP2K4, MAP2K7, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MYC, NCK1, NCK2, NRAS, NRG1, NRG2, NRG3, NRG4, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLCG1, PLCG2, PRKCA, PRKCB1, PRKCG, PTK2, RAF1, RPS6KB1, RPS6KB2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SRC, STAT5A, STAT5B, TGFA	85	ABL1(4), ABL2(7), AKT1(2), AKT2(6), AKT3(1), ARAF(3), BAD(1), BRAF(23), BTC(2), CAMK2A(1), CAMK2B(2), CAMK2D(3), CAMK2G(2), CBL(5), CBLB(8), CDKN1A(1), CDKN1B(3), CRKL(2), EGF(3), EGFR(11), ERBB2(10), ERBB3(14), ERBB4(21), EREG(1), GAB1(6), GRB2(3), GSK3B(8), HBEGF(1), KRAS(96), MAP2K1(4), MAP2K2(1), MAP2K4(11), MAPK1(2), MAPK10(8), MAPK3(3), MAPK8(7), MAPK9(5), NCK1(1), NRAS(20), NRG1(15), NRG2(6), NRG3(7), NRG4(1), PAK1(5), PAK2(3), PAK3(5), PAK6(1), PAK7(7), PIK3CA(40), PIK3CB(2), PIK3CD(3), PIK3CG(14), PIK3R1(10), PIK3R2(1), PIK3R3(4), PIK3R5(1), PLCG1(4), PLCG2(13), PRKCA(4), PRKCG(10), PTK2(5), RAF1(6), RPS6KB1(3), RPS6KB2(2), SHC1(3), SHC2(1), SHC3(1), SHC4(5), SOS1(7), SOS2(11), SRC(3), STAT5B(3)	33296728	518	175	369	98	118	227	115	5	51	2	<1.00e-15	<4.11e-14
9	TGFBPATHWAY	The TGF-beta receptor responds to ligand binding by activating the SMAD family of transcriptional regulations, commonly blocking cell growth.	APC, CDH1, CREBBP, EP300, MADH2, MADH3, MADH4, MADH7, MADHIP, MAP2K1, MAP3K7, MAP3K7IP1, MAPK3, SKIL, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2	13	APC(187), CDH1(5), CREBBP(25), EP300(15), MAP2K1(4), MAP3K7(4), MAPK3(3), SKIL(1), TGFB1(1), TGFB2(9), TGFBR1(9), TGFBR2(7)	8403558	270	175	210	25	34	35	30	1	118	52	<1.00e-15	<4.11e-14
10	HSA04662_B_CELL_RECEPTOR_SIGNALING_PATHWAY	Genes involved in B cell receptor signaling pathway	AKT1, AKT2, AKT3, BCL10, BLNK, BTK, CARD11, CD19, CD22, CD72, CD79A, CD79B, CD81, CHP, CHUK, CR2, FCGR2B, FOS, GSK3B, HRAS, IFITM1, IKBKB, IKBKG, INPP5D, JUN, KRAS, LILRB3, LYN, MALT1, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NFKB1, NFKB2, NFKBIA, NFKBIB, NFKBIE, NRAS, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLCG2, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKCB1, PTPN6, RAC1, RAC2, RAC3, RASGRP3, SYK, VAV1, VAV2, VAV3	62	AKT1(2), AKT2(6), AKT3(1), BCL10(3), BLNK(1), BTK(7), CARD11(9), CD19(3), CD22(10), CD72(4), CD79A(3), CD79B(1), CHUK(6), CR2(11), FOS(1), GSK3B(8), IFITM1(1), IKBKB(4), INPP5D(4), KRAS(96), LILRB3(2), LYN(4), MALT1(7), NFAT5(5), NFATC1(2), NFATC2(5), NFATC3(5), NFATC4(5), NFKB1(6), NFKB2(4), NFKBIB(1), NFKBIE(2), NRAS(20), PIK3CA(40), PIK3CB(2), PIK3CD(3), PIK3CG(14), PIK3R1(10), PIK3R2(1), PIK3R3(4), PIK3R5(1), PLCG2(13), PPP3CA(3), PPP3CB(5), PPP3CC(4), PPP3R1(1), PPP3R2(1), PTPN6(4), RASGRP3(7), SYK(3), VAV1(13), VAV2(4), VAV3(12)	23448894	394	157	272	64	111	195	57	1	28	2	<1.00e-15	<4.11e-14

