Colon/Rectal Adenocarcinoma: Mutation Analysis (MutSig)

Maintained by Dan DiCara (Broad Institute)

Overview

Introduction

This report serves to describe the mutational landscape and properties of a given individual set, as well as rank genes and genesets according to mutational significance. MutSig v2.0 was used to generate the results found in this report.

Working with individual set: COADREAD.

Number of patients in set: 122

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): 86

Mutations seen in COSMIC: 389

Significantly mutated genes in COSMIC territory: 53

Genes with clustered mutations (&le 3 aa apart): 302

Significantly mutated genesets: 183

Significantly mutated genesets: (excluding sig. mutated genes): 40

Results

Breakdown of Mutations by Type

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

type	count
De_novo_Start_InFrame	4
De_novo_Start_OutOfFrame	30
Frame_Shift_Del	242
Frame_Shift_Ins	402
In_Frame_Del	79
In_Frame_Ins	17
Missense_Mutation	21881
Nonsense_Mutation	2293
Nonstop_Mutation	6
Read-through	10
Silent	7583
Splice_Site	52
Total	32599

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	7597	192102810	4e-05	40	5.7
*Cp(A/C/T)->mut	9192	1626891368	5.7e-06	5.7	0.81
A->mut	4845	1771575676	2.7e-06	2.7	0.39
*CpG->(G/A)	247	192102810	1.3e-06	1.3	0.18
indel+null	2965	3590569976	8.3e-07	0.83	0.12
double_null	170	3590569976	4.7e-08	0.047	0.0068
Total	25016	3590569976	7e-06	7	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.

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

Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 86. Number of genes displayed: 35

rank	gene	description	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p_classic	p_ks	p_cons	p_joint	p	q
1	APC	adenomatous polyposis coli	1048224	104	88	79	0	4	8	7	0	59	26	<1.00e-15	2e-07	0.97	0.000025	<0.00	<0.00
2	SMAD4	SMAD family member 4	207766	15	15	10	0	6	3	5	0	0	1	<1.00e-15	0.0032	0.0059	0.00032	<0.00	<0.00
3	FBXW7	F-box and WD repeat domain containing 7	315248	23	19	17	1	11	4	2	1	5	0	<1.00e-15	0.015	0.036	0.0074	<3.33e-16	<1.49e-12
4	FAM123B	family with sequence similarity 123B	407466	14	12	13	1	0	2	2	0	10	0	<1.00e-15	0.0018	0.73	0.0074	<3.33e-16	<1.49e-12
5	TP53	tumor protein p53	158956	73	72	42	1	34	12	7	2	18	0	<1.00e-15	2e-07	2e-07	0	<1.00e-15	<1.99e-12
6	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	86254	55	55	9	0	0	51	3	0	1	0	<1.00e-15	2e-07	0.00055	0	<1.00e-15	<1.99e-12
7	MUTYH	mutY homolog (E. coli)	208940	2	2	2	2	1	0	0	0	1	0	0.14	0.25	0.022	0	<1.00e-15	<1.99e-12
8	SLAMF8	SLAM family member 8	107116	2	2	2	0	1	0	0	0	1	0	0.029	0.0013	0.074	0	<1.00e-15	<1.99e-12
9	TYMS	thymidylate synthetase	96224	2	2	2	0	0	0	1	0	1	0	0.048	0.15	0.063	0	<1.00e-15	<1.99e-12
10	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	71492	9	9	4	0	0	6	3	0	0	0	6.23e-13	0.000074	0.24	0.00011	2.66e-15	4.77e-12
11	BRAF	v-raf murine sarcoma viral oncogene homolog B1	272182	10	10	3	0	0	0	10	0	0	0	2.72e-07	0.000026	0.0012	0.000011	8.38e-11	1.36e-07
12	ARID1A	AT rich interactive domain 1A (SWI-like)	710692	14	14	12	2	1	2	1	1	9	0	2.54e-11	0.38	0.21	0.33	2.19e-10	3.27e-07
13	KRTAP5-5	keratin associated protein 5-5	58532	4	4	1	0	0	0	0	4	0	0	3.25e-06	0.0019	5.2e-06	5.2e-06	4.36e-10	6.01e-07
14	ZC3H13	zinc finger CCCH-type containing 13	580598	19	14	19	0	6	2	1	0	10	0	6.52e-10	0.5	0.16	0.39	5.80e-09	7.43e-06
15	TCF7L2	transcription factor 7-like 2 (T-cell specific, HMG-box)	248586	8	8	8	2	2	3	1	0	2	0	1.60e-07	0.054	0.019	0.021	6.84e-08	0.000082
16	LRP1B	low density lipoprotein-related protein 1B (deleted in tumors)	1728008	36	19	36	10	4	16	15	0	1	0	1.06e-07	0.031	0.71	0.065	1.36e-07	0.00015
17	KIAA1804		290094	12	10	10	0	8	3	1	0	0	0	8.63e-07	0.03	0.018	0.027	4.27e-07	0.00045
18	KLK2	kallikrein-related peptidase 2	102846	3	3	1	1	0	3	0	0	0	0	0.0088	9e-06	0.24	4e-06	6.42e-07	0.00064
19	SMAD2	SMAD family member 2	176168	6	6	6	1	0	3	2	0	1	0	5.47e-06	0.0064	0.24	0.011	1.04e-06	0.00098
20	DMD	dystrophin (muscular dystrophy, Duchenne and Becker types)	1421048	23	16	23	2	6	7	6	0	4	0	2.04e-07	0.35	0.86	0.51	1.78e-06	0.0016
21	CSMD3	CUB and Sushi multiple domains 3	1399340	23	17	23	11	4	8	6	2	3	0	5.31e-07	0.32	0.16	0.23	2.06e-06	0.0018
22	BAI3	brain-specific angiogenesis inhibitor 3	568698	14	11	13	3	3	7	2	0	2	0	5.08e-07	0.78	0.56	1	7.86e-06	0.0063
23	WBSCR17	Williams-Beuren syndrome chromosome region 17	215530	8	8	8	2	3	3	1	0	1	0	2.08e-06	0.23	0.52	0.25	8.08e-06	0.0063
24	EVC2	Ellis van Creveld syndrome 2 (limbin)	460608	13	11	13	2	6	3	2	0	2	0	2.68e-06	0.13	0.34	0.25	0.000010	0.0075
25	LIFR	leukemia inhibitory factor receptor alpha	410970	13	10	13	2	1	4	5	1	2	0	1.11e-06	0.59	0.32	0.68	0.000011	0.0081
26	OPCML	opioid binding protein/cell adhesion molecule-like	137982	6	6	6	2	1	3	0	0	2	0	1.84e-06	0.48	0.48	0.67	0.000018	0.012
27	CDC27	cell division cycle 27 homolog (S. cerevisiae)	313418	8	6	5	4	1	1	5	0	1	0	0.0031	0.00021	0.99	0.00047	0.000021	0.013
28	TUSC3	tumor suppressor candidate 3	122480	5	5	5	1	2	0	2	0	1	0	0.00010	0.068	0.022	0.014	0.000021	0.013
29	ATP10A	ATPase, class V, type 10A	516958	10	9	10	6	3	4	0	1	2	0	0.000011	0.099	0.83	0.17	0.000025	0.016
30	FAT4	FAT tumor suppressor homolog 4 (Drosophila)	1814656	22	15	22	7	8	9	4	0	1	0	0.00023	0.0031	0.74	0.0081	0.000026	0.016
31	MAPK10	mitogen-activated protein kinase 10	176656	6	6	6	1	0	2	2	0	2	0	2.69e-06	0.65	0.73	0.86	0.000033	0.019
32	SYNE1	spectrin repeat containing, nuclear envelope 1	3302296	41	25	40	12	7	20	10	0	4	0	7.44e-06	0.47	0.16	0.35	0.000036	0.020
33	GPC6	glypican 6	207888	7	7	6	0	4	2	1	0	0	0	0.000030	0.16	0.043	0.09	0.000037	0.020
34	FAT2	FAT tumor suppressor homolog 2 (Drosophila)	1603324	24	13	24	6	4	13	4	0	3	0	0.000047	0.49	0.023	0.061	0.000039	0.021
35	CDH9	cadherin 9, type 2 (T1-cadherin)	294508	9	8	9	1	3	2	3	0	1	0	0.000020	0.087	0.49	0.15	0.000041	0.021

