Mutation Analysis (MutSig v2.0)
Colon Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1JH3J4R
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Colon Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Mutation Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C1JH3J4R
Overview
Introduction

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

  • Working with individual set: COAD-TP

  • Number of patients in set: 155

Input

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

  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:COAD-TP.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 75

  • Mutations seen in COSMIC: 517

  • Significantly mutated genes in COSMIC territory: 23

  • Genes with clustered mutations (≤ 3 aa apart): 350

  • Significantly mutated genesets: 156

  • Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing

  • Read 102 MAFs of type "Broad"

  • Read 53 MAFs of type "Baylor-SOLiD"

  • Total number of mutations in input MAFs: 62560

  • After removing 1112 invalidated mutations: 61448

  • After removing 976 noncoding mutations: 60472

  • After collapsing adjacent/redundant mutations: 60470

Mutation Filtering

  • Number of mutations before filtering: 60470

  • After removing 665 mutations outside gene set: 59805

  • After removing 171 mutations outside category set: 59634

  • After removing 9 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 58789

Results
Breakdown of Mutations by Type

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

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

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

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

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

Figure 1. 

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

Figure 2.  Patients counts and rates file used to generate this plot: COAD-TP.patients.counts_and_rates.txt

CoMut Plot

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

Significantly Mutated Genes

Column Descriptions:

  • N = number of sequenced bases in this gene across the individual set

  • n = number of (nonsilent) mutations in this gene across the individual set

  • npat = number of patients (individuals) with at least one nonsilent mutation

  • nsite = number of unique sites having a non-silent mutation

  • nsil = number of silent mutations in this gene across the individual set

  • n1 = number of nonsilent mutations of type: *CpG->T

  • n2 = number of nonsilent mutations of type: *Np(A/C/T)->transit

  • n3 = number of nonsilent mutations of type: *ApG->G

  • n4 = number of nonsilent mutations of type: transver

  • n5 = number of nonsilent mutations of type: indel+null

  • n6 = number of nonsilent mutations of type: double_null

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

  • p_cons = p-value for enrichment of mutations at evolutionarily most-conserved sites in gene

  • p_joint = p-value for clustering + conservation

  • p = p-value (overall)

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

Table 3.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 75. Number of genes displayed: 35. Click on a gene name to display its stick figure depicting the distribution of mutations and mutation types across the chosen gene (this feature may not be available for all significant genes).

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

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

Table 4.  Get Full Table Significantly mutated genes (COSMIC territory only). To access the database please go to: COSMIC. Number of significant genes found: 23. Number of genes displayed: 10

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

Note:

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

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

n_cos = overlap between n and cos.

N_cos = number of individuals times cos.

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

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

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

Clustered Mutations

Table 5.  Get Full Table Genes with Clustered Mutations

num gene desc n mindist nmuts0 nmuts3 nmuts12 npairs0 npairs3 npairs12
6113 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog 58 0 959 1135 1136 959 1135 1136
1160 BRAF v-raf murine sarcoma viral oncogene homolog B1 21 0 171 171 171 171 171 171
11991 TP53 tumor protein p53 77 0 102 181 290 102 181 290
602 APC adenomatous polyposis coli 121 0 82 105 149 82 105 149
8703 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 33 0 53 81 103 53 81 103
4161 FBXW7 F-box and WD repeat domain containing 7 33 0 41 45 53 41 45 53
7726 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 15 0 26 36 36 26 36 36
10803 SMAD4 SMAD family member 4 21 0 10 14 24 10 14 24
4004 FAM22F family with sequence similarity 22, member F 8 0 10 10 10 10 10 10
3770 ERBB3 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) 11 0 6 10 10 6 10 10

Note:

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

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

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

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

Geneset Analyses

Table 6.  Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 156. Number of genesets displayed: 10

