Ovarian Serous Cystadenocarcinoma: 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: OV.

Number of patients in set: 316

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

MAF used for this analysis: OV.final_analysis_set.maf

Significantly mutated genes (q ≤ 0.1): 12

Mutations seen in COSMIC: 394

Significantly mutated genes in COSMIC territory: 39

Genes with clustered mutations (≤ 3 aa apart): 0

Significantly mutated genesets: 61

Significantly mutated genesets: (excluding sig. mutated genes): 13

Mutation Preprocessing

Read 148 MAFs of type "Broad"

Read 88 MAFs of type "WashU"

Read 80 MAFs of type "Baylor"

Total number of mutations in input MAFs: 20219

Mutation Filtering

Number of mutations before filtering: 20219

After removing 1 non-mutations: 20218

After removing 778 mutations outside gene set: 19440

After removing 9 mutations outside category set: 19431

After removing 4 "impossible" mutations in

gene-patient-category bins of zero coverage: 19427

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 441
Frame_Shift_Ins 155
In_Frame_Del 148
In_Frame_Ins 37
Indel 13
Missense_Mutation 13164
Nonsense_Mutation 800
Nonstop_Mutation 16
Silent 4231
Splice_Site_Del 33
Splice_Site_Ins 5
Splice_Site_SNP 388
Total 19431
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 1860 396729715 4.7e-06 4.7 2.5
*Cp(A/C/T)->T 2187 3661505903 6e-07 0.6 0.32
C->(G/A) 5212 4058235618 1.3e-06 1.3 0.69
A->mut 3901 4115893953 9.5e-07 0.95 0.51
indel+null 2030 8174129610 2.5e-07 0.25 0.13
double_null 7 8174129610 8.6e-10 0.00086 0.00046
Total 15197 8174129610 1.9e-06 1.9 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: OV.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

Table 3.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 12. 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_ks p_cons p_joint p q
1 TP53 tumor protein p53 401524 279 276 143 3 47 31 39 61 101 0 <1.00e-15 2e-07 2e-07 0 <1.00e-15 <8.54e-12
2 ELAVL2 ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B) 347710 2 2 2 0 1 0 0 1 0 0 0.041 0.048 0.0044 0 <1.00e-15 <8.54e-12
3 SRC v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) 372331 4 4 2 0 0 0 4 0 0 0 0.0026 1.6e-06 0.017 1.8e-06 9.54e-08 0.00054
4 BRCA1 breast cancer 1, early onset 1798045 12 12 12 0 0 0 1 0 11 0 1.87e-08 1 0.2 0.77 2.73e-07 0.0012
5 TBP TATA box binding protein 321652 4 4 2 0 0 0 0 0 4 0 0.00023 0.000053 0.99 0.000096 4.07e-07 0.0014
6 CSMD3 CUB and Sushi multiple domains 3 3615081 18 18 18 3 0 2 7 8 1 0 1.78e-06 0.051 0.48 0.092 2.72e-06 0.0078
7 RB1 retinoblastoma 1 (including osteosarcoma) 826059 9 9 9 0 0 1 3 0 5 0 7.71e-07 0.23 0.65 0.39 4.84e-06 0.011
8 NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 2619095 15 14 15 0 1 1 1 3 9 0 1.67e-06 0.3 0.09 0.19 5.13e-06 0.011
9 C9orf171 251675 5 5 5 0 2 0 2 0 1 0 0.000039 0.33 0.014 0.039 0.000022 0.042