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: *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 .

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: 53. Number of genes displayed: 10

rank	gene	description	n	cos	n_cos	N_cos	cos_ev	p	q
1	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	55	51	54	6222	567408	0	0
2	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	9	28	9	3416	10215	0	0
3	FBXW7	F-box and WD repeat domain containing 7	23	91	15	11102	682	0	0
4	APC	adenomatous polyposis coli	104	838	77	102236	1457	0	0
5	BRAF	v-raf murine sarcoma viral oncogene homolog B1	10	88	8	10736	84064	0	0
6	TP53	tumor protein p53	73	823	73	100406	30705	0	0
7	SMAD4	SMAD family member 4	15	159	11	19398	65	0	0
8	KRTAP5-5	keratin associated protein 5-5	4	1	4	122	4	1.4e-14	8.1e-12
9	CDC27	cell division cycle 27 homolog (S. cerevisiae)	8	3	4	366	4	1.7e-12	8.6e-10
10	KLK2	kallikrein-related peptidase 2	3	1	3	122	3	1e-10	4.5e-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
4794	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	55	697	919	962	697	919	962
9344	TP53	tumor protein p53	73	130	206	308	130	206	308
496	APC	adenomatous polyposis coli	104	44	60	112	44	60	112
924	BRAF	v-raf murine sarcoma viral oncogene homolog B1	10	28	28	28	28	28	28
3271	FBXW7	F-box and WD repeat domain containing 7	23	22	24	26	22	24	26
6012	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	9	22	22	22	22	22	22
8446	SMAD4	SMAD family member 4	15	13	16	32	13	16	32
1712	CDC27	cell division cycle 27 homolog (S. cerevisiae)	8	6	6	6	6	6	6
4847	KRTAP5-5	keratin associated protein 5-5	4	6	6	6	6	6	6
2960	ERBB2	v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)	4	3	3	3	3	3	3