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

Table 7.  Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 0. Number of genesets displayed: 10

rank geneset description genes N_genes mut_tally N n npat nsite nsil n1 n2 n3 n4 n5 n6 p q
1 EOSINOPHILSPATHWAY Recruitment of eosinophils in the inflammatory response observed in asthma occurs via the chemoattractant eotaxin binding to the CCR3 receptor. CCL11, CCL5, CCR3, CSF2, HLA-DRA, HLA-DRB1, IL3, IL5 8 CCR3(3), HLA-DRA(4), HLA-DRB1(1), IL3(3) 661548 11 11 10 2 5 1 0 3 0 2 0.0017 0.48
2 HSA04080_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION Genes involved in neuroactive ligand-receptor interaction ADCYAP1R1, ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA2A, ADRA2B, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BRS3, C3AR1, C5AR1, CALCR, CALCRL, CCKAR, CCKBR, CGA, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CNR1, CNR2, CRHR1, CRHR2, CTSG, CYSLTR1, CYSLTR2, DRD1, DRD2, DRD3, DRD4, DRD5, EDG1, EDG2, EDG3, EDG4, EDG5, EDG6, EDG7, EDG8, EDNRA, EDNRB, F2, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHB, FSHR, GABBR1, GABBR2, GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GABRB1, GABRB2, GABRB3, GABRD, GABRE, GABRG1, GABRG2, GABRG3, GABRP, GABRQ, GABRR1, GABRR2, GALR1, GALR2, GALR3, GCGR, GH1, GH2, GHR, GHRHR, GHSR, GIPR, GLP1R, GLP2R, GLRA1, GLRA2, GLRA3, GLRB, GNRHR, GPR156, GPR23, GPR35, GPR50, GPR63, GPR83, GRIA1, GRIA2, GRIA3, GRIA4, GRID1, GRID2, GRIK1, GRIK2, GRIK3, GRIK4, GRIK5, GRIN1, GRIN2A, GRIN2B, GRIN2C, GRIN2D, GRIN3A, GRIN3B, GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, GRM8, GRPR, GZMA, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HRH4, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, KISS1R, LEP, LEPR, LHB, LHCGR, LTB4R, LTB4R2, MAS1, MC1R, MC2R, MC3R, MC4R, MC5R, MCHR1, MCHR2, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPBWR1, NPBWR2, NPFFR1, NPFFR2, NPY1R, NPY2R, NPY5R, NR3C1, NTSR1, NTSR2, OPRD1, OPRK1, OPRL1, OPRM1, OXTR, P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX7, P2RXL1, P2RY1, P2RY10, P2RY11, P2RY13, P2RY14, P2RY2, P2RY4, P2RY5, P2RY6, P2RY8, PARD3, PPYR1, PRL, PRLHR, PRLR, PRSS1, PRSS2, PRSS3, PTAFR, PTGDR, PTGER1, PTGER2, PTGER3, PTGER4, PTGFR, PTGIR, PTH2R, PTHR1, RXFP1, RXFP2, SCTR, SSTR1, SSTR2, SSTR3, SSTR4, SSTR5, TAAR1, TAAR2, TAAR5, TAAR6, TAAR8, TAAR9, TACR1, TACR2, TACR3, TBXA2R, THRA, THRB, TRHR, TRPV1, TSHB, TSHR, TSPO, UTS2R, VIPR1, VIPR2 232 