10 GABRA6 gamma-aminobutyric acid (GABA) A receptor, alpha 6 440417 6 6 6 1 1 3 1 1 0 0 0.000045 0.035 0.32 0.059 0.000037 0.063
11 CDK12 1351667 9 9 9 0 0 0 1 3 5 0 0.000057 0.047 0.25 0.071 0.000054 0.084
12 FAT3 FAT tumor suppressor homolog 3 (Drosophila) 3706784 20 19 20 1 4 2 3 10 1 0 0.000012 0.74 0.28 0.62 0.000094 0.12
13 ARHGEF9 Cdc42 guanine nucleotide exchange factor (GEF) 9 494011 5 5 5 0 0 1 2 1 1 0 0.00041 0.015 0.33 0.018 0.000095 0.12
14 EFEMP1 EGF-containing fibulin-like extracellular matrix protein 1 475456 5 5 5 0 1 0 3 0 1 0 0.00036 0.25 0.012 0.028 0.00012 0.15
15 CYP11B1 cytochrome P450, family 11, subfamily B, polypeptide 1 456589 7 7 6 0 1 0 3 3 0 0 0.000019 0.45 0.8 0.65 0.00015 0.17
16 LAIR1 leukocyte-associated immunoglobulin-like receptor 1 267149 3 3 3 1 0 0 1 1 1 0 0.0033 0.036 0.015 0.0042 0.00017 0.17
17 SLCO1C1 solute carrier organic anion transporter family, member 1C1 717910 6 6 6 0 0 1 4 1 0 0 0.00013 0.047 0.72 0.1 0.00017 0.17
18 CREBBP CREB binding protein (Rubinstein-Taybi syndrome) 1964764 7 7 7 1 0 1 0 3 3 0 0.0055 0.0044 0.071 0.0029 0.00019 0.18
19 GAS2L1 growth arrest-specific 2 like 1 197396 4 4 4 0 0 0 3 1 0 0 0.00017 0.065 0.4 0.1 0.00021 0.19
20 DUSP19 dual specificity phosphatase 19 211393 4 4 4 0 0 0 1 3 0 0 0.000040 0.63 0.47 0.7 0.00032 0.22
21 CHST2 carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2 172127 5 5 5 1 0 2 2 1 0 0 0.000028 1 0.97 1 0.00033 0.22
22 USH2A Usher syndrome 2A (autosomal recessive, mild) 5014417 20 20 20 3 2 5 3 7 3 0 0.000074 0.42 0.2 0.39 0.00033 0.22
23 BRCA2 breast cancer 2, early onset 2896444 11 11 11 0 1 0 0 1 8 1 0.000070 0.27 0.93 0.41 0.00033 0.22
24 PPP1R3A protein phosphatase 1, regulatory (inhibitor) subunit 3A 1053877 8 8 8 2 1 1 2 4 0 0 0.000060 0.92 0.093 0.49 0.00034 0.22
25 SLC35F5 solute carrier family 35, member F5 489083 2 2 1 0 0 0 0 0 2 0 0.050 0.00062 0.098 0.00062 0.00036 0.22
26 ATP5B ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide 467672 2 2 1 1 0 0 0 2 0 0 0.072 0.0018 0.22 0.00045 0.00037 0.22
27 FAM171B 744587 7 7 7 0 1 1 2 2 1 0 0.000084 0.22 0.64 0.4 0.00038 0.22
28 C6orf142 chromosome 6 open reading frame 142 449405 5 5 5 3 0 2 1 1 1 0 0.00013 0.16 0.7 0.25 0.00038 0.22
29 PDAP1 PDGFA associated protein 1 170027 2 2 1 0 0 0 0 0 2 0 0.0036 0.0017 0.89 0.0095 0.00038 0.22
30 MYO19 myosin XIX 675465 2 1 2 1 0 0 1 0 1 0 0.44 0.00019 0.19 0.000083 0.00041 0.22
31 GLI2 GLI-Kruppel family member GLI2 947026 10 9 10 0 2 3 3 1 1 0 0.000078 0.6 0.25 0.53 0.00046 0.22
32 ODAM odontogenic, ameloblast asssociated 257049 3 3 3 0 0 0 1 2 0 0 0.0014 0.49 0.0057 0.03 0.00047 0.22
33 COL5A3 collagen, type V, alpha 3 1408232 7 7 7 1 0 3 3 0 1 0 0.0092 0.037 0.0041 0.0047 0.00047 0.22
34 LCOR ligand dependent nuclear receptor corepressor 396634 4 4 4 0 0 1 1 0 2 0 0.0010 0.5 0.012 0.043 0.00048 0.22
35 KCNJ12 potassium inwardly-rectifying channel, subfamily J, member 12 281754 5 5 3 2 5 0 0 0 0 0 0.00022 0.14 0.21 0.2 0.00048 0.22