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	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(2), CD3D(1), CD3G(2), CD80(1), CTLA4(2), GRB2(3), HLA-DRA(5), HLA-DRB1(2), ICOS(1), IL2(4), ITK(11), LCK(3), PIK3R1(10), PTPN11(5)	3423989	52	30	50	10	15	19	7	0	7	4	0.0011	0.33
2	COMPLEMENT_ACTIVATION_CLASSICAL		C1QA, C1QB, C1QG, C1R, C1S, C2, C3, C4A, C4B, C5, C6, C7, C8A, C8B, C9, DAF, MASP1	13	C1QB(1), C1R(3), C1S(6), C2(4), C3(11), C5(13), C6(13), C7(5), C8A(6), C8B(10), C9(5), MASP1(12)	6638726	89	45	89	26	29	32	16	0	11	1	0.0015	0.33
3	CREMPATHWAY	The transcription factor CREM activates a post-meiotic transcriptional cascade culminating in spermatogenesis.	ADCY1, CREM, FHL5, FSHB, FSHR, GNAS, XPO1	7	ADCY1(8), CREM(4), FHL5(4), FSHB(2), FSHR(7), GNAS(6), XPO1(2)	3039066	33	29	33	12	13	9	7	1	3	0	0.0016	0.33
4	ALTERNATIVEPATHWAY	The alternative complement pathway is an antibody-independent mechanism of immune activation that results in cell lysis via the membrane attack complex.	BF, C3, C5, C6, C7, C8A, C9, DF, PFC	6	C3(11), C5(13), C6(13), C7(5), C8A(6), C9(5)	4019457	53	30	53	14	16	19	10	0	7	1	0.0059	0.65
5	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	229	ADCYAP1R1(2), ADORA1(8), ADORA2A(5), ADORA2B(1), ADORA3(3), ADRA1A(5), ADRA1B(5), ADRA2A(3), ADRA2B(1), ADRB1(3), ADRB3(1), AGTR1(5), AGTR2(5), AVPR1A(4), AVPR1B(3), AVPR2(6), BDKRB2(3), BRS3(3), C3AR1(4), C5AR1(3), CALCR(5), CALCRL(6), CCKAR(2), CCKBR(5), CGA(2), CHRM1(3), CHRM3(4), CHRM4(1), CHRM5(2), CNR1(5), CRHR1(2), CRHR2(5), CTSG(3), CYSLTR1(3), CYSLTR2(4), DRD1(1), DRD2(5), DRD3(3), DRD5(6), EDNRA(4), F2(3), F2RL1(1), F2RL2(3), FPR1(2), FSHB(2), FSHR(7), GABBR1(6), GABBR2(7), GABRA1(4), GABRA2(9), GABRA3(5), GABRA4(8), GABRA6(5), GABRB1(7), GABRB2(7), GABRB3(9), GABRE(5), GABRG1(9), GABRG2(11), GABRG3(5), GABRP(4), GABRQ(8), GABRR1(2), GABRR2(4), GALR1(2), GH1(2), GH2(3), GHR(6), GHRHR(2), GHSR(5), GLP1R(7), GLP2R(5), GLRA1(2), GLRA2(3), GLRA3(8), GLRB(7), GNRHR(4), GPR156(8), GPR50(5), GPR63(4), GPR83(1), GRIA2(13), GRIA3(8), GRIA4(19), GRID1(16), GRID2(12), GRIK1(5), GRIK2(14), GRIK4(12), GRIK5(6), GRIN1(1), GRIN2A(21), GRIN2B(10), GRIN2C(4), GRIN2D(5), GRIN3A(6), GRM1(12), GRM2(4), GRM3(7), GRM4(7), GRM5(11), GRM6(10), GRM7(12), GRM8(9), GRPR(3), GZMA(3), HCRTR1(1), HCRTR2(1), HRH1(1), HRH2(4), HRH4(2), HTR1A(5), HTR1B(5), HTR1D(2), HTR1E(7), HTR1F(2), HTR2A(3), HTR2B(1), HTR2C(8), HTR4(3), HTR5A(5), HTR7(7), LEP(1), LEPR(9), LHB(1), LHCGR(4), LTB4R(1), MAS1(2), MC2R(5), MC3R(1), MC4R(4), MC5R(6), MCHR1(6), MCHR2(3), MLNR(3), MTNR1B(3), NMUR1(4), NMUR2(9), NPBWR1(3), NPFFR2(4), NPY1R(4), NPY2R(5), NPY5R(2), NR3C1(4), NTSR1(1), NTSR2(5), OPRD1(1), OPRK1(5), OPRM1(3), OXTR(3), P2RX1(1), P2RX2(2), P2RX3(2), P2RX4(3), P2RX5(1), P2RX7(3), P2RY1(6), P2RY13(2), P2RY14(6), P2RY2(3), P2RY4(6), P2RY6(1), PARD3(7), PPYR1(4), PRL(3), PRLR(4), PRSS1(3), PRSS2(1), PRSS3(4), PTAFR(1), PTGDR(1), PTGER2(1), PTGER3(7), PTGFR(7), PTGIR(1), PTH2R(7), RXFP1(3), RXFP2(10), SCTR(3), SSTR1(5), SSTR2(3), SSTR4(4), TAAR1(4), TAAR2(2), TAAR5(6), TAAR6(5), TAAR8(2), TAAR9(3), TACR1(2), TACR2(1), TACR3(7), THRA(2), THRB(4), TRHR(8), TRPV1(4), TSHB(1), TSHR(7), VIPR1(4), VIPR2(3)	