Kidney Renal Clear Cell Carcinoma: Mutation Analysis (MutSig)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

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

Working with individual set: KIRC.

Number of patients in set: 327

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): 32

Mutations seen in COSMIC: 0

Significantly mutated genes in COSMIC territory: 0

Genes with clustered mutations (&le 3 aa apart): 0

Significantly mutated genesets: 200

Significantly mutated genesets: (excluding sig. mutated genes): 125

Results
Breakdown of Mutations by Type

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

type count
De_novo_Start_OutOfFrame 3
Frame_Shift_Del 468
Frame_Shift_Ins 170
In_Frame_Del 152
In_Frame_Ins 38
Indel 7
Missense_Mutation 8498
Nonsense_Mutation 583
Nonstop_Mutation 5
Silent 3652
Splice_Site 289
Translation_Start_Site 1
Total 13866
Breakdown of Mutation Rates by Category Type

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

category n N rate rate_per_mb relative_rate
(A/T)p*A->T 1065 1916153150 5.6e-07 0.56 0.53
(A/T)p*N->nonflip 2841 4225809399 6.7e-07 0.67 0.64
(C/G)p*N->mut 4075 5479976350 7.4e-07 0.74 0.71
(A/T)p*C->G 512 2309656249 2.2e-07 0.22 0.21
indel+null 1704 9705786076 1.8e-07 0.18 0.17
double_null 17 9705786076 1.8e-09 0.0018 0.0017
Total 10214 9705786076 1.1e-06 1.1 1
Target Coverage for Each Individual

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

Figure 1. 

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

Figure 2. 

Significantly Mutated Genes

Table 3.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 32. Number of genes displayed: 35

rank gene description N n npat nsite nsil n1 n2 n3 n4 n5 n6 p q
1 VHL von Hippel-Lindau tumor suppressor 123578 102 99 71 1 1 10 22 5 64 0 <1.00e-15 <1.80e-11
2 SETD2 SET domain containing 2 2325969 26 25 26 0 1 6 0 2 17 0 1.01e-14 9.09e-11
3 PBRM1 polybromo 1 1641867 79 78 75 2 0 5 7 1 66 0 1.94e-14 1.17e-10
4 KRTAP5-5 keratin associated protein 5-5 175966 8 8 3 0 0 0 0 0 8 0 4.71e-14 1.50e-10
5 KDM5C 1535300 17 16 17 1 1 4 3 0 9 0 4.80e-14 1.50e-10
6 BAP1 BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase) 711601 20 20 20 1 0 2 7 1 10 0 5.01e-14 1.50e-10
7 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 408096 11 11 11 5 2 0 4 0 5 0 6.51e-14 1.67e-10
8 TP53 tumor protein p53 424318 11 9 11 4 0 3 6 0 2 0 2.02e-11 4.54e-08
9 MUC4 mucin 4, cell surface associated 2136226 14 12 14 10 0 4 1 0 6 3 1.13e-08 0.000023
10 KANK3 KN motif and ankyrin repeat domains 3 317542 5 5 2 0 0 0 0 0 5 0 1.55e-08 0.000028
11 POLDIP2 polymerase (DNA-directed), delta interacting protein 2 320208 4 4 3 0 0 0 0 0 4 0 1.97e-07 0.00032
12 NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 2860923 13 13 13 3 1 4 4 1 3 0 6.65e-07 0.00100
13 TSPAN19 tetraspanin 19 219248 4 4 4 0 1 1 0 0 2 0 8.47e-07 0.0012
14 PTPN18 protein tyrosine phosphatase, non-receptor type 18 (brain-derived) 372926 5 5 3 0 0 1 1 0 3 0 2.92e-06 0.0038
15 KRTAP4-1 keratin associated protein 4-1 126824 3 3 3 0 0 1 0 0 2 0 8.86e-06 0.011
16 FAM200A 339714 5 5 5 0 1 1 2 0 1 0 0.000011 0.012
17 CD300E CD300e molecule 207318 4 4 4 0 1 1 2 0 0 0 0.000014 0.014
18 LGALS9B 159260 3 3 2 0 0 0 1 0 2 0 0.000016 0.016
19 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 1074849 8 8 8 2 1 5 1 0 1 0 0.000019 0.018
20 CRIPAK cysteine-rich PAK1 inhibitor 334428 3 3 3 1 0 0 0 0 3 0 0.000025 0.022
21 FMN2 formin 2 1396218 7 7 7 2 0 1 3 0 3 0 0.000038 0.033
22 NDUFA13 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13 135911 3 3 3 0 0 0 3 0 0 0 0.000055 0.044
23 NAT8 N-acetyltransferase 8 224976 3 3 3 0 0 1 1 0 1 0 0.000056 0.044
24 ADAMTS20 ADAM metallopeptidase with thrombospondin type 1 motif, 20 1919663 8 8 8 2 2 2 1 0 3 0 0.000059 0.045
25 STAG2 stromal antigen 2 1288053 7 7 7 2 0 1 2 0 4 0 0.000072 0.052
26 KRT1 keratin 1 (epidermolytic hyperkeratosis) 599661 4 4 2 0 0 1 0 0 3 0 0.000079 0.054
27 JMJD6 jumonji domain containing 6 414009 4 4 4 0 0 1 1 0 2 0 0.00011 0.070
28 RECQL5 RecQ protein-like 5 918684 4 4 2 1 0 0 1 0 3 0 0.00011 0.070
29 TGM5 transglutaminase 5 724305 5 5 5 1 0 1 3 0 1 0 0.00012 0.070
30 NF2 neurofibromin 2 (merlin) 570236 4 4 4 3 0 0 0 0 4 0 0.00012 0.070
31 C5orf13 chromosome 5 open reading frame 13 71613 2 2 2 0 0 0 0 0 2 0 0.00012 0.070
32 LHFPL1 lipoma HMGIC fusion partner-like 1 220725 3 3 3 0 0 1 1 0 1 0 0.00020 0.11
33 ZNF800 zinc finger protein 800 658905 5 5 5 1 2 1 1 0 1 0 0.00020 0.11
34 MCPH1 microcephalin 1 830844 6 5 6 0 0 0 2 0 2 2 0.00023 0.12
35 NKAIN3 Na+/K+ transporting ATPase interacting 3 183120 3 3 3 0 2 0 1 0 0 0 0.00023 0.12

Note:

N - number of sequenced bases in this gene across the individual set.