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)->T .

n3 - number of nonsilent mutations of type: C->(G/A) .

n4 - number of nonsilent mutations of type: A->mut .

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: 39. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 TP53 tumor protein p53 279 823 278 260068 70907 0 0
2 RB1 retinoblastoma 1 (including osteosarcoma) 9 267 8 84372 16 9.6e-12 2.1e-08
3 NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 15 285 6 90060 8 2.7e-08 0.000039
4 MYO3A myosin IIIA 7 14 3 4424 3 9.2e-08 0.0001
5 KLK10 kallikrein-related peptidase 10 2 2 2 632 2 6.9e-07 0.0006
6 CDC27 cell division cycle 27 homolog (S. cerevisiae) 4 3 2 948 2 1.5e-06 0.0011
7 ERBB2 v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) 4 41 3 12956 4 2.3e-06 0.0014
8 MLL4 4 6 2 1896 2 6.2e-06 0.0034
9 NIPBL Nipped-B homolog (Drosophila) 5 7 2 2212 2 8.4e-06 0.0041
10 EGFR epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) 7 218 4 68888 53 1e-05 0.0044

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

There were no clustered mutations discovered.

Geneset Analyses

Table 5.  Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 61. 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 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 232 ACVR1B(1), ACVR1C(2), BRAF(2), CACNA1A(5), CACNA1B(1), CACNA1C(9), CACNA1D(6), CACNA1E(4), CACNA1F(4), CACNA1G(3), CACNA1S(5), CACNA2D1(4), CACNA2D2(1), CACNA2D3(1), CACNA2D4(1), CACNB1(1), CACNB2(1), CACNB4(1), CACNG3(1), CACNG6(2), CDC25B(2), CHUK(1), DAXX(1), DDIT3(2), DUSP1(2), DUSP7(1), DUSP9(2), ECSIT(1), EGFR(7), ELK1(2), FGF12(1), FGF2(1), FGF23(2), FGF5(1), FGF6(1), FGFR4(1), FLNA(1), FLNB(3), FLNC(3), FOS(1), GADD45A(1), GADD45B(1), GNA12(1), GRB2(2), IKBKB(1), KRAS(2), MAP2K3(1), MAP2K4(1), MAP2K6(1), MAP3K1(1), MAP3K10(2), MAP3K12(1), MAP3K13(2), MAP3K14(1), MAP3K2(2), MAP3K3(1), MAP3K4(2), MAP3K5(2), MAP3K6(1), MAP3K7(3), MAP4K1(1), MAP4K3(3), MAPK14(1), MAPK8(1), MAPK8IP1(1), MAPK9(1), MAPKAPK3(1), MAPKAPK5(1), MEF2C(1), MKNK1(1), MOS(1), MRAS(1), NF1(15), NFATC2(1), NFATC4(1), NFKB1(1), NLK(1), NRAS(2), NTF3(1), NTRK1(4), NTRK2(1), PAK2(1), PDGFRA(3), PDGFRB(3), PLA2G12A(1), PLA2G12B(1), PLA2G2F(1), PLA2G4A(1), PLA2G6(1), PPP3CC(1), PPP5C(1), PRKACG(1), PRKCA(1), PRKCG(1), PTPN5(3), PTPRR(1), RAPGEF2(1), RASA1(1), RASA2(2), RASGRF1(2), RASGRF2(4), RASGRP1(1), RASGRP2(1), RASGRP3(2), RPS6KA1(1), RPS6KA2(1), RPS6KA4(1), RPS6KA5(1), RRAS(1), SOS1(3), SOS2(1), SRF(1), STK4(1), TAOK1(1), TAOK3(1), TGFBR2(3), TNF(1), TNFRSF1A(1), TP53(279), TRAF2(1), TRAF6(2) 116594517 496 293 358 53 79 59 109 115 134 0 <1.00e-15 <3.08e-14
2 HSA04110_CELL_CYCLE Genes involved in cell cycle ABL1, ANAPC1, ANAPC10, ANAPC11, ANAPC2, ANAPC4, ANAPC5, ANAPC7, ATM, ATR, BUB1, BUB1B, BUB3, CCNA1, CCNA2, CCNB1, CCNB2, CCNB3, CCND1, CCND2, CCND3, CCNE1, CCNE2, CCNH, CDC14A, CDC14B, CDC16, CDC2, CDC20, CDC23, CDC25A, CDC25B, CDC25C, CDC26, CDC27, CDC45L, CDC6, CDC7, CDK2, CDK4, CDK6, CDK7, CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B, CDKN2C, CDKN2D, CHEK1, CHEK2, CREBBP, CUL1, DBF4, E2F1, E2F2, E2F3, EP300, ESPL1, FZR1, GADD45A, GADD45B, GADD45G, GSK3B, hCG_1982709, HDAC1, HDAC2, LOC440917, LOC728919, MAD1L1, MAD2L1, MAD2L2, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MDM2, ORC1L, ORC2L, ORC3L, ORC4L, ORC5L, ORC6L, PCNA, PKMYT1, PLK1, PRKDC, PTTG1, PTTG2, RB1, RBL1, RBL2, RBX1, SFN, SKP1, SKP2, SMAD2, SMAD3, SMAD4, SMC1A, SMC1B, TFDP1, TGFB1, TGFB2, TGFB3, TP53, WEE1, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ 106 ABL1(1), ANAPC1(1), ANAPC2(1), ANAPC4(1), ANAPC5(1), ATM(5), ATR(2), BUB1(1), BUB1B(2), BUB3(1), CCNA1(2), CCNA2(1), CCNB3(3), CCNH(1), CDC20(1), CDC25B(2), CDC27(4), CDC6(1), CDC7(2), CDK2(1), CDKN1A(1), CDKN1B(1), CDKN2C(2), CDKN2D(1), CHEK2(1), CREBBP(7), E2F2(1), EP300(1), GADD45A(1), GADD45B(1), GSK3B(1), HDAC1(1), MAD2L2(1), MCM2(2), MCM3(1), MCM4(2), MCM5(2), ORC1L(1), ORC4L(1), PRKDC(8), RB1(9), RBL1(1), RBL2(3), SKP2(2), SMC1A(5), SMC1B(3), TFDP1(2), TP53(279), YWHAB(1), YWHAE(2), YWHAG(2) 59044916 380 287 244 28 60 44 71 84 121 0 <1.00e-15 <3.08e-14
3 G1_TO_S_CELL_CYCLE_REACTOME ATM, CCNA1, CCNB1, CCND1, CCND2, CCND3, CCNE1, CCNE2, CCNG2, CCNH, CDC25A, CDC45L, CDK2, CDK4, CDK7, CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B, CDKN2C, CDKN2D, CREB3, CREB3L1, CREB3L3, CREB3L4, CREBL1, CREBL1, TNXB, E2F1, E2F2, E2F3, E2F4, E2F5, E2F6, FLJ14001, GADD45A, GBA2, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MDM2, MNAT1, MYC, MYT1, NACA, NACA, FKSG17, ORC1L, ORC2L, ORC3L, ORC4L, ORC5L, ORC6L, PCNA, POLA2, POLE, POLE2, PRIM1, PRIM2A, RB1, RBL1, RPA1, RPA2, RPA3, TFDP1, TFDP2, TP53, WEE1 64 ATM(5), CCNA1(2), CCNG2(1), CCNH(1), CDK2(1), CDKN1A(1), CDKN1B(1), CDKN2C(2), CDKN2D(1), CREB3L1(1), CREB3L4(1), E2F2(1), E2F5(1), GADD45A(1), GBA2(2), MCM2(2), MCM3(1), MCM4(2), MCM5(2), MNAT1(1), MYT1(2), NACA(4), ORC1L(1), ORC4L(1), POLE(2), POLE2(1), RB1(9), RBL1(1), RPA1(2), RPA2(1), TFDP1(2), TNXB(4), TP53(279) 32487850 339 286 203 24 56 38 60 70 115 0 <1.00e-15 <3.08e-14
4 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 138 APC(8), AXIN2(1), BTRC(2), CAMK2B(2), CAMK2D(1), CAMK2G(1), CHD8(5), CREBBP(7), CSNK1A1L(1), CSNK1E(1), CSNK2A1(1), CSNK2B(1), CTBP1(1), CTBP2(1), CTNNB1(2), CXXC4(1), DAAM1(2), DAAM2(2), DKK2(2), DVL3(1), EP300(1), FBXW11(1), FOSL1(1), FZD5(2), FZD7(2), GSK3B(1), LRP5(3), LRP6(1), MAP3K7(3), MAPK8(1), MAPK9(1), MMP7(1), NFAT5(1), NFATC1(1), NFATC2(1), NFATC4(1), NLK(1), PLCB1(4), PLCB2(4), PLCB3(2), PLCB4(1), PORCN(2), PPARD(2), PPP2CA(2), PPP2R1A(4), PPP2R2A(1), PPP2R2B(1), PPP3CC(1), PRICKLE1(3), PRICKLE2(2), PRKACG(1), PRKCA(1), PRKCG(1), RHOA(2), SFRP2(1), SFRP5(1), TBL1X(1), TBL1XR1(1), TCF7L2(2), TP53(279), VANGL2(1), WIF1(3), WNT11(2), WNT16(3), WNT2(1), WNT2B(1), WNT4(1), WNT6(2), WNT7A(2), WNT7B(2), WNT8A(1), WNT9A(2), WNT9B(1) 65706417 407 284 270 37 65 52 80 90 120 0 <1.00e-15 <3.08e-14
5 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(1), ATM(5), BUB1(1), BUB1B(2), BUB3(1), CCNA1(2), CCNA2(1), CCNB3(3), CCNH(1), CDAN1(2), CDC20(1), CDC25B(2), CDC6(1), CDC7(2), CDH1(2), CDK2(1), CDKN1A(1), CHEK2(1), E2F2(1), E2F5(1), EP300(1), GADD45A(1), GSK3B(1), HDAC1(1), HDAC3(2), HDAC4(2), HDAC5(1), HDAC6(2), MAD2L2(1), MCM2(2), MCM3(1), MCM4(2), MCM5(2), MPEG1(1), ORC1L(1), ORC4L(1), PRKDC(8), RB1(9), RBL1(1), SKP2(2), TBC1D8(3), TFDP1(2), TP53(279) 48736010 358 283 222 27 56 42 65 80 115 0 <1.00e-15 <3.08e-14