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: 183. 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(104), AXIN1(1), AXIN2(5), BTRC(3), CACYBP(1), CAMK2D(2), CCND2(1), CCND3(1), CHD8(2), CREBBP(8), CSNK2A2(1), CTNNB1(8), CUL1(5), DAAM1(1), DAAM2(4), DKK1(2), DKK2(3), DKK4(3), DVL2(2), DVL3(2), EP300(8), FBXW11(4), FZD1(1), FZD10(2), FZD2(1), FZD3(7), FZD4(1), FZD6(4), FZD7(1), GSK3B(2), LEF1(1), LRP5(3), LRP6(8), MAP3K7(2), MAPK10(6), MAPK8(6), MAPK9(2), MMP7(2), NFATC1(1), NFATC2(3), NFATC3(1), NFATC4(2), NKD1(1), PLCB1(1), PLCB3(3), PLCB4(2), PPARD(1), PPP2CA(1), PPP2CB(2), PPP2R1A(1), PPP2R1B(1), PPP2R2B(2), PPP2R2C(2), PPP3CA(2), PPP3CB(2), PPP3CC(3), PRICKLE1(5), PRICKLE2(3), PRKACA(1), PRKACG(1), PRKCA(3), PRKCG(5), RBX1(1), RHOA(1), ROCK1(8), ROCK2(4), RUVBL1(4), SENP2(2), SFRP1(2), SFRP2(2), SFRP4(1), SIAH1(1), SMAD2(6), SMAD3(3), SMAD4(15), TBL1X(1), TBL1Y(1), TCF7(5), TCF7L1(1), TCF7L2(8), TP53(73), VANGL1(1), VANGL2(1), WIF1(1), WNT10B(1), WNT11(1), WNT16(1), WNT2(1), WNT2B(2), WNT3(1), WNT4(1), WNT6(1), WNT8A(1), WNT9B(2)	28815720	423	119	360	61	118	101	63	5	109	27	<1.00e-15	<1.28e-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	201	ABI2(1), ACTN1(2), ACTN2(5), ACTN3(1), ACTN4(3), APC(104), ARAF(1), ARHGEF1(2), ARHGEF12(2), ARHGEF4(2), ARHGEF6(3), ARHGEF7(3), ARPC1B(1), ARPC2(1), ARPC5L(2), BAIAP2(1), BDKRB2(1), BRAF(10), CDC42(1), CHRM1(1), CHRM2(3), CHRM4(1), CHRM5(2), CSK(2), CYFIP1(3), CYFIP2(1), DIAPH2(6), DIAPH3(2), DOCK1(2), EGFR(5), F2(2), FGD1(3), FGD3(1), FGF11(1), FGF12(1), FGF13(1), FGF14(2), FGF19(1), FGF20(1), FGF3(1), FGF5(2), FGFR1(1), FGFR2(5), FN1(6), GIT1(1), GRLF1(5), IQGAP1(8), IQGAP2(8), IQGAP3(4), ITGA1(1), ITGA10(4), ITGA11(2), ITGA2(2), ITGA2B(3), ITGA4(5), ITGA5(2), ITGA6(2), ITGA8(3), ITGA9(3), ITGAD(2), ITGAE(3), ITGAL(4), ITGAM(3), ITGAV(4), ITGAX(2), ITGB2(2), ITGB3(2), ITGB4(1), ITGB5(4), ITGB6(2), ITGB7(2), ITGB8(1), KRAS(55), LIMK1(2), LIMK2(1), MAP2K1(2), MAP2K2(1), MAPK3(1), MOS(1), MRAS(1), MSN(3), MYH10(6), MYH14(3), MYH9(6), MYL9(2), MYLK(5), MYLK2(2), NCKAP1(3), NCKAP1L(6), NRAS(9), PAK1(1), PAK2(3), PAK3(3), PAK7(3), PDGFRA(4), PDGFRB(2), PIK3CA(7), PIK3CB(1), PIK3CD(2), PIK3CG(5), PIK3R1(6), PIK3R3(4), PIP4K2C(1), PIP5K1B(1), PIP5K1C(3), PPP1CB(1), PPP1CC(1), PPP1R12A(1), PPP1R12B(4), PTK2(1), RAF1(4), RDX(1), RHOA(1), ROCK1(8), ROCK2(4), RRAS2(1), SCIN(1), SLC9A1(2), SOS1(3), SOS2(6), SSH1(2), SSH2(1), SSH3(1), TIAM1(6), TIAM2(5), VAV1(7), VAV2(3), VAV3(3), VCL(2), WASF1(2), WASF2(1), WASL(2)	51109242	516	116	433	111	120	186	79	4	99	28	<1.00e-15	<1.28e-14
3	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	246	ACVR1B(3), ACVR1C(1), AKT1(1), AKT2(2), AKT3(1), ATF2(1), ATF4(1), BRAF(10), CACNA1A(9), CACNA1B(4), CACNA1C(2), CACNA1D(3), CACNA1E(6), CACNA1F(5), CACNA1I(2), CACNA1S(7), CACNA2D1(6), CACNA2D3(3), CACNB2(2), CACNB3(1), CACNB4(2), CACNG1(1), CACNG2(1), CACNG3(3), CACNG6(1), CACNG7(3), CACNG8(1), CASP3(1), CDC25B(2), CDC42(1), CHUK(4), DAXX(1), DUSP1(2), DUSP10(3), DUSP16(4), DUSP3(1), DUSP5(2), DUSP6(3), DUSP7(2), ECSIT(1), EGFR(5), ELK4(1), FAS(2), FGF11(1), FGF12(1), FGF13(1), FGF14(2), FGF19(1), FGF20(1), FGF3(1), FGF5(2), FGFR1(1), FGFR2(5), FLNA(1), FLNB(6), FLNC(2), FOS(1), GRB2(2), IKBKB(2), IL1B(1), IL1R1(1), IL1R2(5), KRAS(55), MAP2K1(2), MAP2K2(1), MAP2K3(4), MAP2K4(2), MAP2K5(2), MAP2K6(1), MAP3K1(2), MAP3K10(1), MAP3K12(2), MAP3K13(1), MAP3K14(1), MAP3K2(1), MAP3K3(2), MAP3K4(8), MAP3K5(3), MAP3K6(2), MAP3K7(2), MAP3K8(1), MAP4K1(1), MAP4K2(1), MAP4K3(1), MAP4K4(3), MAPK10(6), MAPK13(1), MAPK3(1), MAPK8(6), MAPK8IP3(1), MAPK9(2), MAPT(1), MEF2C(2), MKNK1(1), MKNK2(1), MOS(1), MRAS(1), NF1(5), NFATC2(3), NFATC4(2), NFKB1(4), NFKB2(2), NR4A1(2), NRAS(9), NTRK1(3), NTRK2(1), PAK1(1), PAK2(3), PDGFRA(4), PDGFRB(2), PLA2G4A(4), PLA2G6(2), PPM1B(2), PPP3CA(2), PPP3CB(2), PPP3CC(3), PPP5C(1), PRKACA(1), PRKACG(1), PRKCA(3), PRKCG(5), PTPN7(2), PTPRR(4), RAF1(4), RAP1A(1), RAP1B(1), RAPGEF2(5), RASA1(5), RASA2(2), RASGRF1(6), RASGRF2(4), RASGRP1(3), RASGRP2(2), RASGRP3(3), RASGRP4(1), RPS6KA2(4), RPS6KA3(2), RPS6KA5(4), RPS6KA6(3), RRAS2(1), SOS1(3), SOS2(6), STMN1(1), TAOK1(2), TAOK2(1), TGFB1(1), TGFB2(4), TGFBR1(5), TGFBR2(2), TP53(73), TRAF6(1), ZAK(2)	53006312	502	115	413	125	163	169	102	6	57	5	<1.00e-15	<1.28e-14