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

npat - number of patients (individuals) with at least one nonsilent mutation.

nsite - number of unique sites having a non-silent mutation.

nsil - number of silent mutations in this gene across the individual set.

n1 - number of nonsilent mutations of type: (A/T)p*A->T .

n2 - number of nonsilent mutations of type: (A/T)p*N->nonflip .

n3 - number of nonsilent mutations of type: (C/G)p*N->mut .

n4 - number of nonsilent mutations of type: (A/T)p*C->G .

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

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

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

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

p = p-value (overall)

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

COSMIC analyses

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

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

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

Note:

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

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

n_cos = overlap between n and cos.

N_cos = number of individuals times cos.

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

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

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

Clustered Mutations

Table 5.  Get Full Table Genes with Clustered Mutations

num gene desc n mindist npairs3 npairs12
2787 KDM5C 17 7 0 1
2868 KIF15 kinesin family member 15 5 24 0 0
1035 CDCP1 CUB domain containing protein 1 3 172 0 0
2876 KIF20B 4 188 0 0
6312 ZFYVE16 zinc finger, FYVE domain containing 16 2 304 0 0
3500 MUC6 mucin 6, oligomeric mucus/gel-forming 3 309 0 0
4022 PBRM1 polybromo 1 79 553 0 0
1955 FBN2 fibrillin 2 (congenital contractural arachnodactyly) 6 1111 0 0
5699 TLN1 talin 1 3 1315 0 0
1 A2BP1 3 Inf 0 0

Note:

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

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

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

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

Geneset Analyses

Table 6.  Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 200. 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 HSA04510_FOCAL_ADHESION Genes involved in focal adhesion ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, ARHGAP5, BAD, BCAR1, BCL2, BIRC2, BIRC3, BIRC4, BRAF, CAPN2, CAV1, CAV2, CAV3, CCND1, CCND2, CCND3, CDC42, CHAD, COL11A1, COL11A2, COL1A1, COL1A2, COL2A1, COL3A1, COL4A1, COL4A2, COL4A4, COL4A6, COL5A1, COL5A2, COL5A3, COL6A1, COL6A2, COL6A3, COL6A6, COMP, CRK, CRKL, CTNNB1, DIAPH1, DOCK1, EGF, EGFR, ELK1, ERBB2, FARP2, FIGF, FLNA, FLNB, FLNC, FLT1, FN1, FYN, GRB2, GRLF1, GSK3B, HGF, HRAS, IBSP, IGF1, IGF1R, ILK, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAV, ITGB1, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, JUN, KDR, LAMA1, LAMA2, LAMA3, LAMA4, LAMA5, LAMB1, LAMB2, LAMB3, LAMB4, LAMC1, LAMC2, LAMC3, LOC653852, MAP2K1, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MET, MLCK, MRCL3, MRLC2, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLK, MYLK2, MYLPF, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PARVA, PARVB, PARVG, PDGFA, PDGFB, PDGFC, PDGFD, PDGFRA, PDGFRB, PDPK1, PGF, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIP5K1C, PPP1CA, PPP1CB, PPP1CC, PPP1R12A, PRKCA, PRKCB1, PRKCG, PTEN, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, RAP1A, RAP1B, RAPGEF1, RELN, RHOA, ROCK1, ROCK2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SPP1, SRC, THBS1, THBS2, THBS3, THBS4, TLN1, TLN2, TNC, TNN, TNR, TNXB, VASP, VAV1, VAV2, VAV3, VCL, VEGFA, VEGFB, VEGFC, VTN, VWF, ZYX 192 ACTN2(2), AKT1(2), AKT2(2), ARHGAP5(1), BCAR1(2), BIRC2(2), BIRC3(1), BRAF(3), CCND2(1), CHAD(1), COL11A1(2), COL1A2(6), COL2A1(3), COL4A1(1), COL4A4(2), COL4A6(2), COL5A1(2), COL5A2(1), COL5A3(2), COL6A3(5), COL6A6(5), DIAPH1(1), DOCK1(1), EGF(1), EGFR(4), ERBB2(3), FARP2(2), FIGF(2), FLNA(2), FLNB(1), FLNC(3), FLT1(2), FN1(2), FYN(1), GRLF1(2), GSK3B(1), HGF(1), HRAS(2), ILK(1), ITGA1(1), ITGA11(2), ITGA3(2), ITGA6(2), ITGA8(1), ITGA9(2), ITGB1(2), ITGB5(3), ITGB6(2), ITGB7(1), JUN(1), KDR(2), LAMA1(3), LAMA2(5), LAMA3(1), LAMA4(3), LAMA5(4), LAMB1(3), LAMB2(1), LAMB4(4), LAMC2(3), LAMC3(3), MAPK10(1), MAPK9(1), MET(1), MYL7(1), MYL9(1), MYLK(2), PAK1(1), PAK4(2), PAK6(1), PAK7(1), PARVG(1), PDGFD(1), PDGFRA(3), PGF(1), PIK3CA(8), PIK3CB(1), PIK3CD(1), PIK3CG(4), PIK3R1(2), PIP5K1C(1), PRKCG(2), PTEN(11), PTK2(1), RELN(3), ROCK1(2), SOS1(4), SOS2(2), THBS1(4), THBS2(1), THBS3(1), THBS4(1), TLN1(3), TLN2(4), TNC(2), TNN(2), TNR(3), TNXB(1), VAV1(1), VAV3(1), VCL(1), VEGFA(1), VTN(1), VWF(5) 181072482 223 145 223 95 26 61 92 10 34 0 <1.00e-15 <2.05e-13
2 VEGFPATHWAY Vascular endothelial growth factor (VEGF) is upregulated by hypoxic conditions and promotes normal blood vessel formation and angiogenesis related to tumor growth or cardiac disease. ARNT, EIF1, EIF1A, EIF2B1, EIF2B2, EIF2B3, EIF2B4, EIF2B5, EIF2S1, EIF2S2, EIF2S3, ELAVL1, FLT1, FLT4, HIF1A, HRAS, KDR, NOS3, PIK3CA, PIK3R1, PLCG1, PRKCA, PRKCB1, PTK2, PXN, SHC1, VEGF, VHL 25 ARNT(1), EIF1(1), EIF2B1(2), EIF2B2(1), EIF2S2(1), FLT1(2), FLT4(3), HIF1A(1), HRAS(2), KDR(2), NOS3(1), PIK3CA(8), PIK3R1(2), PLCG1(1), PTK2(1), VHL(102) 16366258 131 119 100 14 7 21 31 6 66 0 <1.00e-15 <2.05e-13
3 HIFPATHWAY Under normal conditions, hypoxia inducible factor HIF-1 is degraded; under hypoxic conditions, it activates transcription of genes controlled by hpoxic response elements (HREs). ARNT, ASPH, COPS5, CREB1, EDN1, EP300, EPO, HIF1A, HSPCA, JUN, LDHA, NOS3, P4HB, VEGF, VHL 13 ARNT(1), ASPH(2), EP300(3), HIF1A(1), JUN(1), NOS3(1), VHL(102) 8099514 111 104 80 6 2 13 26 5 65 0 <1.00e-15 <2.05e-13
4 HSA04120_UBIQUITIN_MEDIATED_PROTEOLYSIS Genes involved in ubiquitin mediated proteolysis ANAPC1, ANAPC10, ANAPC11, ANAPC2, ANAPC4, ANAPC5, ANAPC7, BTRC, CDC16, CDC20, CDC23, CDC26, CDC27, CUL1, CUL2, CUL3, FBXW11, FBXW7, FZR1, ITCH, LOC728919, RBX1, SKP1, SKP2, SMURF1, SMURF2, TCEB1, TCEB2, UBA1, UBE2C, UBE2D1, UBE2D2, UBE2D3, UBE2D4, UBE2E1, UBE2E2, UBE2E3, VHL, WWP1, WWP2 39 ANAPC1(3), ANAPC4(1), CDC27(1), CUL1(2), CUL3(1), FBXW11(1), FBXW7(3), SMURF2(2), TCEB1(1), UBA1(1), UBE2E2(1), VHL(102), WWP2(1) 19910346 120 109 89 8 1 14 32 6 67 0 1.18e-14 1.45e-12