6 HSA04210_APOPTOSIS Genes involved in apoptosis AIFM1, AKT1, AKT2, AKT3, APAF1, ATM, BAD, BAX, BCL2, BCL2L1, BID, BIRC2, BIRC3, BIRC4, CAPN1, CAPN2, CASP10, CASP3, CASP6, CASP7, CASP8, CASP9, CFLAR, CHP, CHUK, CSF2RB, CYCS, DFFA, DFFB, ENDOG, FADD, FAS, FASLG, IKBKB, IKBKG, IL1A, IL1B, IL1R1, IL1RAP, IL3, IL3RA, IRAK1, IRAK2, IRAK3, IRAK4, MAP3K14, MYD88, NFKB1, NFKB2, NFKBIA, NGFB, NTRK1, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKACA, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, RELA, RIPK1, TNF, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFRSF1A, TNFSF10, TP53, TRADD, TRAF2 78 AIFM1(2), APAF1(2), ATM(5), BID(1), BIRC3(2), CASP6(1), CASP7(1), CASP9(1), CHUK(1), CSF2RB(3), FADD(1), IKBKB(1), IRAK1(2), IRAK2(1), IRAK3(2), IRAK4(1), MAP3K14(1), NFKB1(1), NTRK1(4), PIK3CA(2), PIK3CB(1), PIK3CG(3), PIK3R1(1), PIK3R2(2), PIK3R5(1), PPP3CC(1), PRKACG(1), PRKAR2A(1), PRKAR2B(1), RELA(1), TNF(1), TNFRSF10A(2), TNFRSF10D(1), TNFRSF1A(1), TNFSF10(1), TP53(279), TRAF2(1) 35255671 334 282 198 25 53 42 59 75 105 0 <1.00e-15 <3.08e-14
7 TELPATHWAY Telomerase is a ribonucleotide protein that adds telomeric repeats to the 3' ends of chromosomes. AKT1, BCL2, EGFR, G22P1, HSPCA, IGF1R, KRAS2, MYC, POLR2A, PPP2CA, PRKCA, RB1, TEP1, TERF1, TERT, TNKS, TP53, XRCC5 15 EGFR(7), IGF1R(1), PPP2CA(2), PRKCA(1), RB1(9), TEP1(5), TERF1(1), TERT(1), TNKS(1), TP53(279) 12360237 307 281 171 10 50 33 49 65 110 0 <1.00e-15 <3.08e-14
8 APOPTOSIS_GENMAPP APAF1, BAK1, BCL2L7P1, BAX, BCL2, BCL2L1, BID, BIRC2, BIRC3, BIRC4, CASP2, CASP3, CASP6, CASP7, CASP8, CASP9, CYCS, FADD, FAS, FASLG, GZMB, IKBKG, JUN, MAP2K4, MAP3K1, MAP3K14, MAPK10, MCL1, MDM2, MYC, NFKB1, NFKBIA, PARP1, PRF1, RELA, RIPK1, TNF, TNFRSF1A, TNFRSF1B, TNFSF10, TP53, TRADD, TRAF1, TRAF2 40 APAF1(2), BAK1(1), BID(1), BIRC3(2), CASP2(1), CASP6(1), CASP7(1), CASP9(1), FADD(1), MAP2K4(1), MAP3K1(1), MAP3K14(1), NFKB1(1), PRF1(2), RELA(1), TNF(1), TNFRSF1A(1), TNFSF10(1), TP53(279), TRAF1(4), TRAF2(1) 16033981 305 280 169 10 50 36 48 67 104 0 <1.00e-15 <3.08e-14
9 G1PATHWAY CDK4/6-cyclin D and CDK2-cyclin E phosphorylate Rb, which allows the transcription of genes needed for the G1/S cell cycle transition. ABL1, ATM, ATR, CCNA1, CCND1, CCNE1, CDC2, CDC25A, CDK2, CDK4, CDK6, CDKN1A, CDKN1B, CDKN2A, CDKN2B, DHFR, E2F1, GSK3B, HDAC1, MADH3, MADH4, RB1, SKP2, TFDP1, TGFB1, TGFB2, TGFB3, TP53 25 ABL1(1), ATM(5), ATR(2), CCNA1(2), CDK2(1), CDKN1A(1), CDKN1B(1), GSK3B(1), HDAC1(1), RB1(9), SKP2(2), TFDP1(2), TP53(279) 13302114 307 280 171 8 48 37 47 66 109 0 <1.00e-15 <3.08e-14
10 G2PATHWAY Activated Cdc2-cyclin B kinase regulates the G2/M transition; DNA damage stimulates the DNA-PK/ATM/ATR kinases, which inactivate Cdc2. ATM, ATR, BRCA1, CCNB1, CDC2, CDC25A, CDC25B, CDC25C, CDC34, CDKN1A, CDKN2D, CHEK1, CHEK2, EP300, GADD45A, MDM2, MYT1, PLK, PRKDC, RPS6KA1, TP53, WEE1, YWHAH, YWHAQ 21 ATM(5), ATR(2), BRCA1(12), CDC25B(2), CDKN1A(1), CDKN2D(1), CHEK2(1), EP300(1), GADD45A(1), MYT1(2), PRKDC(8), RPS6KA1(1), TP53(279) 18900608 316 280 180 7 49 34 46 71 116 0 <1.00e-15 <3.08e-14