4	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(1), APC(104), AR(3), ASAH1(1), BRAF(10), DAG1(3), EGFR(5), GNA11(1), GNA15(1), GNAI1(1), GNAQ(1), ITPR1(8), ITPR2(6), ITPR3(7), KCNJ5(1), KCNJ9(2), MAPK10(6), PHKA2(3), PIK3CA(7), PIK3CD(2), PIK3R1(6), PTX3(2), RAF1(4), SRC(3)	9838080	188	101	156	21	34	30	29	0	66	29	<1.00e-15	<1.28e-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(104), ATF2(1), AXIN1(1), BMP10(1), BMP2(1), BMP4(2), BMP5(3), BMP7(2), BMPR1A(1), BMPR2(8), CTNNB1(8), FZD1(1), GSK3B(2), MAP3K7(2), MEF2C(2), NPPB(1), RFC1(4), TGFB1(1), TGFB2(4), TGFBR1(5), TGFBR2(2), TGFBR3(3)	6473550	162	100	136	8	22	30	15	0	69	26	<1.00e-15	<1.28e-14
6	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(104), AXIN1(1), CCND2(1), CCND3(1), CTNNB1(8), DVL2(2), DVL3(2), FBXW2(1), FZD1(1), FZD10(2), FZD2(1), FZD3(7), FZD6(4), FZD7(1), GSK3B(2), LDLR(1), MAPK10(6), MAPK9(2), PLAU(1), PPP2R5C(1), PPP2R5E(2), PRKCA(3), PRKCE(2), PRKCG(5), PRKCH(1), PRKCI(1), PRKCQ(2), PRKD1(5), RHOA(1), SFRP4(1), TCF7(5), WNT10B(1), WNT11(1), WNT16(1), WNT2(1), WNT2B(2), WNT3(1), WNT4(1), WNT6(1)	10472464	186	100	161	22	28	41	19	0	72	26	<1.00e-15	<1.28e-14
7	HSA04360_AXON_GUIDANCE	Genes involved in axon guidance	ABL1, ABLIM1, ABLIM2, ABLIM3, ARHGEF12, CDC42, CDK5, CFL1, CFL2, CHP, CXCL12, CXCR4, DCC, DPYSL2, DPYSL5, EFNA1, EFNA2, EFNA3, EFNA4, EFNA5, EFNB1, EFNB2, EFNB3, EPHA1, EPHA2, EPHA3, EPHA4, EPHA5, EPHA6, EPHA7, EPHA8, EPHB1, EPHB2, EPHB3, EPHB4, EPHB6, FES, FYN, GNAI1, GNAI2, GNAI3, GSK3B, HRAS, ITGB1, KRAS, L1CAM, LIMK1, LIMK2, LRRC4C, MAPK1, MAPK3, MET, NCK1, NCK2, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NGEF, NRAS, NRP1, NTN1, NTN2L, NTN4, NTNG1, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PLXNA1, PLXNA2, PLXNA3, PLXNB1, PLXNB2, PLXNB3, PLXNC1, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PTK2, RAC1, RAC2, RAC3, RASA1, RGS3, RHOA, RHOD, RND1, ROBO1, ROBO2, ROBO3, ROCK1, ROCK2, SEMA3A, SEMA3B, SEMA3C, SEMA3D, SEMA3E, SEMA3F, SEMA3G, SEMA4A, SEMA4B, SEMA4C, SEMA4D, SEMA4F, SEMA4G, SEMA5A, SEMA5B, SEMA6A, SEMA6B, SEMA6C, SEMA6D, SEMA7A, SLIT1, SLIT2, SLIT3, SRGAP1, SRGAP2, SRGAP3, UNC5A, UNC5B, UNC5C, UNC5D	127	ABL1(2), ABLIM1(4), ABLIM3(2), ARHGEF12(2), CDC42(1), CXCR4(1), DCC(5), DPYSL2(4), DPYSL5(1), EFNA5(3), EFNB2(1), EFNB3(1), EPHA1(4), EPHA2(2), EPHA3(7), EPHA4(3), EPHA5(9), EPHA7(4), EPHA8(3), EPHB1(3), EPHB2(3), EPHB3(1), EPHB4(4), FYN(1), GNAI1(1), GSK3B(2), KRAS(55), L1CAM(2), LIMK1(2), LIMK2(1), LRRC4C(3), MAPK3(1), MET(1), NCK1(1), NFATC1(1), NFATC2(3), NFATC3(1), NFATC4(2), NRAS(9), NRP1(1), NTN1(2), NTN4(2), NTNG1(3), PAK1(1), PAK2(3), PAK3(3), PAK7(3), PLXNA2(5), PLXNA3(1), PLXNB1(2), PLXNB3(1), PLXNC1(3), PPP3CA(2), PPP3CB(2), PPP3CC(3), PTK2(1), RASA1(5), RGS3(3), RHOA(1), ROBO1(9), ROBO2(3), ROBO3(3), ROCK1(8), ROCK2(4), SEMA3A(4), SEMA3C(1), SEMA3D(5), SEMA3E(6), SEMA3G(1), SEMA4A(2), SEMA4B(1), SEMA4D(4), SEMA4F(5), SEMA4G(4), SEMA5A(5), SEMA5B(5), SEMA6B(2), SEMA6C(2), SEMA6D(5), SEMA7A(2), SLIT1(3), SLIT2(4), SLIT3(4), SRGAP1(2), SRGAP3(1), UNC5A(1), UNC5B(1), UNC5C(4)	35300578	304	99	253	73	100	122	49	3	30	0	<1.00e-15	<1.28e-14
8	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(104), AXIN1(1), CREBBP(8), CTNNB1(8), EP300(8), FZD1(1), GSK3B(2), HDAC1(2), LDB1(2), LEF1(1), TRRAP(9)	5920936	146	98	121	6	19	22	15	1	63	26	<1.00e-15	<1.28e-14
9	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(1), AKT2(2), AKT3(1), APC(104), AXIN1(1), AXIN2(5), CTNNB1(8), DACT1(1), DKK1(2), DKK2(3), DKK3(1), DKK4(3), FSTL1(2), GSK3B(2), LRP1(7), MVP(3), NKD1(1), PIN1(1), PTPRA(1), SENP2(2), SFRP1(2), TSHB(1), WIF1(1)	7337384	155	98	130	8	20	25	24	0	60	26	<1.00e-15	<1.28e-14
10	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(1), APC(104), AXIN1(1), CTNNB1(8), FZD1(1), GJA1(4), GNAI1(1), GSK3B(2), LEF1(1), MYD88(1), NFKB1(4), PDPK1(1), PIK3CA(7), PIK3R1(6), PPP2CA(1), TLR4(4), TOLLIP(1)	5399076	148	96	123	9	19	21	20	0	60	28	<1.00e-15	<1.28e-14