5 HSA04530_TIGHT_JUNCTION Genes involved in tight junction ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, AMOTL1, ASH1L, CASK, CDC42, CDK4, CGN, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CRB3, CSDA, CSNK2A1, CSNK2A2, CSNK2B, CTNNA1, CTNNA2, CTNNA3, CTNNB1, CTTN, EPB41, EPB41L1, EPB41L2, EPB41L3, EXOC3, EXOC4, F11R, GNAI1, GNAI2, GNAI3, HCLS1, HRAS, IGSF5, INADL, JAM2, JAM3, KRAS, LLGL1, LLGL2, MAGI1, MAGI2, MAGI3, MLLT4, MPDZ, MPP5, MRAS, MRCL3, MRLC2, MYH1, MYH10, MYH11, MYH13, MYH14, MYH15, MYH2, MYH3, MYH4, MYH6, MYH7, MYH7B, MYH8, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLPF, NRAS, OCLN, PARD3, PARD6A, PARD6B, PARD6G, PPM1J, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP2R3A, PPP2R3B, PPP2R4, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCQ, PRKCZ, PTEN, RAB13, RAB3B, RHOA, RRAS, RRAS2, SPTAN1, SRC, SYMPK, TJAP1, TJP1, TJP2, TJP3, VAPA, YES1, ZAK 130 ACTN2(2), AKT1(2), AKT2(2), ASH1L(2), CDK4(1), CLDN10(2), CLDN16(1), CLDN2(2), CLDN4(1), CSNK2A2(1), CTNNA1(2), CTNNA2(4), CTNNA3(3), EPB41(1), EPB41L2(2), EPB41L3(2), EXOC4(2), F11R(1), HCLS1(1), HRAS(2), INADL(2), LLGL1(1), LLGL2(1), MAGI1(2), MAGI2(1), MAGI3(1), MLLT4(1), MPDZ(3), MRAS(1), MYH1(4), MYH10(2), MYH11(5), MYH13(2), MYH14(2), MYH2(5), MYH3(3), MYH4(2), MYH6(3), MYH7(2), MYH7B(2), MYH8(1), MYH9(2), MYL7(1), MYL9(1), PARD3(1), PARD6B(1), PPM1J(1), PPP2CA(2), PPP2R1A(1), PPP2R2B(1), PPP2R3A(2), PPP2R4(1), PRKCD(2), PRKCG(2), PRKCH(2), PRKCI(1), PRKCQ(2), PRKCZ(1), PTEN(11), SPTAN1(1), TJP1(1), TJP2(1), ZAK(1) 95510705 121 100 121 61 9 38 40 6 28 0 1.19e-14 1.45e-12
6 HISTONE_METHYLTRANSFERASE Genes with HMT activity AOF2, KDM6A, ASH1L, ASH2L, C17orf79, CARM1, CTCFL, DOT1L, EED, EHMT1, EHMT2, EZH1, EZH2, FBXL10, FBXL11, FBXO11, HCFC1, HSF4, JMJD1A, JMJD1B, JMJD2A, JMJD2B, JMJD2C, JMJD2D, JMJD3, JMJD4, JMJD6, MEN1, MLL, MLL2, MLL3, MLL4, MLL5, NSD1, OGT, PAXIP1, PPP1CA, PPP1CB, PPP1CC, PRDM2, PRDM6, PRDM7, PRDM9, PRMT1, PRMT5, PRMT6, PRMT7, PRMT8, RBBP5, SATB1, SETD1A, SETD1B, SETD2, SETD7, SETD8, SETDB1, SETDB2, SETMAR, SMYD3, STK38, SUV39H1, SUV39H2, SUV420H1, SUV420H2, SUZ12, WHSC1, WHSC1L1 55 ASH1L(2), ASH2L(1), DOT1L(2), EHMT2(2), EZH1(1), EZH2(2), FBXO11(2), HCFC1(1), HSF4(1), JMJD6(4), KDM6A(3), MLL(1), MLL2(6), MLL3(9), MLL4(2), MLL5(4), NSD1(2), OGT(3), PRDM9(2), PRMT1(1), PRMT5(1), PRMT6(1), PRMT7(2), PRMT8(1), RBBP5(2), SETD1A(1), SETD2(26), SETDB1(1), SETMAR(1), SUV420H1(1), SUZ12(2), WHSC1(1), WHSC1L1(4) 59129401 95 82 95 30 8 22 26 3 36 0 1.41e-14 1.45e-12
7 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), ACTN2(2), APC(5), APC2(3), ARHGEF7(1), ARPC2(1), ARPC3(1), BCAR1(2), BDKRB1(1), BRAF(3), CHRM2(1), CHRM5(2), CSK(1), CYFIP1(2), CYFIP2(1), DIAPH1(1), DIAPH2(1), DIAPH3(1), DOCK1(1), EGF(1), EGFR(4), F2(2), FGD1(3), FGF20(1), FGF6(1), FGFR1(1), FGFR2(2), FGFR3(1), FGFR4(1), FN1(2), GIT1(2), GNA13(1), GNG12(1), GRLF1(2), HRAS(2), IQGAP1(1), IQGAP2(1), IQGAP3(3), ITGA1(1), ITGA11(2), ITGA3(2), ITGA6(2), ITGA8(1), ITGA9(2), ITGAE(2), ITGAL(2), ITGAX(1), ITGB1(2), ITGB5(3), ITGB6(2), ITGB7(1), LIMK2(1), MRAS(1), MSN(2), MYH10(2), MYH14(2), MYH9(2), MYL7(1), MYL9(1), MYLK(2), NCKAP1(1), NCKAP1L(1), PAK1(1), PAK4(2), PAK6(1), PAK7(1), PDGFRA(3), PIK3CA(8), PIK3CB(1), PIK3CD(1), PIK3CG(4), PIK3R1(2), PIP4K2A(2), PIP5K1C(1), PPP1R12B(1), PTK2(1), ROCK1(2), SLC9A1(1), SOS1(4), SOS2(2), SSH2(2), SSH3(1), TIAM1(2), TIAM2(2), VAV1(1), VAV3(1), VCL(1), WASL(2) 137704604 152 114 152 62 14 41 68 3 26 0 1.97e-13 1.73e-11
8 MTORPATHWAY Mammalian target of rapamycin (mTOR) senses mitogenic factors and nutrients, including ATP, and induces cell proliferation. AKT1, EIF3S10, EIF4A1, EIF4A2, EIF4B, EIF4E, EIF4EBP1, EIF4G1, EIF4G2, EIF4G3, FKBP1A, FRAP1, MKNK1, PDK2, PDPK1, PIK3CA, PIK3R1, PPP2CA, PTEN, RPS6, RPS6KB1, TSC1, TSC2 21 AKT1(2), EIF4A2(1), EIF4E(1), EIF4G1(2), EIF4G2(2), EIF4G3(1), PIK3CA(8), PIK3R1(2), PPP2CA(2), PTEN(11), RPS6KB1(2), TSC1(2), TSC2(2) 13388837 38 37 38 11 6 12 8 2 10 0 3.76e-12 2.89e-10
9 HSA00562_INOSITOL_PHOSPHATE_METABOLISM Genes involved in inositol phosphate metabolism CARKL, FN3K, IMPA1, IMPA2, INPP1, INPP4A, INPP4B, INPP5A, INPP5B, INPP5E, INPPL1, IPMK, ISYNA1, ITGB1BP3, ITPK1, ITPKA, ITPKB, MINPP1, MIOX, OCRL, PI4KA, PI4KB, PIB5PA, PIK3C3, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIP4K2A, PIP4K2B, PIP4K2C, PIP5K1A, PIP5K1B, PIP5K1C, PIP5K3, PLCB1, PLCB2, PLCB3, PLCB4, PLCD1, PLCD3, PLCD4, PLCE1, PLCG1, PLCG2, PLCZ1, PTEN, PTPMT1, SKIP, SYNJ1, SYNJ2 47 INPP4A(1), INPP4B(2), INPP5A(1), INPP5B(1), ITPKA(1), ITPKB(1), MIOX(1), OCRL(2), PI4KA(2), PI4KB(2), PIK3C3(3), PIK3CA(8), PIK3CB(1), PIK3CD(1), PIK3CG(4), PIP4K2A(2), PIP5K1C(1), PLCB1(1), PLCB2(1), PLCB4(3), PLCD1(1), PLCD4(2), PLCE1(1), PLCG1(1), PLCG2(1), PTEN(11), PTPMT1(1), SYNJ1(4) 36528872 61 53 61 23 5 18 18 1 17 2 4.55e-12 3.12e-10
10 SA_PTEN_PATHWAY PTEN is a tumor suppressor that dephosphorylates the lipid messenger phosphatidylinositol triphosphate. AKT1, AKT2, AKT3, BPNT1, GRB2, ILK, MAPK1, MAPK3, PDK1, PIK3CA, PIK3CD, PIP3-E, PTEN, PTK2B, RBL2, SHC1, SOS1 16 AKT1(2), AKT2(2), ILK(1), PDK1(1), PIK3CA(8), PIK3CD(1), PTEN(11), PTK2B(2), RBL2(1), SOS1(4) 9973858 33 32 33 8 4 10 11 1 7 0 1.59e-11 9.04e-10