Table 6.  Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 13. 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 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 220 ADCYAP1R1(1), ADORA2B(2), ADORA3(2), ADRA1A(1), ADRA2B(3), ADRB2(1), AGTR2(2), AVPR1B(3), AVPR2(1), BDKRB1(4), BDKRB2(3), BRS3(1), C5AR1(2), CALCR(3), CALCRL(1), CCKBR(1), CGA(1), CHRM2(4), CHRM3(3), CHRM5(1), CTSG(1), CYSLTR1(1), DRD1(2), DRD3(1), EDNRA(1), F2(3), F2R(2), F2RL2(1), FPR1(1), FSHB(1), FSHR(4), GABBR1(2), GABBR2(2), GABRA1(2), GABRA2(2), GABRA3(1), GABRA4(1), GABRA5(1), GABRB1(2), GABRB3(1), GABRE(3), GABRG1(2), GABRG2(2), GABRQ(2), GALR1(1), GH2(1), GHR(1), GHRHR(1), GHSR(1), GLP2R(1), GLRA1(1), GLRA2(1), GLRA3(4), GPR156(1), GPR35(1), GPR50(2), GRIA1(1), GRIA2(2), GRIA3(2), GRIA4(3), GRID1(3), GRID2(2), GRIK1(1), GRIK2(2), GRIK3(2), GRIK5(2), GRIN2A(3), GRIN2B(3), GRIN2C(1), GRIN2D(3), GRIN3A(3), GRM1(4), GRM3(1), GRM4(1), GRM5(2), GRM6(1), GRM7(4), GRM8(3), GRPR(1), GZMA(2), HCRTR1(1), HCRTR2(1), HRH1(1), HRH4(2), HTR1A(2), HTR1E(2), HTR1F(3), HTR2A(3), HTR2C(4), HTR4(2), HTR5A(2), HTR6(1), LEPR(1), LHCGR(3), MAS1(1), MC2R(3), MC3R(2), MC4R(1), MC5R(2), MCHR2(2), MLNR(1), MTNR1A(1), NMBR(1), NMUR2(2), NPBWR1(1), NPFFR2(2), NR3C1(2), OPRD1(2), OPRK1(1), P2RX1(1), P2RX5(1), P2RY10(2), P2RY13(4), P2RY2(2), P2RY6(1), PARD3(2), PPYR1(2), PRLHR(1), PRLR(2), PRSS2(1), PRSS3(1), PTGDR(1), PTGFR(3), PTH2R(1), RXFP2(1), SCTR(1), SSTR1(1), TAAR6(2), TACR1(1), TACR2(2), TACR3(1), TRPV1(1), TSHR(4), VIPR2(1) 92059511 241 147 240 74 46 26 84 64 21 0 9.8e-08 6e-05
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 127 ACTG1(2), ACTN2(3), ACTN3(2), AMOTL1(1), ASH1L(3), CASK(2), CGN(2), CLDN10(1), CLDN11(2), CLDN15(1), CLDN16(1), CLDN17(2), CLDN18(2), CLDN2(1), CLDN6(1), CLDN9(1), CSDA(1), CSNK2A1(1), CSNK2B(1), CTNNA1(2), CTNNA3(1), CTNNB1(2), CTTN(1), EPB41(2), EPB41L3(5), EXOC3(1), EXOC4(4), F11R(2), GNAI2(1), INADL(2), JAM3(1), KRAS(2), LLGL2(3), MAGI1(2), MAGI2(4), MAGI3(3), MLLT4(2), MPDZ(4), MPP5(1), MRAS(1), MYH1(9), MYH10(3), MYH11(7), MYH13(6), MYH14(2), MYH15(5), MYH2(5), MYH3(4), MYH4(9), MYH7(3), MYH7B(5), MYH8(3), MYH9(3), MYL2(1), NRAS(2), PARD3(2), PARD6A(1), PPP2CA(2), PPP2R1A(4), PPP2R2A(1), PPP2R2B(1), PPP2R3A(2), PPP2R4(1), PRKCA(1), PRKCE(1), PRKCG(1), PRKCH(1), PRKCI(2), PRKCQ(3), PRKCZ(2), PTEN(2), RAB3B(1), RHOA(2), RRAS(1), SPTAN1(5), TJAP1(1), TJP1(3), TJP3(1), YES1(1) 82023148 185 138 183 38 29 15 64 50 27 0 1.6e-06 0.00049
3 GPCRDB_CLASS_A_RHODOPSIN_LIKE ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA1D, ADRA2A, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BLR1, BRS3, C3AR1, C5R1, CCBP2, CCKAR, CCKBR, CCR1, CCR10, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CCRL1, CCRL2, CHML, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CMKLR1, CMKOR1, CNR1, CNR2, CX3CR1, CXCR3, CXCR4, DRD1, DRD2, DRD3, DRD4, DRD5, EDNRA, EDNRB, ELA3A, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHR, GALR1, GALR2, GALR3, GALT, GHSR, GNB2L1, GPR10, GPR147, GPR17, GPR173, GPR174, GPR23, GPR24, GPR27, GPR3, GPR30, GPR35, GPR37, GPR37L1, GPR4, GPR44, GPR50, GPR6, GPR63, GPR74, GPR77, GPR83, GPR85, GPR87, GPR92, GRPR, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, HTR7, LOC93164, IL8RA, IL8RB, LHCGR, LTB4R, MAS1, MC1R, MC3R, MC4R, MC5R, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPY1R, NPY2R, NPY5R, NPY6R, NTSR1, NTSR2, OPN1SW, OPN3, OPRD1, OPRK1, OPRL1, OPRM1, OR10A5, OR11A1, OR12D3, OR1C1, OR1F1, OR1Q1, OR2H1, OR5V1, OR5V1, OR12D3, OR7A5, OR7C1, OR8B8, OXTR, P2RY1, P2RY10, P2RY11, P2RY12, P2RY13, P2RY14, P2RY2, P2RY5, P2RY6, PPYR1, PTAFR, PTGDR, PTGER1, PTGER2, PTGER4, PTGFR, PTGIR, Rgr, RGR, RHO, RRH, SSTR1, SSTR2, SSTR3, SSTR4, SUCNR1, TBXA2R, TRHR 