Table 7. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 40. 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	HSA00240_PYRIMIDINE_METABOLISM	Genes involved in pyrimidine metabolism	AICDA, AK3, CAD, CANT1, CDA, CMPK, CTPS, CTPS2, DCK, DCTD, DHODH, DPYD, DPYS, DTYMK, DUT, ECGF1, ENTPD1, ENTPD3, ENTPD4, ENTPD5, ENTPD6, ENTPD8, ITPA, NME1, NME2, NME4, NME6, NME7, NP, NT5C, NT5C1A, NT5C1B, NT5C2, NT5C3, NT5E, NT5M, NUDT2, PNPT1, POLA1, POLA2, POLD1, POLD2, POLD3, POLD4, POLE, POLE2, POLE3, POLE4, POLR1A, POLR1B, POLR1C, POLR1D, POLR2A, POLR2B, POLR2C, POLR2D, POLR2E, POLR2F, POLR2G, POLR2H, POLR2I, POLR2J, POLR2K, POLR2L, POLR3A, POLR3B, POLR3G, POLR3GL, POLR3H, POLR3K, PRIM1, PRIM2, RFC5, RRM1, RRM2, RRM2B, TK1, TK2, TXNRD1, TXNRD2, TYMS, UCK1, UCK2, UMPS, UPB1, UPP1, UPP2, UPRT, ZNRD1	85	AICDA(1), CAD(4), CDA(1), CTPS(1), DCK(1), DCTD(2), DHODH(1), DPYD(9), DPYS(1), DTYMK(1), ENTPD1(1), ENTPD5(2), ENTPD6(2), NME6(3), NME7(2), NT5C1A(1), NT5C1B(5), NT5C2(2), NT5E(1), PNPT1(6), POLA1(3), POLA2(2), POLD1(2), POLD2(1), POLD3(1), POLE(10), POLE2(1), POLR1A(3), POLR1B(5), POLR1C(2), POLR1D(2), POLR2A(1), POLR2B(3), POLR2D(1), POLR2K(1), POLR3A(6), POLR3B(9), POLR3GL(1), POLR3K(1), PRIM2(3), RFC5(1), RRM1(2), TK2(1), TXNRD1(1), TXNRD2(1), UCK2(1), UMPS(1), UPB1(2), UPP2(1), UPRT(2)	14952294	118	49	116	26	39	38	22	0	19	0	2.9e-11	1.8e-08
2	HSA00230_PURINE_METABOLISM	Genes involved in purine metabolism	ADA, ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ADK, ADSL, ADSS, ADSSL1, AK1, AK2, AK3L1, AK5, AK7, ALLC, AMPD1, AMPD2, AMPD3, APRT, ATIC, CANT1, DCK, DGUOK, ECGF1, ENPP1, ENPP3, ENTPD1, ENTPD2, ENTPD3, ENTPD4, ENTPD5, ENTPD6, ENTPD8, FHIT, GART, GDA, GMPR, GMPR2, GMPS, GUCY1A2, GUCY1A3, GUCY1B3, GUCY2C, GUCY2D, GUCY2F, GUK1, HPRT1, IMPDH1, IMPDH2, ITPA, NME1, NME2, NME4, NME6, NME7, NP, NPR1, NPR2, NT5C, NT5C1A, NT5C1B, NT5C2, NT5C3, NT5E, NT5M, NUDT2, NUDT5, NUDT9, PAICS, PAPSS1, PAPSS2, PDE10A, PDE11A, PDE1A, PDE1C, PDE2A, PDE3B, PDE4A, PDE4B, PDE4C, PDE4D, PDE5A, PDE6D, PDE6G, PDE6H, PDE7A, PDE7B, PDE8A, PDE8B, PDE9A, PFAS, PKLR, PKM2, PNPT1, POLA1, POLA2, POLD1, POLD2, POLD3, POLD4, POLE, POLE2, POLE3, POLE4, POLR1A, POLR1B, POLR1C, POLR1D, POLR2A, POLR2B, POLR2C, POLR2D, POLR2E, POLR2F, POLR2G, POLR2H, POLR2I, POLR2J, POLR2K, POLR2L, POLR3A, POLR3B, POLR3G, POLR3GL, POLR3H, POLR3K, PPAT, PRIM1, PRIM2, PRPS1, PRPS1L1, PRPS2, PRUNE, RFC5, RRM1, RRM2, RRM2B, SAC, XDH, ZNRD1	142	ADA(1), ADCY1(5), ADCY2(8), ADCY3(2), ADCY4(2), ADCY5(6), ADCY7(2), ADCY8(3), ADCY9(2), ADSL(2), ADSS(1), AK2(1), AK5(2), AK7(1), ALLC(2), AMPD1(6), AMPD2(3), AMPD3(1), ATIC(1), DCK(1), ENPP3(2), ENTPD1(1), ENTPD5(2), ENTPD6(2), GART(1), GMPR(1), GUCY1A2(6), GUCY1A3(5), GUCY1B3(2), GUCY2C(3), GUCY2D(6), GUCY2F(6), IMPDH1(2), IMPDH2(3), NME6(3), NME7(2), NPR1(2), NPR2(2), NT5C1A(1), NT5C1B(5), NT5C2(2), NT5E(1), NUDT9(1), PAICS(1), PAPSS1(1), PAPSS2(2), PDE10A(7), PDE11A(2), PDE1A(2), PDE1C(5), PDE3B(1), PDE4A(1), PDE4B(3), PDE4D(1), PDE5A(3), PDE7B(1), PDE8B(2), PDE9A(2), PNPT1(6), POLA1(3), POLA2(2), POLD1(2), POLD2(1), POLD3(1), POLE(10), POLE2(1), POLR1A(3), POLR1B(5), POLR1C(2), POLR1D(2), POLR2A(1), POLR2B(3), POLR2D(1), POLR2K(1), POLR3A(6), POLR3B(9), POLR3GL(1), POLR3K(1), PPAT(5), PRIM2(3), PRPS1(1), PRPS2(1), PRUNE(1), RFC5(1), RRM1(2), XDH(1)	30197542	223	64	221	75	79	69	42	1	32	0	2.2e-09	6.9e-07