Table 7.  Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 125. 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 HSA04510_FOCAL_ADHESION Genes involved in focal adhesion ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, ARHGAP5, BAD, BCAR1, BCL2, BIRC2, BIRC3, BIRC4, BRAF, CAPN2, CAV1, CAV2, CAV3, CCND1, CCND2, CCND3, CDC42, CHAD, COL11A1, COL11A2, COL1A1, COL1A2, COL2A1, COL3A1, COL4A1, COL4A2, COL4A4, COL4A6, COL5A1, COL5A2, COL5A3, COL6A1, COL6A2, COL6A3, COL6A6, COMP, CRK, CRKL, CTNNB1, DIAPH1, DOCK1, EGF, EGFR, ELK1, ERBB2, FARP2, FIGF, FLNA, FLNB, FLNC, FLT1, FN1, FYN, GRB2, GRLF1, GSK3B, HGF, HRAS, IBSP, IGF1, IGF1R, ILK, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAV, ITGB1, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, JUN, KDR, LAMA1, LAMA2, LAMA3, LAMA4, LAMA5, LAMB1, LAMB2, LAMB3, LAMB4, LAMC1, LAMC2, LAMC3, LOC653852, MAP2K1, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MET, MLCK, MRCL3, MRLC2, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLK, MYLK2, MYLPF, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PARVA, PARVB, PARVG, PDGFA, PDGFB, PDGFC, PDGFD, PDGFRA, PDGFRB, PDPK1, PGF, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIP5K1C, PPP1CA, PPP1CB, PPP1CC, PPP1R12A, PRKCA, PRKCB1, PRKCG, PTEN, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, RAP1A, RAP1B, RAPGEF1, RELN, RHOA, ROCK1, ROCK2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SPP1, SRC, THBS1, THBS2, THBS3, THBS4, TLN1, TLN2, TNC, TNN, TNR, TNXB, VASP, VAV1, VAV2, VAV3, VCL, VEGFA, VEGFB, VEGFC, VTN, VWF, ZYX 190 ACTN2(2), AKT1(2), AKT2(2), ARHGAP5(1), BCAR1(2), BIRC2(2), BIRC3(1), BRAF(3), CCND2(1), CHAD(1), COL11A1(2), COL1A2(6), COL2A1(3), COL4A1(1), COL4A4(2), COL4A6(2), COL5A1(2), COL5A2(1), COL5A3(2), COL6A3(5), COL6A6(5), DIAPH1(1), DOCK1(1), EGF(1), EGFR(4), ERBB2(3), FARP2(2), FIGF(2), FLNA(2), FLNB(1), FLNC(3), FLT1(2), FN1(2), FYN(1), GRLF1(2), GSK3B(1), HGF(1), HRAS(2), ILK(1), ITGA1(1), ITGA11(2), ITGA3(2), ITGA6(2), ITGA8(1), ITGA9(2), ITGB1(2), ITGB5(3), ITGB6(2), ITGB7(1), JUN(1), KDR(2), LAMA1(3), LAMA2(5), LAMA3(1), LAMA4(3), LAMA5(4), LAMB1(3), LAMB2(1), LAMB4(4), LAMC2(3), LAMC3(3), MAPK10(1), MAPK9(1), MET(1), MYL7(1), MYL9(1), MYLK(2), PAK1(1), PAK4(2), PAK6(1), PAK7(1), PARVG(1), PDGFD(1), PDGFRA(3), PGF(1), PIK3CB(1), PIK3CD(1), PIK3CG(4), PIK3R1(2), PIP5K1C(1), PRKCG(2), PTK2(1), RELN(3), ROCK1(2), SOS1(4), SOS2(2), THBS1(4), THBS2(1), THBS3(1), THBS4(1), TLN1(3), TLN2(4), TNC(2), TNN(2), TNR(3), TNXB(1), VAV1(1), VAV3(1), VCL(1), VEGFA(1), VTN(1), VWF(5) 179589537 204 138 204 88 23 56 87 10 28 0 6e-15 3.7e-12
2 HSA04530_TIGHT_JUNCTION Genes involved in tight junction ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, AMOTL1, ASH1L, CASK, CDC42, CDK4, CGN, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CRB3, CSDA, CSNK2A1, CSNK2A2, CSNK2B, CTNNA1, CTNNA2, CTNNA3, CTNNB1, CTTN, EPB41, EPB41L1, EPB41L2, EPB41L3, EXOC3, EXOC4, F11R, GNAI1, GNAI2, GNAI3, HCLS1, HRAS, IGSF5, INADL, JAM2, JAM3, KRAS, LLGL1, LLGL2, MAGI1, MAGI2, MAGI3, MLLT4, MPDZ, MPP5, MRAS, MRCL3, MRLC2, MYH1, MYH10, MYH11, MYH13, MYH14, MYH15, MYH2, MYH3, MYH4, MYH6, MYH7, MYH7B, MYH8, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLPF, NRAS, OCLN, PARD3, PARD6A, PARD6B, PARD6G, PPM1J, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP2R3A, PPP2R3B, PPP2R4, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCQ, PRKCZ, PTEN, RAB13, RAB3B, RHOA, RRAS, RRAS2, SPTAN1, SRC, SYMPK, TJAP1, TJP1, TJP2, TJP3, VAPA, YES1, ZAK 