Mutation Analysis (MutSig v1.5)
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
23 May 2013
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analyses__2013_05_23
Maintainer Information
Citation Information
Maintained by Dan DiCara
(Broad Institute)
Cite as
Broad Institute TCGA Genome Data Analysis Center
(2013):
Mutation Analysis (MutSig v1.5).
Broad Institute of MIT and Harvard.
doi:10.7908/C1NG4NP4
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Overview
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Introduction
This report serves to describe the mutational landscape and properties of a given individual set, as well as rank genes and genesets according to mutational significance. MutSig v1.5 was used to generate the results found in this report.
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Working with individual set: OV-TP
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Number of patients in set: 316
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Input
The input for this pipeline is a set of individuals with the following files associated for each:
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An annotated .maf file describing the mutations called for the respective individual, and their properties.
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A .wig file that contains information about the coverage of the sample.
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Summary
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MAF used for this analysis:OV-TP.final_analysis_set.maf
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Significantly mutated genes (q ≤ 0.1): 9
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Mutations seen in COSMIC: 394
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Significantly mutated genes in COSMIC territory: 39
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Genes with clustered mutations (≤ 3 aa apart): 132
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Significantly mutated genesets: 39
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Significantly mutated genesets: (excluding sig. mutated genes):0
Mutation Preprocessing
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Read 148 MAFs of type "Broad"
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Read 88 MAFs of type "WashU"
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Read 80 MAFs of type "Baylor-SOLiD"
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Total number of mutations in input MAFs: 20219
Mutation Filtering
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Number of mutations before filtering: 20219
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After removing 1 non-mutations: 20218
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After removing 778 mutations outside gene set: 19440
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After removing 9 mutations outside category set: 19431
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After removing 4 "impossible" mutations in
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gene-patient-category bins of zero coverage: 18640
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Results
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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 |
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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 |
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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.
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Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples
Figure 2. Patients counts and rates file used to generate this plot: OV-TP.patients.counts_and_rates.txt
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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.