ADCYAP1R1(1), ADORA1(5), ADORA2A(3), ADORA2B(1), ADORA3(3), ADRA1A(5), ADRA1B(4), ADRA2A(3), ADRB1(2), ADRB3(1), AGTR1(3), AGTR2(4), AVPR1A(3), AVPR1B(3), AVPR2(6), BDKRB2(2), BRS3(1), C3AR1(2), C5AR1(2), CALCR(3), CALCRL(5), CCKAR(1), CCKBR(3), CGA(1), CHRM1(3), CHRM2(8), CHRM3(4), CHRM5(1), CNR1(3), CRHR1(1), CRHR2(4), CTSG(2), CYSLTR1(3), CYSLTR2(3), DRD1(1), DRD2(3), DRD3(3), DRD5(2), EDNRA(4), EDNRB(7), F2(2), F2RL2(2), FPR1(2), FSHB(1), FSHR(6), GABBR1(4), GABBR2(3), GABRA1(2), GABRA2(6), GABRA3(4), GABRA4(6), GABRA6(4), GABRB1(6), GABRB2(4), GABRB3(5), GABRE(5), GABRG1(7), GABRG2(8), GABRG3(5), GABRP(2), GABRQ(7), GABRR1(2), GABRR2(3), GALR1(1), GH1(1), GH2(1), GHR(6), GHRHR(2), GHSR(5), GLP1R(2), GLP2R(3), GLRA1(2), GLRA2(2), GLRA3(7), GLRB(6), GNRHR(4), GPR156(6), GPR50(5), GPR63(2), GPR83(1), GRIA2(10), GRIA3(5), GRIA4(12), GRID1(15), GRID2(10), GRIK1(5), GRIK2(10), GRIK4(11), GRIK5(5), GRIN1(1), GRIN2A(15), GRIN2B(8), GRIN2C(2), GRIN2D(3), GRIN3A(3), GRM1(9), GRM2(3), GRM3(5), GRM4(7), GRM5(8), GRM6(9), GRM7(8), GRM8(7), GRPR(3), GZMA(2), HCRTR1(1), HCRTR2(1), HRH1(1), HRH2(4), HRH4(2), HTR1A(3), HTR1B(3), HTR1D(2), HTR1E(5), HTR1F(2), HTR2A(2), HTR2B(1), HTR2C(6), HTR4(2), HTR5A(2), HTR7(6), LEP(1), LEPR(5), LHB(1), LHCGR(4), MAS1(1), MC2R(2), MC3R(1), MC4R(3), MC5R(4), MCHR1(6), MCHR2(2), MLNR(3), MTNR1B(3), NMUR1(4), NMUR2(6), NPBWR1(3), NPFFR2(3), NPY1R(4), NPY2R(5), NPY5R(1), NR3C1(3), NTSR1(1), NTSR2(4), OPRD1(1), OPRK1(5), OPRM1(1), OXTR(2), P2RX1(1), P2RX2(1), P2RX3(2), P2RX4(2), P2RX5(1), P2RX7(2), P2RY1(3), P2RY10(6), P2RY13(2), P2RY14(4), P2RY2(2), P2RY4(6), PARD3(5), PPYR1(1), PRL(2), PRLR(2), PRSS1(3), PRSS2(1), PRSS3(4), PTAFR(1), PTGER2(1), PTGER3(6), PTGFR(6), PTGIR(1), PTH2R(6), RXFP1(2), RXFP2(8), SCTR(3), SSTR1(4), SSTR2(2), SSTR4(2), TAAR1(3), TAAR2(2), TAAR5(5), TAAR6(2), TAAR8(1), TAAR9(1), TACR1(2), TACR2(1), TACR3(4), THRA(2), THRB(4), TRHR(6), TRPV1(3), TSHR(6), VIPR1(3), VIPR2(3) 48166910 709 118 706 266 272 154 15 210 58 0 0.0022 0.48
3 PITX2PATHWAY The bicoid-related transcription factor Pitx2 is activated by Wnt binding to the Frizzled receptor and induces tissue-specific cell proliferation. APC, AXIN1, CREBBP, CTNNB1, DVL1, EP300, FZD1, GSK3B, HDAC1, HTATIP, LDB1, LEF1, PITX2, PPARBP, TRRAP, WNT1 13 AXIN1(1), CREBBP(21), CTNNB1(8), EP300(13), GSK3B(7), HDAC1(2), LDB1(3), LEF1(4), PITX2(2), TRRAP(17), WNT1(1) 6009423 79 46 78 21 33 25 1 8 12 0 0.0028 0.48
4 PELP1PATHWAY Pelp1 acts downstream of activated estrogen receptor to promote cell proliferation and is overexpressed in many breast tumors. CREBBP, EP300, ESR1, MAPK1, MAPK3, PELP1, SRC 7 CREBBP(21), EP300(13), ESR1(12), MAPK1(2), MAPK3(2), PELP1(2), SRC(3) 3251889 55 34 55 13 18 20 1 9 7 0 0.0032 0.48