3	HSA04514_CELL_ADHESION_MOLECULES	Genes involved in cell adhesion molecules (CAMs)	ALCAM, CADM1, CADM3, CD2, CD22, CD226, CD274, CD276, CD28, CD34, CD4, CD40, CD40LG, CD58, CD6, CD80, CD86, CD8A, CD8B, CD99, CDH1, CDH15, CDH2, CDH3, CDH4, CDH5, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CNTN1, CNTN2, CNTNAP1, CNTNAP2, CTLA4, ESAM, F11R, GLG1, HLA-A, HLA-A29.1, HLA-B, HLA-C, HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-E, HLA-F, HLA-G, ICAM1, ICAM2, ICAM3, ICOS, ICOSLG, ITGA4, ITGA6, ITGA8, ITGA9, ITGAL, ITGAM, ITGAV, ITGB1, ITGB2, ITGB7, ITGB8, JAM2, JAM3, L1CAM, MADCAM1, MAG, MPZ, MPZL1, NCAM1, NCAM2, NEGR1, NEO1, NFASC, NLGN1, NLGN2, NLGN3, NRCAM, NRXN1, NRXN2, NRXN3, OCLN, PDCD1, PDCD1LG2, PECAM1, PTPRC, PTPRF, PTPRM, PVR, PVRL1, PVRL2, PVRL3, SDC1, SDC2, SDC3, SDC4, SELE, SELL, SELP, SELPLG, SIGLEC1, SPN, VCAM1, VCAN	126	CADM3(4), CD22(4), CD226(2), CD274(2), CD28(1), CD40(1), CD40LG(4), CD58(1), CD6(1), CD80(1), CDH1(2), CDH15(1), CDH2(8), CDH3(3), CDH4(5), CDH5(1), CLDN10(3), CLDN16(2), CLDN17(3), CLDN2(1), CLDN8(2), CNTN1(7), CNTN2(4), CNTNAP1(3), CNTNAP2(5), CTLA4(1), ESAM(1), GLG1(1), HLA-A(2), HLA-B(1), HLA-DMB(1), HLA-DOA(1), HLA-DPB1(2), HLA-DQA2(2), HLA-DQB1(1), HLA-DRA(3), HLA-DRB1(1), HLA-DRB5(1), HLA-F(1), HLA-G(1), ITGA4(5), ITGA6(2), ITGA8(3), ITGA9(3), ITGAL(4), ITGAM(3), ITGAV(4), ITGB2(2), ITGB7(2), ITGB8(1), L1CAM(2), MAG(2), NCAM1(4), NCAM2(7), NEGR1(3), NEO1(3), NFASC(6), NLGN1(4), NLGN2(2), NLGN3(1), NRCAM(1), NRXN1(4), NRXN2(2), PDCD1LG2(1), PECAM1(1), PTPRC(9), PTPRF(5), PTPRM(14), PVRL1(4), PVRL2(1), PVRL3(1), SDC1(1), SDC2(3), SDC3(1), SDC4(1), SELE(2), SELL(3), SELP(2), SELPLG(1), SIGLEC1(2), SPN(1), VCAM1(2)	24479520	216	59	216	70	67	86	33	4	26	0	7.8e-09	1.6e-06
4	HSA04360_AXON_GUIDANCE	Genes involved in axon guidance	ABL1, ABLIM1, ABLIM2, ABLIM3, ARHGEF12, CDC42, CDK5, CFL1, CFL2, CHP, CXCL12, CXCR4, DCC, DPYSL2, DPYSL5, EFNA1, EFNA2, EFNA3, EFNA4, EFNA5, EFNB1, EFNB2, EFNB3, EPHA1, EPHA2, EPHA3, EPHA4, EPHA5, EPHA6, EPHA7, EPHA8, EPHB1, EPHB2, EPHB3, EPHB4, EPHB6, FES, FYN, GNAI1, GNAI2, GNAI3, GSK3B, HRAS, ITGB1, KRAS, L1CAM, LIMK1, LIMK2, LRRC4C, MAPK1, MAPK3, MET, NCK1, NCK2, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NGEF, NRAS, NRP1, NTN1, NTN2L, NTN4, NTNG1, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PLXNA1, PLXNA2, PLXNA3, PLXNB1, PLXNB2, PLXNB3, PLXNC1, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PTK2, RAC1, RAC2, RAC3, RASA1, RGS3, RHOA, RHOD, RND1, ROBO1, ROBO2, ROBO3, ROCK1, ROCK2, SEMA3A, SEMA3B, SEMA3C, SEMA3D, SEMA3E, SEMA3F, SEMA3G, SEMA4A, SEMA4B, SEMA4C, SEMA4D, SEMA4F, SEMA4G, SEMA5A, SEMA5B, SEMA6A, SEMA6B, SEMA6C, SEMA6D, SEMA7A, SLIT1, SLIT2, SLIT3, SRGAP1, SRGAP2, SRGAP3, UNC5A, UNC5B, UNC5C, UNC5D	125	