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Significantly Mutated Genes
Column Descriptions:
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N = number of sequenced bases in this gene across the individual set
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n = number of (nonsilent) mutations in this gene across the individual set
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npat = number of patients (individuals) with at least one nonsilent mutation
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nsite = number of unique sites having a non-silent mutation
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nsil = number of silent mutations in this gene across the individual set
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n1 = number of nonsilent mutations of type: *CpG->T
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n2 = number of nonsilent mutations of type: *Cp(A/C/T)->T
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n3 = number of nonsilent mutations of type: C->(G/A)
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n4 = number of nonsilent mutations of type: A->mut
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n5 = number of nonsilent mutations of type: indel+null
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n6 = number of nonsilent mutations of type: double_null
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p = p-value (overall)
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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: 9. 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 | q |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | TP53 | tumor protein p53 | 401524 | 279 | 276 | 143 | 3 | 47 | 31 | 39 | 61 | 101 | 0 | 2.3e-15 | 4e-11 |
| 2 | RB1 | retinoblastoma 1 (including osteosarcoma) | 826059 | 9 | 9 | 9 | 0 | 0 | 1 | 3 | 0 | 5 | 0 | 2.5e-06 | 0.021 |
| 3 | BRCA1 | breast cancer 1, early onset | 1798045 | 12 | 12 | 12 | 0 | 0 | 0 | 1 | 0 | 11 | 0 | 7.2e-06 | 0.041 |
| 4 | NF1 | neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) | 2619095 | 15 | 14 | 15 | 0 | 1 | 1 | 1 | 3 | 9 | 0 | 0.000021 | 0.088 |
| 5 | GABRA6 | gamma-aminobutyric acid (GABA) A receptor, alpha 6 | 440417 | 6 | 6 | 6 | 1 | 1 | 3 | 1 | 1 | 0 | 0 | 0.000031 | 0.088 |
| 6 | FAT3 | FAT tumor suppressor homolog 3 (Drosophila) | 3706784 | 20 | 19 | 20 | 1 | 4 | 2 | 3 | 10 | 1 | 0 | 0.000035 | 0.088 |
| 7 | CHST2 | carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2 | 172127 | 5 | 5 | 5 | 1 | 0 | 2 | 2 | 1 | 0 | 0 | 4e-05 | 0.088 |
| 8 | CYP11B1 | cytochrome P450, family 11, subfamily B, polypeptide 1 | 456589 | 7 | 7 | 6 | 0 | 1 | 0 | 3 | 3 | 0 | 0 | 0.000043 | 0.088 |
| 9 | CSMD3 | CUB and Sushi multiple domains 3 | 3615081 | 18 | 18 | 18 | 3 | 0 | 2 | 7 | 8 | 1 | 0 | 0.000046 | 0.088 |
| 10 | GLI2 | GLI-Kruppel family member GLI2 | 947026 | 10 | 9 | 10 | 0 | 2 | 3 | 3 | 1 | 1 | 0 | 0.000081 | 0.12 |
| 11 | FAM171B | family with sequence similarity 171, member B | 744587 | 7 | 7 | 7 | 0 | 1 | 1 | 2 | 2 | 1 | 0 | 0.000086 | 0.12 |
| 12 | KCNJ12 | potassium inwardly-rectifying channel, subfamily J, member 12 | 281754 | 5 | 5 | 3 | 2 | 5 | 0 | 0 | 0 | 0 | 0 | 0.000087 | 0.12 |
| 13 | PPP1R3A | protein phosphatase 1, regulatory (inhibitor) subunit 3A | 1053877 | 8 | 8 | 8 | 2 | 1 | 1 | 2 | 4 | 0 | 0 | 0.00015 | 0.2 |
| 14 | C9orf171 | chromosome 9 open reading frame 171 | 251675 | 5 | 5 | 5 | 0 | 2 | 0 | 2 | 0 | 1 | 0 | 0.00017 | 0.2 |
| 15 | TACC3 | transforming, acidic coiled-coil containing protein 3 | 311979 | 5 | 5 | 5 | 0 | 0 | 1 | 0 | 2 | 2 | 0 | 0.00019 | 0.2 |
| 16 | SI | sucrase-isomaltase (alpha-glucosidase) | 1778977 | 10 | 10 | 10 | 0 | 1 | 1 | 4 | 4 | 0 | 0 | 0.0002 | 0.2 |
| 17 | ZNF479 | zinc finger protein 479 | 365518 | 5 | 5 | 5 | 0 | 0 | 2 | 2 | 1 | 0 | 0 | 0.0002 | 0.2 |
