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
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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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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