68119460	920	158	910	348	352	303	180	9	75	1	0.0066	0.65
6	ERBB3PATHWAY	Neuregulins bind to the receptor tyrosine kinases ErbB3 and ErbB4, surface-localized receptors whose overexpression induces tumor formation.	EGF, EGFR, ERBB3, NRG1, UBE2D1	5	EGF(3), EGFR(11), ERBB3(14), NRG1(15), UBE2D1(1)	3378947	44	33	40	7	18	8	11	1	6	0	0.0071	0.65
7	HSA04012_ERBB_SIGNALING_PATHWAY	Genes involved in ErbB signaling pathway	ABL1, ABL2, AKT1, AKT2, AKT3, ARAF, AREG, BAD, BRAF, BTC, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CBL, CBLB, CBLC, CDKN1A, CDKN1B, CRK, CRKL, EGF, EGFR, EIF4EBP1, ELK1, ERBB2, ERBB3, ERBB4, EREG, FRAP1, GAB1, GRB2, GSK3B, HBEGF, HRAS, JUN, KRAS, MAP2K1, MAP2K2, MAP2K4, MAP2K7, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MYC, NCK1, NCK2, NRAS, NRG1, NRG2, NRG3, NRG4, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLCG1, PLCG2, PRKCA, PRKCB1, PRKCG, PTK2, RAF1, RPS6KB1, RPS6KB2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SRC, STAT5A, STAT5B, TGFA	79	ABL1(4), ABL2(7), AKT1(2), AKT2(6), AKT3(1), ARAF(3), BAD(1), BTC(2), CAMK2A(1), CAMK2B(2), CAMK2D(3), CAMK2G(2), CBL(5), CBLB(8), CDKN1A(1), CDKN1B(3), CRKL(2), EGF(3), EGFR(11), ERBB2(10), ERBB3(14), EREG(1), GAB1(6), GRB2(3), GSK3B(8), HBEGF(1), MAP2K1(4), MAP2K2(1), MAPK1(2), MAPK10(8), MAPK3(3), MAPK8(7), MAPK9(5), NCK1(1), NRG1(15), NRG2(6), NRG3(7), NRG4(1), PAK1(5), PAK2(3), PAK3(5), PAK6(1), PAK7(7), PIK3CB(2), PIK3CD(3), PIK3CG(14), PIK3R1(10), PIK3R2(1), PIK3R3(4), PIK3R5(1), PLCG1(4), PLCG2(13), PRKCA(4), PRKCG(10), PTK2(5), RAF1(6), RPS6KB1(3), RPS6KB2(2), SHC1(3), SHC2(1), SHC3(1), SHC4(5), SOS1(7), SOS2(11), SRC(3), STAT5B(3)	30746680	307	104	294	88	106	87	62	4	46	2	0.009	0.65
8	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(4), HLA-DRA(5), HLA-DRB1(2), IL3(3)	949081	14	12	13	4	7	5	0	0	0	2	0.011	0.65
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(4), GABRA2(9), GABRA3(5), GABRA4(8), GABRA6(5), GPX1(1), PRKCE(6)	2175145	38	22	37	6	11	17	6	0	4	0	0.012	0.65
10	PLCPATHWAY	Phospholipase C hydrolyzes the membrane lipid PIP2 to DAG, which activates protein kinase C, and IP3, which causes calcium influx.	AKT1, PIK3CA, PIK3R1, PLCB1, PLCG1, PRKCA, PRKCB1, VAV1	6	AKT1(2), PIK3R1(10), PLCB1(8), PLCG1(4), PRKCA(4), VAV1(13)	3510211	41	31	40	12	16	9	7	1	6	2	0.014	0.65

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)

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