| 18 | CDK12 | cyclin-dependent kinase 12 | 1351667 | 9 | 9 | 9 | 0 | 0 | 0 | 1 | 3 | 5 | 0 | 0.00027 | 0.23 |
| 19 | PAOX | polyamine oxidase (exo-N4-amino) | 205136 | 4 | 4 | 4 | 0 | 1 | 0 | 0 | 1 | 2 | 0 | 0.00029 | 0.23 |
| 20 | DUSP19 | dual specificity phosphatase 19 | 211393 | 4 | 4 | 4 | 0 | 0 | 0 | 1 | 3 | 0 | 0 | 0.0003 | 0.23 |
| 21 | USH2A | Usher syndrome 2A (autosomal recessive, mild) | 5014417 | 20 | 20 | 20 | 3 | 2 | 5 | 3 | 7 | 3 | 0 | 0.00031 | 0.23 |
| 22 | TBP | TATA box binding protein | 321652 | 4 | 4 | 2 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 0.00031 | 0.23 |
| 23 | VN1R5 | vomeronasal 1 receptor 5 | 296700 | 4 | 4 | 4 | 0 | 0 | 2 | 1 | 1 | 0 | 0 | 0.00032 | 0.23 |
| 24 | C6orf142 | chromosome 6 open reading frame 142 | 449405 | 5 | 5 | 5 | 3 | 0 | 2 | 1 | 1 | 1 | 0 | 0.00034 | 0.23 |
| 25 | SNTG1 | syntrophin, gamma 1 | 505767 | 5 | 5 | 5 | 1 | 0 | 1 | 1 | 0 | 3 | 0 | 0.00036 | 0.23 |
| 26 | OR5D16 | olfactory receptor, family 5, subfamily D, member 16 | 307171 | 4 | 4 | 4 | 0 | 2 | 0 | 1 | 1 | 0 | 0 | 0.00036 | 0.23 |
| 27 | SLCO1C1 | solute carrier organic anion transporter family, member 1C1 | 717910 | 6 | 6 | 6 | 0 | 0 | 1 | 4 | 1 | 0 | 0 | 0.00037 | 0.23 |
| 28 | HIST1H1C | histone cluster 1, H1c | 195033 | 4 | 4 | 4 | 0 | 0 | 1 | 2 | 0 | 1 | 0 | 0.00046 | 0.28 |
| 29 | C1orf95 | chromosome 1 open reading frame 95 | 81558 | 3 | 3 | 3 | 0 | 0 | 0 | 2 | 0 | 1 | 0 | 0.00047 | 0.28 |
| 30 | MAS1L | MAS1 oncogene-like | 357934 | 4 | 4 | 4 | 1 | 1 | 2 | 1 | 0 | 0 | 0 | 0.00059 | 0.34 |
| 31 | GAS2L1 | growth arrest-specific 2 like 1 | 197396 | 4 | 4 | 4 | 0 | 0 | 0 | 3 | 1 | 0 | 0 | 0.00066 | 0.34 |
| 32 | EPHA7 | EPH receptor A7 | 941078 | 7 | 7 | 7 | 1 | 0 | 1 | 4 | 2 | 0 | 0 | 0.00067 | 0.34 |
| 33 | C10orf140 | chromosome 10 open reading frame 140 | 424809 | 5 | 5 | 3 | 1 | 0 | 0 | 2 | 0 | 3 | 0 | 0.00068 | 0.34 |
| 34 | HAS2 | hyaluronan synthase 2 | 527414 | 5 | 5 | 5 | 0 | 0 | 1 | 3 | 0 | 1 | 0 | 0.00069 | 0.34 |
| 35 | GPR149 | G protein-coupled receptor 149 | 595318 | 6 | 6 | 6 | 1 | 1 | 2 | 1 | 2 | 0 | 0 | 0.0007 | 0.34 |
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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 | 824 | 278 | 260384 | 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 | 42 | 3 | 13272 | 4 | 2.5e-06 | 0.0015 |
| 8 | MLL4 | myeloid/lymphoid or mixed-lineage leukemia 2 | 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 | FBXW7 | F-box and WD repeat domain containing 7 | 4 | 91 | 3 | 28756 | 118 | 0.000024 | 0.011 |
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)
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Clustered Mutations
Table 5. Get Full Table Genes with Clustered Mutations
| num | gene | desc | n | mindist | nmuts0 | nmuts3 | nmuts12 | npairs0 | npairs3 | npairs12 |
|---|---|---|---|---|---|---|---|---|---|---|
| 7338 | TP53 | tumor protein p53 | 277 | 0 | 575 | 1491 | 3592 | 575 | 1491 | 3592 |
| 2019 | DNAH5 | dynein, axonemal, heavy chain 5 | 15 | 0 | 3 | 3 | 6 | 3 | 3 | 6 |
| 6808 | SRC | v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) | 4 | 0 | 3 | 3 | 6 | 3 | 3 | 6 |
| 4502 | MYO3A | myosin IIIA | 7 | 0 | 3 | 3 | 3 | 3 | 3 | 3 |
| 3565 | KCNJ12 | potassium inwardly-rectifying channel, subfamily J, member 12 | 5 | 0 | 2 | 2 | 2 | 2 | 2 | 2 |
| 4432 | MTOR | mechanistic target of rapamycin (serine/threonine kinase) | 7 | 0 | 1 | 6 | 6 | 1 | 6 | 6 |
| 5431 | PLA2G4F | phospholipase A2, group IVF | 4 | 0 | 1 | 3 | 3 | 1 | 3 | 3 |
| 151 | ADAMTS4 | ADAM metallopeptidase with thrombospondin type 1 motif, 4 | 4 | 0 | 1 | 2 | 2 | 1 | 2 | 2 |
| 166 | ADCY2 | adenylate cyclase 2 (brain) | 6 | 0 | 1 | 2 | 2 | 1 | 2 | 2 |
| 3475 | ITGB7 | integrin, beta 7 | 4 | 0 | 1 | 1 | 3 | 1 | 1 | 3 |
Note:
n - number of mutations in this gene in the individual set.