129 ACTN2(2), AKT1(2), AKT2(2), ASH1L(2), CDK4(1), CLDN10(2), CLDN16(1), CLDN2(2), CLDN4(1), CSNK2A2(1), CTNNA1(2), CTNNA2(4), CTNNA3(3), EPB41(1), EPB41L2(2), EPB41L3(2), EXOC4(2), F11R(1), HCLS1(1), HRAS(2), INADL(2), LLGL1(1), LLGL2(1), MAGI1(2), MAGI2(1), MAGI3(1), MLLT4(1), MPDZ(3), MRAS(1), MYH1(4), MYH10(2), MYH11(5), MYH13(2), MYH14(2), MYH2(5), MYH3(3), MYH4(2), MYH6(3), MYH7(2), MYH7B(2), MYH8(1), MYH9(2), MYL7(1), MYL9(1), PARD3(1), PARD6B(1), PPM1J(1), PPP2CA(2), PPP2R1A(1), PPP2R2B(1), PPP2R3A(2), PPP2R4(1), PRKCD(2), PRKCG(2), PRKCH(2), PRKCI(1), PRKCQ(2), PRKCZ(1), SPTAN1(1), TJP1(1), TJP2(1), ZAK(1) 95102609 110 91 110 56 7 38 36 6 23 0 9.3e-12 1.9e-09
3 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 202 ABI2(1), ACTN2(2), APC(5), APC2(3), ARHGEF7(1), ARPC2(1), ARPC3(1), BCAR1(2), BDKRB1(1), BRAF(3), CHRM2(1), CHRM5(2), CSK(1), CYFIP1(2), CYFIP2(1), DIAPH1(1), DIAPH2(1), DIAPH3(1), DOCK1(1), EGF(1), EGFR(4), F2(2), FGD1(3), FGF20(1), FGF6(1), FGFR1(1), FGFR2(2), FGFR3(1), FGFR4(1), FN1(2), GIT1(2), GNA13(1), GNG12(1), GRLF1(2), HRAS(2), IQGAP1(1), IQGAP2(1), IQGAP3(3), ITGA1(1), ITGA11(2), ITGA3(2), ITGA6(2), ITGA8(1), ITGA9(2), ITGAE(2), ITGAL(2), ITGAX(1), ITGB1(2), ITGB5(3), ITGB6(2), ITGB7(1), LIMK2(1), MRAS(1), MSN(2), MYH10(2), MYH14(2), MYH9(2), MYL7(1), MYL9(1), MYLK(2), NCKAP1(1), NCKAP1L(1), PAK1(1), PAK4(2), PAK6(1), PAK7(1), PDGFRA(3), PIK3CB(1), PIK3CD(1), PIK3CG(4), PIK3R1(2), PIP4K2A(2), PIP5K1C(1), PPP1R12B(1), PTK2(1), ROCK1(2), SLC9A1(1), SOS1(4), SOS2(2), SSH2(2), SSH3(1), TIAM1(2), TIAM2(2), VAV1(1), VAV3(1), VCL(1), WASL(2) 136629755 144 108 144 60 13 36 67 3 25 0 9.4e-12 1.9e-09
4 HSA04020_CALCIUM_SIGNALING_PATHWAY Genes involved in calcium signaling pathway ADCY1, ADCY2, ADCY3, ADCY4, ADCY7, ADCY8, ADCY9, ADORA2A, ADORA2B, ADRA1A, ADRA1B, ADRA1D, ADRB1, ADRB2, ADRB3, AGTR1, ATP2A1, ATP2A2, ATP2A3, ATP2B1, ATP2B2, ATP2B3, ATP2B4, AVPR1A, AVPR1B, BDKRB1, BDKRB2, BST1, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1F, CACNA1G, CACNA1H, CACNA1I, CACNA1S, CALM1, CALM2, CALM3, CALML3, CALML6, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CAMK4, CCKAR, CCKBR, CD38, CHP, CHRM1, CHRM2, CHRM3, CHRM5, CHRNA7, CYSLTR1, CYSLTR2, DRD1, EDNRA, EDNRB, EGFR, ERBB2, ERBB3, ERBB4, F2R, GNA11, GNA14, GNA15, GNAL, GNAQ, GNAS, GRIN1, GRIN2A, GRIN2C, GRIN2D, GRM1, GRM5, GRPR, HRH1, HRH2, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, ITPKA, ITPKB, ITPR1, ITPR2, ITPR3, LHCGR, LTB4R2, MLCK, MYLK, MYLK2, NOS1, NOS2A, NOS3, NTSR1, OXTR, P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX7, P2RXL1, PDE1A, PDE1B, PDE1C, PDGFRA, PDGFRB, PHKA1, PHKA2, PHKB, PHKG1, PHKG2, PLCB1, PLCB2, PLCB3, PLCB4, PLCD1, PLCD3, PLCD4, PLCE1, PLCG1, PLCG2, PLCZ1, PLN, PPID, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PTAFR, PTGER1, PTGER3, PTGFR, PTK2B, RYR1, RYR2, RYR3, SLC25A4, SLC25A5, SLC25A6, SLC8A1, SLC8A2, SLC8A3, SPHK1, SPHK2, TACR1, TACR2, TACR3, TBXA2R, TNNC1, TNNC2, TRHR, TRPC1, VDAC1, VDAC2, VDAC3 167 