5 CTLA4PATHWAY T cell activation requires interaction with an antigen-MHC-I complex on an antigen-presenting cell (APC), as well as CD28 interaction with the APC's CD80 or 86. CD28, CD3D, CD3E, CD3G, CD3Z, CD80, CD86, CTLA4, GRB2, HLA-DRA, HLA-DRB1, ICOS, ICOSL, IL2, ITK, LCK, PIK3CA, PIK3R1, PTPN11, TRA@, TRB@ 16 CD28(1), CD3D(1), CD3G(2), CTLA4(1), GRB2(2), HLA-DRA(4), HLA-DRB1(1), ICOS(1), IL2(3), ITK(8), LCK(2), PIK3R1(5), PTPN11(2) 2385350 33 23 32 7 7 9 2 8 5 2 0.0044 0.48
6 GPCRDB_CLASS_A_RHODOPSIN_LIKE ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA1D, ADRA2A, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BLR1, BRS3, C3AR1, C5R1, CCBP2, CCKAR, CCKBR, CCR1, CCR10, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CCRL1, CCRL2, CHML, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CMKLR1, CMKOR1, CNR1, CNR2, CX3CR1, CXCR3, CXCR4, DRD1, DRD2, DRD3, DRD4, DRD5, EDNRA, EDNRB, ELA3A, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHR, GALR1, GALR2, GALR3, GALT, GHSR, GNB2L1, GPR10, GPR147, GPR17, GPR173, GPR174, GPR23, GPR24, GPR27, GPR3, GPR30, GPR35, GPR37, GPR37L1, GPR4, GPR44, GPR50, GPR6, GPR63, GPR74, GPR77, GPR83, GPR85, GPR87, GPR92, GRPR, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, HTR7, LOC93164, IL8RA, IL8RB, LHCGR, LTB4R, MAS1, MC1R, MC3R, MC4R, MC5R, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPY1R, NPY2R, NPY5R, NPY6R, NTSR1, NTSR2, OPN1SW, OPN3, OPRD1, OPRK1, OPRL1, OPRM1, OR10A5, OR11A1, OR12D3, OR1C1, OR1F1, OR1Q1, OR2H1, OR5V1, OR5V1, OR12D3, OR7A5, OR7C1, OR8B8, OXTR, P2RY1, P2RY10, P2RY11, P2RY12, P2RY13, P2RY14, P2RY2, P2RY5, P2RY6, PPYR1, PTAFR, PTGDR, PTGER1, PTGER2, PTGER4, PTGFR, PTGIR, Rgr, RGR, RHO, RRH, SSTR1, SSTR2, SSTR3, SSTR4, SUCNR1, TBXA2R, TRHR 162 ADORA1(5), ADORA2A(3), ADORA2B(1), ADORA3(3), ADRA1A(5), ADRA1B(4), ADRA1D(2), ADRA2A(3), ADRB1(2), ADRB3(1), AGTR1(3), AGTR2(4), AVPR1A(3), AVPR1B(3), AVPR2(6), BDKRB2(2), BRS3(1), C3AR1(2), CCBP2(5), CCKAR(1), CCKBR(3), CCR1(5), CCR3(3), CCR5(1), CCR6(2), CCR7(1), CCR8(4), CCR9(4), CCRL1(2), CHML(4), CHRM1(3), CHRM2(8), CHRM3(4), CHRM5(1), CMKLR1(2), CNR1(3), CX3CR1(1), CXCR4(3), DRD1(1), DRD2(3), DRD3(3), DRD5(2), EDNRA(4), EDNRB(7), F2RL2(2), FPR1(2), FSHR(6), GALR1(1), GALT(2), GHSR(5), GPR17(1), GPR173(2), GPR174(2), GPR37(6), GPR37L1(3), GPR4(1), GPR50(5), GPR6(5), GPR63(2), GPR77(1), GPR83(1), GPR85(1), GPR87(4), GRPR(3), HCRTR1(1), HCRTR2(1), HRH1(1), HRH2(4), HTR1A(3), HTR1B(3), HTR1D(2), HTR1E(5), HTR1F(2), HTR2A(2), HTR2B(1), HTR2C(6), HTR4(2), HTR5A(2), HTR7(6), LHCGR(4), MAS1(1), MC3R(1), MC4R(3), MC5R(4), MLNR(3), MTNR1B(3), NMUR1(4), NMUR2(6), NPY1R(4), NPY2R(5), NPY5R(1), NTSR1(1), NTSR2(4), OPN1SW(3), OPN3(1), OPRD1(1), OPRK1(5), OPRM1(1), OR12D3(1), OR1C1(1), OR1F1(2), OR2H1(3), OR5V1(2), OR7A5(3), OR8B8(2), OXTR(2), P2RY1(3), P2RY10(6), P2RY12(3), P2RY13(2), P2RY14(4), P2RY2(2), PPYR1(1), PTAFR(1), PTGER2(1), PTGFR(6), PTGIR(1), RGR(2), RHO(2), RRH(2), SSTR1(4), SSTR2(2), SSTR4(2), TRHR(6) 