151 ADORA2B(2), ADORA3(2), ADRA1A(1), ADRB2(1), AGTR2(2), AVPR1B(3), AVPR2(1), BDKRB1(4), BDKRB2(3), BRS3(1), CCKBR(1), CCR3(2), CCR6(1), CCR8(1), CCR9(1), CHML(3), CHRM2(4), CHRM3(3), CHRM5(1), CXCR3(2), DRD1(2), DRD3(1), EDNRA(1), F2R(2), F2RL2(1), FPR1(1), FSHR(4), GALR1(1), GHSR(1), GPR173(1), GPR174(1), GPR35(1), GPR37(2), GPR37L1(1), GPR4(2), GPR50(2), GPR77(1), GRPR(1), HCRTR1(1), HCRTR2(1), HRH1(1), HTR1A(2), HTR1E(2), HTR1F(3), HTR2A(3), HTR2C(4), HTR4(2), HTR5A(2), HTR6(1), LHCGR(3), MAS1(1), MC3R(2), MC4R(1), MC5R(2), MLNR(1), MTNR1A(1), NMBR(1), NMUR2(2), OPN1SW(2), OPRD1(2), OPRK1(1), OR10A5(1), OR11A1(1), OR12D3(2), OR5V1(3), OR7C1(2), OR8B8(1), P2RY10(2), P2RY12(1), P2RY13(4), P2RY2(2), P2RY6(1), PPYR1(2), PTGDR(1), PTGFR(3), RRH(1), SSTR1(1), SUCNR1(1) 48728343 135 103 135 30 22 12 52 38 11 0 0.000061 0.013
4 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 192 ACTN2(3), ACTN3(2), APC(8), ARHGEF1(3), ARHGEF12(1), ARHGEF4(2), ARHGEF7(2), ARPC1A(1), ARPC3(1), BDKRB1(4), BDKRB2(3), BRAF(2), CHRM2(4), CHRM3(3), CHRM5(1), CSK(1), CYFIP1(5), CYFIP2(2), DIAPH2(4), DIAPH3(2), DOCK1(4), EGFR(7), F2(3), F2R(2), FGD1(3), FGD3(1), FGF12(1), FGF2(1), FGF23(2), FGF5(1), FGF6(1), FGFR4(1), FN1(1), GNA12(1), GRLF1(6), GSN(1), IQGAP1(2), IQGAP2(6), IQGAP3(2), ITGA1(1), ITGA10(2), ITGA2B(4), ITGA3(2), ITGA4(3), ITGA5(1), ITGA6(1), ITGA8(3), ITGAD(1), ITGAE(1), ITGAL(3), ITGAV(2), ITGAX(1), ITGB2(2), ITGB6(1), ITGB7(4), KRAS(2), LIMK1(1), LIMK2(1), MOS(1), MRAS(1), MSN(2), MYH10(3), MYH14(2), MYH9(3), MYL2(1), MYLK(6), MYLK2(1), NCKAP1(2), NCKAP1L(3), NRAS(2), PAK2(1), PAK3(5), PAK6(2), PAK7(1), PDGFRA(3), PDGFRB(3), PFN2(1), PFN4(1), PIK3CA(2), PIK3CB(1), PIK3CG(3), PIK3R1(1), PIK3R2(2), PIK3R5(1), PIP4K2A(1), PIP4K2B(1), PIP5K1A(1), PIP5K1C(1), PPP1R12A(2), PPP1R12B(4), PTK2(1), PXN(5), RHOA(2), RRAS(1), SCIN(2), SOS1(3), SOS2(1), SSH1(4), SSH2(1), SSH3(3), TIAM1(1), TIAM2(3), VAV1(2), VAV2(4), VAV3(3), VCL(2), WAS(1), WASF2(1) 116072989 240 159 237 64 31 29 88 64 28 0 0.0002 0.021
5 AMIPATHWAY Endogenous anti-thrombosis pathways are overwhelmed in plaque-narrowed blood vessels, resulting in potentially lethal myocardial infarction. ADCY1, CD3D, CD3E, CD3G, CD3Z, CD4, CREBBP, CSK, GNAS, GNB1, GNGT1, HLA-DRA, HLA-DRB1, LCK, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PTPRC, TRA@, TRB@, ZAP70 21 ADCY1(4), CD3E(2), CD4(1), CREBBP(7), CSK(1), GNAS(3), HLA-DRA(1), HLA-DRB1(1), LCK(1), PRKACG(1), PRKAR2A(1), PRKAR2B(1), PTPRC(3), ZAP70(1) 9488232 28 28 27 3 5 3 6 6 8 0 0.0002 0.021
6 CSKPATHWAY Csk inhibits T-cell activation by phosphorylating Lck; Csk is regulated by cAMP-dependent kinases and is opposed by the T-cell activator CD45. ADCY1, CD3D, CD3E, CD3G, CD3Z, CD4, CREBBP, CSK, GNAS, GNB1, GNGT1, HLA-DRA, HLA-DRB1, LCK, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PTPRC, TRA@, TRB@, ZAP70 21 ADCY1(4), CD3E(2), CD4(1), CREBBP(7), CSK(1), GNAS(3), HLA-DRA(1), HLA-DRB1(1), LCK(1), PRKACG(1), PRKAR2A(1), PRKAR2B(1), PTPRC(3), ZAP70(1) 9488232 28 28 27 3 5 3 6 6 8 0 0.0002 0.021