ADCY2(1), ADCY7(1), ADCY8(4), ADCY9(2), ADORA2A(1), ADRB2(1), ATP2A1(2), ATP2A2(2), ATP2B3(1), ATP2B4(1), AVPR1A(2), BDKRB1(1), CACNA1A(1), CACNA1C(5), CACNA1D(4), CACNA1E(1), CACNA1F(3), CACNA1H(3), CACNA1I(3), CACNA1S(1), CALM2(1), CAMK2G(2), CCKAR(2), CCKBR(1), CD38(1), CHRM2(1), CHRM5(2), CHRNA7(1), DRD1(1), EGFR(4), ERBB2(3), ERBB3(3), ERBB4(3), GNAL(1), GNAS(1), GRIN1(1), GRIN2A(3), GRM1(1), GRM5(1), HTR2A(1), HTR2C(1), HTR5A(1), HTR6(1), HTR7(1), ITPKA(1), ITPKB(1), ITPR1(1), ITPR2(4), ITPR3(1), MYLK(2), NOS1(5), NOS3(1), NTSR1(1), P2RX1(1), PDE1B(2), PDE1C(1), PDGFRA(3), PHKA1(1), PHKB(2), PHKG1(1), PLCB1(1), PLCB2(1), PLCB4(3), PLCD1(1), PLCD4(2), PLCE1(1), PLCG1(1), PLCG2(1), PPP3CC(1), PRKACA(1), PRKACB(1), PRKCG(2), PTAFR(1), PTGFR(1), PTK2B(2), RYR1(3), RYR2(3), RYR3(3), SLC25A4(1), SLC8A1(1), SLC8A3(1), SPHK2(1), TACR1(1), TACR2(1), TACR3(2), TRPC1(1), VDAC3(1) 134793666 145 121 145 59 14 44 59 5 23 0 5e-11 7.7e-09
5 HSA04520_ADHERENS_JUNCTION Genes involved in adherens junction ACP1, ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, ACVR1B, ACVR1C, BAIAP2, CDC42, CDH1, CREBBP, CSNK2A1, CSNK2A2, CSNK2B, CTNNA1, CTNNA2, CTNNA3, CTNNB1, CTNND1, EGFR, EP300, ERBB2, FARP2, FER, FGFR1, FYN, IGF1R, INSR, IQGAP1, LEF1, LMO7, MAP3K7, MAPK1, MAPK3, MET, MLLT4, NLK, PARD3, PTPN1, PTPN6, PTPRB, PTPRF, PTPRJ, PTPRM, PVRL1, PVRL2, PVRL3, PVRL4, RAC1, RAC2, RAC3, RHOA, SMAD2, SMAD3, SMAD4, SNAI1, SNAI2, SORBS1, SRC, SSX2IP, TCF7, TCF7L1, TCF7L2, TGFBR1, TGFBR2, TJP1, VCL, WAS, WASF1, WASF2, WASF3, WASL, YES1 75 ACTN2(2), ACVR1B(3), ACVR1C(2), CDH1(2), CREBBP(3), CSNK2A2(1), CTNNA1(2), CTNNA2(4), CTNNA3(3), CTNND1(3), EGFR(4), EP300(3), ERBB2(3), FARP2(2), FER(2), FGFR1(1), FYN(1), INSR(4), IQGAP1(1), LMO7(3), MAP3K7(1), MET(1), MLLT4(1), PARD3(1), PTPRB(2), PTPRF(3), PTPRJ(4), PTPRM(1), PVRL3(2), SMAD2(1), SMAD4(4), SNAI1(1), SNAI2(1), SORBS1(1), SSX2IP(1), TCF7(2), TGFBR2(2), TJP1(1), VCL(1), WASL(2) 58917089 82 69 81 29 7 26 30 6 13 0 2.2e-09 2.7e-07
6 HSA04670_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION Genes involved in Leukocyte transendothelial migration ACTN1, ACTN2, ACTN3, ACTN4, ARHGAP5, BCAR1, CD99, CDC42, CDH5, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CTNNA1, CTNNA2, CTNNA3, CTNNB1, CTNND1, CXCL12, CXCR4, CYBA, CYBB, ESAM, EZR, F11R, GNAI1, GNAI2, GNAI3, GRLF1, ICAM1, ITGA4, ITGAL, ITGAM, ITGB1, ITGB2, ITK, JAM2, JAM3, MAPK11, MAPK12, MAPK13, MAPK14, MLLT4, MMP2, MMP9, MRCL3, MRLC2, MSN, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLPF, NCF1, NCF2, NCF4, NOX1, NOX3, OCLN, PECAM1, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLCG1, PLCG2, PRKCA, PRKCB1, PRKCG, PTK2, PTK2B, PTPN11, PXN, RAC1, RAC2, RAP1A, RAP1B, RAPGEF3, RAPGEF4, RASSF5, RHOA, RHOH, ROCK1, ROCK2, SIPA1, THY1, TXK, VASP, VAV1, VAV2, VAV3, VCAM1, VCL 108 ACTN2(2), ARHGAP5(1), BCAR1(2), CDH5(1), CLDN10(2), CLDN16(1), CLDN2(2), CLDN4(1), CTNNA1(2), CTNNA2(4), CTNNA3(3), CTNND1(3), F11R(1), GRLF1(2), ITGAL(2), ITGB1(2), ITK(2), MLLT4(1), MSN(2), MYL7(1), MYL9(1), NCF1(1), NOX1(1), NOX3(2), PIK3CB(1), PIK3CD(1), PIK3CG(4), PIK3R1(2), PLCG1(1), PLCG2(1), PRKCG(2), PTK2(1), PTK2B(2), PTPN11(1), RAPGEF3(2), RAPGEF4(1), RASSF5(1), ROCK1(2), VAV1(1), VAV3(1), VCAM1(1), VCL(1) 60319616 68 54 68 26 8 14 28 2 16 0 4.7e-08 4.8e-06