ABL1(2), ABLIM1(4), ABLIM3(2), ARHGEF12(2), CDC42(1), CXCR4(1), DCC(5), DPYSL2(4), DPYSL5(1), EFNA5(3), EFNB2(1), EFNB3(1), EPHA1(4), EPHA2(2), EPHA3(7), EPHA4(3), EPHA5(9), EPHA7(4), EPHA8(3), EPHB1(3), EPHB2(3), EPHB3(1), EPHB4(4), FYN(1), GNAI1(1), GSK3B(2), L1CAM(2), LIMK1(2), LIMK2(1), LRRC4C(3), MAPK3(1), MET(1), NCK1(1), NFATC1(1), NFATC2(3), NFATC3(1), NFATC4(2), NRP1(1), NTN1(2), NTN4(2), NTNG1(3), PAK1(1), PAK2(3), PAK3(3), PAK7(3), PLXNA2(5), PLXNA3(1), PLXNB1(2), PLXNB3(1), PLXNC1(3), PPP3CA(2), PPP3CB(2), PPP3CC(3), PTK2(1), RASA1(5), RGS3(3), RHOA(1), ROBO1(9), ROBO2(3), ROBO3(3), ROCK1(8), ROCK2(4), SEMA3A(4), SEMA3C(1), SEMA3D(5), SEMA3E(6), SEMA3G(1), SEMA4A(2), SEMA4B(1), SEMA4D(4), SEMA4F(5), SEMA4G(4), SEMA5A(5), SEMA5B(5), SEMA6B(2), SEMA6C(2), SEMA6D(5), SEMA7A(2), SLIT1(3), SLIT2(4), SLIT3(4), SRGAP1(2), SRGAP3(1), UNC5A(1), UNC5B(1), UNC5C(4)	35142832	240	67	240	73	100	65	43	3	29	0	3.5e-07	0.000054
5	HSA04350_TGF_BETA_SIGNALING_PATHWAY	Genes involved in TGF-beta signaling pathway	ACVR1, ACVR1B, ACVR1C, ACVR2A, ACVR2B, ACVRL1, AMH, AMHR2, BMP2, BMP4, BMP5, BMP6, BMP7, BMP8A, BMP8B, BMPR1A, BMPR1B, BMPR2, CDKN2B, CHRD, COMP, CREBBP, CUL1, DCN, E2F4, E2F5, EP300, FST, GDF5, GDF6, GDF7, hCG_1982709, ID1, ID2, ID3, ID4, IFNG, INHBA, INHBB, INHBC, INHBE, LEFTY1, LEFTY2, LTBP1, MAPK1, MAPK3, MYC, NODAL, NOG, PITX2, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, RBL1, RBL2, RBX1, RHOA, ROCK1, ROCK2, RPS6KB1, RPS6KB2, SKP1, SMAD1, SMAD2, SMAD3, SMAD4, SMAD5, SMAD6, SMAD7, SMAD9, SMURF1, SMURF2, SP1, TFDP1, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, THBS1, THBS2, THBS3, THBS4, TNF, ZFYVE16, ZFYVE9	86	ACVR1(3), ACVR1B(3), ACVR1C(1), ACVR2A(2), ACVR2B(2), ACVRL1(2), BMP2(1), BMP4(2), BMP5(3), BMP6(1), BMP7(2), BMPR1A(1), BMPR1B(1), BMPR2(8), CREBBP(8), CUL1(5), DCN(2), EP300(8), FST(2), GDF5(2), GDF6(1), INHBA(3), INHBC(1), INHBE(1), LTBP1(3), MAPK3(1), NODAL(1), PPP2CA(1), PPP2CB(2), PPP2R1A(1), PPP2R1B(1), PPP2R2B(2), PPP2R2C(2), RBL1(4), RBL2(3), RBX1(1), RHOA(1), ROCK1(8), ROCK2(4), RPS6KB2(1), SMAD1(1), SMAD3(3), SMAD5(1), SMAD9(1), SMURF1(2), SMURF2(2), SP1(1), TFDP1(1), TGFB1(1), TGFB2(4), TGFBR1(5), TGFBR2(2), THBS1(3), THBS2(8), THBS3(2), THBS4(1), ZFYVE16(4), ZFYVE9(4)	17535458	147	47	145	36	48	50	24	1	23	1	3.8e-06	0.00047
6	CREMPATHWAY	The transcription factor CREM activates a post-meiotic transcriptional cascade culminating in spermatogenesis.	ADCY1, CREM, FHL5, FSHB, FSHR, GNAS, XPO1	7	ADCY1(5), CREM(2), FHL5(3), FSHB(2), FSHR(2), GNAS(2), XPO1(1)	1676768	17	16	17	7	7	2	4	1	3	0	0.000031	0.0028
7	ERBB4PATHWAY	ErbB4 (aka HER4) is a receptor tyrosine kinase that binds neuregulins as well as members of the EGF family, which also target EGF receptors.	ADAM17, ERBB4, NRG2, NRG3, PRKCA, PRKCB1, PSEN1	6	ADAM17(3), ERBB4(7), NRG2(3), NRG3(5), PRKCA(3)	1646150	21	16	21	4	5	8	2	1	5	0	0.000034	0.0028
8	HSA01030_GLYCAN_STRUCTURES_BIOSYNTHESIS_1	Genes involved in glycan structures - biosynthesis 1	A4GNT, ALG1, ALG10, ALG10B, ALG11, ALG12, ALG13, ALG14, ALG2, ALG3, ALG6, ALG8, ALG9, B3GALT6, B3GNT1, B3GNT2, B3GNT6, B3GNT7, B4GALT1, B4GALT2, B4GALT3, B4GALT4, B4GALT5, B4GALT7, C1GALT1, C1GALT1C1, ChGn, CHPF, CHST1, CHST11, CHST12, CHST13, CHST14, CHST2, CHST3, CHST4, CHST6, CHST7, CHSY-2, CHSY1, CSGlcA-T, DAD1, DDOST, DPAGT1, EXT1, EXT2, EXTL1, EXTL2, EXTL3, FUT11, FUT8, GALNAC4S-6ST, GALNACT-2, GALNT1, GALNT10, GALNT11, GALNT12, GALNT13, GALNT14, GALNT17, GALNT2, GALNT3, GALNT4, GALNT5, GALNT6, GALNT7, GALNT8, GALNT9, GALNTL1, GALNTL2, GALNTL4, GALNTL5, GANAB, GCNT1, GCNT3, GCNT4, GCS1, HS2ST1, HS3ST1, HS3ST2, HS3ST3A1, HS3ST3B1, HS3ST5, HS6ST1, HS6ST2, HS6ST3, LOC728969, MAN1A1, MAN1A2, MAN1B1, MAN1C1, MAN2A1, MGAT1, MGAT2, MGAT3, MGAT4A, MGAT4B, MGAT5, MGAT5B, NDST1, NDST2, NDST3, NDST4, OGT, RPN1, RPN2, ST3GAL1, ST3GAL2, ST3GAL3, ST3GAL4, ST6GAL1, ST6GALNAC1, STT3B, UST, WBSCR17, XYLT1, XYLT2	