7 GPCRDB_OTHER ADORA3, ALG6, C5R1, CCKBR, CCR2, CCR3, CCR5, CELSR1, CELSR2, CELSR3, CHRM2, CHRM3, CIDEB, CXCR3, DRD4, EBI2, EDG1, EDNRA, ELA3A, EMR2, EMR3, F2R, FSHR, FY, GHRHR, GNRHR, GPR, GPR116, GPR132, GPR133, GPR135, GPR143, GPR145, GPR17, GPR18, GPR55, GPR56, GPR61, GPR73L1, GPR77, GPR84, GPR88, GRCA, GRM1, GRPR, HRH4, IL8RA, IL8RB, LGR6, LGR7, LPHN2, LPHN3, LTB4R2, MASS1, NTSR1, OR2A9P, OR2M4, OR5E1P, OR7E19P, OR7E47P, OR7E37P, OR7E18P, OR7E35P, LOC441453, OR8G1, LOC442754, OR8G2, P2RY11, P2RY13, PTGFR, RLN3R1, SMO, SSTR2, TAAR5, TSHR, VN1R1 50 ADORA3(2), CCKBR(1), CCR3(2), CELSR1(1), CELSR2(4), CELSR3(6), CHRM2(4), CHRM3(3), CXCR3(2), EDNRA(1), EMR2(1), EMR3(5), F2R(2), FSHR(4), GHRHR(1), GPR116(1), GPR132(2), GPR133(2), GPR55(1), GPR77(1), GRM1(4), GRPR(1), HRH4(2), LGR6(3), LPHN2(1), LPHN3(4), OR8G2(1), P2RY13(4), PTGFR(3), TSHR(4) 25452491 73 60 73 20 11 10 27 19 6 0 0.0005 0.039
8 FXRPATHWAY The nuclear receptor transcription factors FXR and LXR are activated by cholesterol metabolites and regulate cholesterol homeostasis. FABP6, LDLR, NR0B2, NR1H3, NR1H4, RXRA 6 LDLR(3), NR1H3(4), NR1H4(3), RXRA(2) 2264708 12 12 12 0 2 2 3 2 3 0 0.0005 0.039
9 HSA04916_MELANOGENESIS Genes involved in melanogenesis ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ASIP, CALM1, CALM2, CALM3, CALML3, CALML6, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CREB1, CREB3, CREB3L1, CREB3L2, CREB3L3, CREB3L4, CREBBP, CTNNB1, DCT, DVL1, DVL2, DVL3, EDN1, EDNRB, EP300, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GNAI1, GNAI2, GNAI3, GNAO1, GNAQ, GNAS, GSK3B, HRAS, KIT, KITLG, KRAS, LEF1, LOC652788, MAP2K1, MAP2K2, MAPK1, MAPK3, MC1R, MITF, NRAS, PLCB1, PLCB2, PLCB3, PLCB4, POMC, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, RAF1, TCF7, TCF7L1, TCF7L2, TYR, TYRP1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B 96 ADCY1(4), ADCY2(6), ADCY3(2), ADCY4(1), ADCY5(3), ADCY7(1), ADCY9(5), CALM3(1), CAMK2B(2), CAMK2D(1), CAMK2G(1), CREB3L1(1), CREB3L4(1), CREBBP(7), CTNNB1(2), DCT(2), DVL3(1), EP300(1), FZD5(2), FZD7(2), GNAI2(1), GNAS(3), GSK3B(1), KIT(7), KITLG(1), KRAS(2), MITF(2), NRAS(2), PLCB1(4), PLCB2(4), PLCB3(2), PLCB4(1), POMC(1), PRKACG(1), PRKCA(1), PRKCG(1), TCF7L2(2), TYR(1), WNT11(2), WNT16(3), WNT2(1), WNT2B(1), WNT4(1), WNT6(2), WNT7A(2), WNT7B(2), WNT8A(1), WNT9A(2), WNT9B(1) 43571057 101 86 96 28 21 14 30 20 16 0 0.00073 0.05
10 HSA04340_HEDGEHOG_SIGNALING_PATHWAY Genes involved in Hedgehog signaling pathway BMP2, BMP4, BMP5, BMP6, BMP7, BMP8A, BMP8B, BTRC, CSNK1A1, CSNK1A1L, CSNK1D, CSNK1E, CSNK1G1, CSNK1G2, CSNK1G3, DHH, FBXW11, GAS1, GLI1, GLI2, GLI3, GSK3B, HHIP, IHH, LRP2, PRKACA, PRKACB, PRKACG, PRKX, PRKY, PTCH1, PTCH2, RAB23, SHH, SMO, STK36, SUFU, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B, ZIC2 54 BMP2(1), BMP5(1), BMP6(1), BTRC(2), CSNK1A1L(1), CSNK1E(1), FBXW11(1), GLI1(5), GLI2(10), GLI3(2), GSK3B(1), HHIP(2), LRP2(16), PRKACG(1), PTCH1(6), PTCH2(1), STK36(1), WNT11(2), WNT16(3), WNT2(1), WNT2B(1), WNT4(1), WNT6(2), WNT7A(2), WNT7B(2), WNT8A(1), WNT9A(2), WNT9B(1) 24713567 71 61 70 10 10 14 26 15 6 0 0.00095 0.057
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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