7 HSA04512_ECM_RECEPTOR_INTERACTION Genes involved in ECM-receptor interaction AGRN, CD36, CD44, CD47, CHAD, COL11A1, COL11A2, COL1A1, COL1A2, COL2A1, COL3A1, COL4A1, COL4A2, COL4A4, COL4A6, COL5A1, COL5A2, COL5A3, COL6A1, COL6A2, COL6A3, COL6A6, DAG1, FN1, FNDC1, FNDC3A, FNDC4, FNDC5, GP1BA, GP1BB, GP5, GP6, GP9, HMMR, HSPG2, IBSP, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAV, ITGB1, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, LAMA1, LAMA2, LAMA3, LAMA4, LAMA5, LAMB1, LAMB2, LAMB3, LAMB4, LAMC1, LAMC2, LAMC3, RELN, SDC1, SDC2, SDC3, SDC4, SPP1, SV2A, SV2B, SV2C, THBS1, THBS2, THBS3, THBS4, TNC, TNN, TNR, TNXB, VTN, VWF 86 AGRN(2), CD44(2), CHAD(1), COL11A1(2), COL1A2(6), COL2A1(3), COL4A1(1), COL4A4(2), COL4A6(2), COL5A1(2), COL5A2(1), COL5A3(2), COL6A3(5), COL6A6(5), FN1(2), FNDC1(2), GP1BA(1), HSPG2(1), ITGA1(1), ITGA11(2), ITGA3(2), ITGA6(2), ITGA8(1), ITGA9(2), ITGB1(2), ITGB5(3), ITGB6(2), ITGB7(1), LAMA1(3), LAMA2(5), LAMA3(1), LAMA4(3), LAMA5(4), LAMB1(3), LAMB2(1), LAMB4(4), LAMC2(3), LAMC3(3), RELN(3), SV2C(2), THBS1(4), THBS2(1), THBS3(1), THBS4(1), TNC(2), TNN(2), TNR(3), TNXB(1), VTN(1), VWF(5) 109979156 116 94 116 53 17 30 42 8 19 0 9.1e-08 7.9e-06
8 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 235 ADCYAP1R1(1), ADORA2A(1), ADRB2(1), AVPR1A(2), BDKRB1(1), C3AR1(1), CALCR(1), CCKAR(2), CCKBR(1), CHRM2(1), CHRM5(2), CNR2(1), CRHR2(1), DRD1(1), DRD5(1), F2(2), GABBR1(1), GABRA3(2), GABRA4(2), GABRA5(1), GABRA6(1), GABRB1(1), GABRB3(1), GABRE(3), GABRG2(2), GABRQ(3), GABRR1(2), GABRR2(2), GH2(1), GHR(1), GIPR(1), GLP2R(1), GLRA1(1), GPR35(1), GPR50(1), GPR63(1), GPR83(1), GRIA1(5), GRIA2(1), GRIA4(3), GRID2(5), GRIK1(1), GRIK2(1), GRIK3(1), GRIK5(1), GRIN1(1), GRIN2A(3), GRIN2B(4), GRIN3B(2), GRM1(1), GRM2(2), GRM3(1), GRM4(1), GRM5(1), GRM7(1), GRM8(1), GZMA(1), HRH4(1), HTR1A(1), HTR2A(1), HTR2C(1), HTR5A(1), HTR6(1), HTR7(1), LEPR(1), LTB4R(1), MAS1(1), MC3R(1), MCHR2(3), NMBR(1), NPFFR2(1), NPY1R(1), NTSR1(1), OPRD1(1), OPRM1(1), P2RX1(1), P2RY10(2), P2RY13(1), P2RY2(1), PARD3(1), PRLR(1), PTAFR(1), PTGDR(1), PTGER2(1), PTGFR(1), SSTR1(2), SSTR4(1), TAAR2(1), TACR1(1), TACR2(1), TACR3(2), THRA(1), TSHR(1) 107023493 128 104 128 41 12 34 59 5 18 0 1e-07 7.9e-06
9 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 84 ABL2(2), AKT1(2), AKT2(2), BRAF(3), BTC(1), CAMK2G(2), CBL(1), CBLB(1), CDKN1A(1), EGF(1), EGFR(4), ERBB2(3), ERBB3(3), ERBB4(3), GAB1(1), GSK3B(1), HRAS(2), JUN(1), MAP2K7(1), MAPK10(1), MAPK9(1), NRG1(3), NRG2(1), NRG3(2), PAK1(1), PAK4(2), PAK6(1), PAK7(1), PIK3CB(1), PIK3CD(1), PIK3CG(4), PIK3R1(2), PLCG1(1), PLCG2(1), PRKCG(2), PTK2(1), RPS6KB1(2), SOS1(4), SOS2(2), STAT5B(1) 49422728 70 59 70 29 8 20 30 1 11 0 4.3e-06 0.0003
10 P53HYPOXIAPATHWAY Hypoxia induces p53 accumulation and consequent apoptosis with p53-mediated cell cycle arrest, which is present under conditions of DNA damage. ABCB1, AKT1, ATM, BAX, CDKN1A, CPB2, CSNK1A1, CSNK1D, FHL2, GADD45A, HIC1, HIF1A, HSPA1A, HSPCA, IGFBP3, MAPK8, MDM2, NFKBIB, NQO1, TP53 16 ABCB1(3), AKT1(2), ATM(8), CDKN1A(1), CPB2(1), HIF1A(1), IGFBP3(1), NFKBIB(1) 9340461 18 17 18 8 2 4 6 0 6 0 8.4e-06 0.00051
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 Ð 615 (2011)
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  • Maintainer = Dan DiCara

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