mindist - distance (in aa) between closest pair of mutations in this gene
npairs3 - how many pairs of mutations are within 3 aa of each other.
npairs12 - how many pairs of mutations are within 12 aa of each other.
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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: 39. 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 | 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 | <4.88e-14 |
| 2 | 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 | <4.88e-14 | |
| 3 | 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 | <4.88e-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 | 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 | <4.88e-14 |
| 5 | 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 | <4.88e-14 |
| 6 | CHEMICALPATHWAY | DNA damage promotes Bid cleavage, which stimulates mitochondrial cytochrome c release and consequent caspase activation, resulting in apoptosis. | ADPRT, AKT1, APAF1, ATM, BAD, BAX, BCL2, BCL2L1, BID, CASP3, CASP6, CASP7, CASP9, CYCS, EIF2S1, PRKCA, PRKCB1, PTK2, PXN, STAT1, TLN1, TP53 | 20 | APAF1(2), ATM(5), BID(1), CASP6(1), CASP7(1), CASP9(1), EIF2S1(1), PRKCA(1), PTK2(1), PXN(5), STAT1(2), TLN1(1), TP53(279) | 12296579 | 301 | 279 | 165 | 7 | 49 | 33 | 50 | 66 | 103 | 0 | <1.00e-15 | <4.88e-14 |
| 7 | RBPATHWAY | The ATM protein kinase recognizes DNA damage and blocks cell cycle progression by phosphorylating chk1 and p53, which normally inhibits Rb to allow G1/S transitions. | ATM, CDC2, CDC25A, CDC25B, CDC25C, CDK2, CDK4, CHEK1, MYT1, RB1, TP53, WEE1, YWHAH | 12 | ATM(5), CDC25B(2), CDK2(1), MYT1(2), RB1(9), TP53(279) | 7986534 | 298 | 279 | 162 | 5 | 47 | 33 | 47 | 64 | 107 | 0 | <1.00e-15 | <4.88e-14 |
| 8 | P53PATHWAY | p53 induces cell cycle arrest or apoptosis under conditions of DNA damage. | APAF1, ATM, BAX, BCL2, CCND1, CCNE1, CDK2, CDK4, CDKN1A, E2F1, GADD45A, MDM2, PCNA, RB1, TIMP3, TP53 | 16 | APAF1(2), ATM(5), CDK2(1), CDKN1A(1), GADD45A(1), RB1(9), TP53(279) | 8056664 | 298 | 278 | 162 | 3 | 48 | 34 | 44 | 65 | 107 | 0 | <1.00e-15 | <4.88e-14 |
| 9 | ST_JNK_MAPK_PATHWAY | JNKs are MAP kinases regulated by several levels of kinases (MAPKK, MAPKKK) and phosphorylate transcription factors and regulatory proteins. | AKT1, ATF2, CDC42, DLD, DUSP10, DUSP4, DUSP8, GAB1, GADD45A, GCK, IL1R1, JUN, MAP2K4, MAP2K5, MAP2K7, MAP3K1, MAP3K10, MAP3K11, MAP3K12, MAP3K13, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K7, MAP3K7IP1, MAP3K7IP2, MAP3K9, MAPK10, MAPK7, MAPK8, MAPK9, MYEF2, NFATC3, NR2C2, PAPPA, SHC1, TP53, TRAF6, ZAK | 36 | GADD45A(1), MAP2K4(1), MAP3K1(1), MAP3K10(2), MAP3K12(1), MAP3K13(2), MAP3K2(2), MAP3K3(1), MAP3K4(2), MAP3K5(2), MAP3K7(3), MAP3K9(1), MAPK8(1), MAPK9(1), MYEF2(1), PAPPA(3), SHC1(1), TP53(279), TRAF6(2) | 21375636 | 307 | 278 | 171 | 6 | 51 | 37 | 50 | 65 | 104 | 0 | <1.00e-15 | <4.88e-14 |