26305643 350 94 351 123 144 85 5 90 26 0 0.0059 0.48
7 GABAPATHWAY Gamma-aminobutyric acid (GABA) is an inhibitory neurotransmitter whose receptor is regulated by Plic-1, gephyrin, and GABARAP, which promote receptor clustering. DNM1, GABARAP, GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GPHN, NSF, SRC, UBQLN1 11 DNM1(8), GABRA1(2), GABRA2(6), GABRA3(4), GABRA4(6), GABRA6(4), GPHN(11), NSF(1), SRC(3), UBQLN1(2) 2538782 47 27 45 20 13 9 1 17 7 0 0.0068 0.48
8 1_AND_2_METHYLNAPHTHALENE_DEGRADATION ADH1A, ADH1A, ADH1B, ADH1C, ADH1B, ADH1C, ADH4, ADH6, ADH7, ADHFE1 7 ADH1B(2), ADH1C(3), ADH4(1), ADH6(5), ADH7(2), ADHFE1(6) 1229065 19 16 19 5 3 4 1 11 0 0 0.0074 0.48
9 FLUMAZENILPATHWAY Flumazenil is a benzodiazepine receptor antagonist that may induce protective preconditioning in ischemic cardiomyocytes. GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GPX1, PRKCE, SOD1 8 GABRA1(2), GABRA2(6), GABRA3(4), GABRA4(6), GABRA6(4), GPX1(1), PRKCE(4) 1520965 27 19 27 5 9 5 0 10 3 0 0.0075 0.48
10 CCR3PATHWAY CCR3 is a G-protein coupled receptor that recruits eosinophils to inflammation sites via chemokine ligands. ARHA, CCL11, CCR3, CFL1, GNAQ, GNAS, GNB1, GNGT1, HRAS, LIMK1, MAP2K1, MAPK1, MAPK3, MYL2, NOX1, PIK3C2G, PLCB1, PPP1R12B, PRKCA, PRKCB1, PTK2, RAF1, ROCK2 21 CCR3(3), CFL1(1), GNAQ(3), GNAS(6), GNB1(1), LIMK1(4), MAP2K1(3), MAPK1(2), MAPK3(2), MYL2(1), NOX1(1), PIK3C2G(7), PLCB1(8), PPP1R12B(5), PRKCA(2), PTK2(5), RAF1(4), ROCK2(2) 5505383 60 39 58 11 24 8 2 17 9 0 0.0078 0.48
Methods & Data
Methods

In brief, we tabulate the number of mutations and the number of covered bases for each gene. The counts are broken down by mutation context category: four context categories that are discovered by MutSig, and one for indel and 'null' mutations, which include indels, nonsense mutations, splice-site mutations, and non-stop (read-through) mutations. For each gene, we calculate the probability of seeing the observed constellation of mutations, i.e. the product P1 x P2 x ... x Pm, or a more extreme one, given the background mutation rates calculated across the dataset. [1]

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 - 615 (2011)
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