107	A4GNT(3), ALG1(1), ALG10B(3), ALG11(1), ALG12(1), ALG14(1), ALG2(1), ALG6(1), ALG8(3), ALG9(1), B3GNT2(1), B3GNT7(2), B4GALT1(2), B4GALT3(3), CHPF(1), CHST1(1), CHST11(1), CHST12(1), CHST13(1), CHST4(3), CHSY1(1), DAD1(2), DDOST(1), DPAGT1(1), EXT1(5), EXTL1(1), EXTL2(5), EXTL3(5), FUT11(1), FUT8(2), GALNT11(1), GALNT12(1), GALNT13(1), GALNT14(4), GALNT2(2), GALNT5(5), GALNT6(1), GALNT7(1), GALNT8(1), GALNTL1(2), GALNTL2(3), GALNTL4(1), GALNTL5(3), GANAB(1), GCNT1(2), GCNT3(2), GCNT4(3), HS2ST1(1), HS3ST1(1), HS3ST2(3), HS6ST3(1), MAN1A1(2), MAN1A2(1), MAN1B1(1), MAN1C1(3), MAN2A1(7), MGAT1(1), MGAT4A(1), MGAT5(2), NDST1(2), NDST2(1), NDST3(6), NDST4(1), OGT(2), RPN2(1), ST3GAL2(1), ST3GAL3(3), ST3GAL4(1), ST6GALNAC1(2), STT3B(4), XYLT1(2), XYLT2(1)	19542070	141	49	141	45	41	43	38	2	17	0	0.000037	0.0028
9	PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM		ACVR1, ACVR1B, ACVRL1, AKT1, AURKB, BMPR1A, BMPR2, BUB1, CDC2L5, CDIPT, CDKL1, CDKL2, CDS1, CDS2, CLK1, CLK2, CLK4, COL4A3BP, CSNK2A1, CSNK2A1, CSNK2A1P, CSNK2A2, CSNK2B, DGKA, DGKB, DGKD, DGKE, DGKG, DGKH, DGKQ, DGKZ, IMPA1, INPP1, INPP4A, INPP4B, INPP5A, INPPL1, ITPKA, ITPKB, MAP3K10, MOS, NEK1, NEK3, OCRL, PAK4, PCTK1, PCTK2, PIK3C2A, PIK3C2B, PIK3C2G, PIK3CA, PIK3CB, PIK3CG, PIK4CA, PIK4CA, LOC220686, PIM2, PIP5K2B, PLCB1, PLCB2, PLCB3, PLCB4, PLCD1, PLCG1, PLCG2, PLK3, PRKACA, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCQ, PRKCZ, PRKD1, PRKG1, RAF1, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KA4, RPS6KB1, STK11, TGFBR1, VRK1	80	ACVR1(3), ACVR1B(3), ACVRL1(2), AKT1(1), BMPR1A(1), BMPR2(8), BUB1(2), CDKL1(2), CDS1(2), CDS2(2), CLK1(2), CLK4(2), CSNK2A2(1), DGKA(1), DGKB(2), DGKD(8), DGKE(2), DGKG(2), DGKH(7), DGKZ(1), IMPA1(1), INPP4A(1), INPP4B(2), INPPL1(3), MAP3K10(1), MOS(1), NEK1(2), OCRL(6), PIK3C2A(3), PIK3C2B(6), PIK3C2G(2), PIK3CB(1), PIK3CG(5), PLCB1(1), PLCB3(3), PLCB4(2), PLCD1(4), PLCG1(1), PLCG2(4), PRKACA(1), PRKACG(1), PRKAR1A(4), PRKAR1B(1), PRKAR2B(1), PRKCA(3), PRKCE(2), PRKCG(5), PRKCH(1), PRKCQ(2), PRKD1(5), PRKG1(8), RAF1(4), RPS6KA2(4), RPS6KA3(2), TGFBR1(5), VRK1(2)	20222030	154	54	153	47	49	54	31	2	18	0	0.000047	0.0032
10	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	77	ABL1(2), ABL2(3), AKT1(1), AKT2(2), AKT3(1), ARAF(1), CAMK2D(2), CBL(4), CBLB(3), CDKN1A(1), CDKN1B(2), EGFR(5), ERBB3(6), ERBB4(7), EREG(1), GAB1(1), GRB2(2), GSK3B(2), MAP2K1(2), MAP2K2(1), MAP2K4(2), MAPK3(1), MAPK8(6), MAPK9(2), NCK1(1), NRG2(3), NRG3(5), PAK1(1), PAK2(3), PAK3(3), PAK7(3), PIK3CB(1), PIK3CD(2), PIK3CG(5), PIK3R3(4), PLCG1(1), PLCG2(4), PRKCA(3), PRKCG(5), PTK2(1), RAF1(4), RPS6KB2(1), SHC1(1), SHC2(1), SHC3(1), SHC4(1), SOS1(3), SOS2(6), SRC(3), STAT5B(1)	16575142	127	44	125	38	39	43	23	3	19	0	0.000054	0.0033

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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