| 10 | PMLPATHWAY | Ring-shaped PML nuclear bodies regulate transcription and are required co-activators in p53- and DAXX-mediated apoptosis. | CREBBP, DAXX, HRAS, PAX3, PML, PRAM-1, RARA, RB1, SIRT1, SP100, TNF, TNFRSF1A, TNFRSF1B, TNFRSF6, TNFSF6, TP53, UBL1 | 13 | CREBBP(7), DAXX(1), PAX3(5), RARA(1), RB1(9), SP100(4), TNF(1), TNFRSF1A(1), TP53(279) | 8081303 | 308 | 277 | 172 | 6 | 49 | 34 | 47 | 66 | 112 | 0 | <1.00e-15 | <4.88e-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 | 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 | 0.00088 | 0.54 |
| 2 | 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 | 0.0022 | 0.54 | |
| 3 | 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 | 0.0043 | 0.54 |
| 4 | 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 | 0.0043 | 0.54 |
| 5 | HSA04530_TIGHT_JUNCTION | Genes involved in tight junction | ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, AMOTL1, ASH1L, CASK, CDC42, CDK4, CGN, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CRB3, CSDA, CSNK2A1, CSNK2A2, CSNK2B, CTNNA1, CTNNA2, CTNNA3, CTNNB1, CTTN, EPB41, EPB41L1, EPB41L2, EPB41L3, EXOC3, EXOC4, F11R, GNAI1, GNAI2, GNAI3, HCLS1, HRAS, IGSF5, INADL, JAM2, JAM3, KRAS, LLGL1, LLGL2, MAGI1, MAGI2, MAGI3, MLLT4, MPDZ, MPP5, MRAS, MRCL3, MRLC2, MYH1, MYH10, MYH11, MYH13, MYH14, MYH15, MYH2, MYH3, MYH4, MYH6, MYH7, MYH7B, MYH8, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLPF, NRAS, OCLN, PARD3, PARD6A, PARD6B, PARD6G, PPM1J, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP2R3A, PPP2R3B, PPP2R4, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCQ, PRKCZ, PTEN, RAB13, RAB3B, RHOA, RRAS, RRAS2, SPTAN1, SRC, SYMPK, TJAP1, TJP1, TJP2, TJP3, VAPA, YES1, ZAK | 128 | 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), SRC(4), TJAP1(1), TJP1(3), TJP3(1), YES1(1) | 82395479 | 189 | 141 | 185 | 38 | 29 | 15 | 68 | 50 | 27 | 0 | 0.0044 | 0.54 |
| 6 | 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 | 0.0066 | 0.67 |
| 7 | 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 | 0.0084 | 0.68 |
| 8 | CREMPATHWAY | The transcription factor CREM activates a post-meiotic transcriptional cascade culminating in spermatogenesis. | ADCY1, CREM, FHL5, FSHB, FSHR, GNAS, XPO1 | 7 | ADCY1(4), FHL5(2), FSHB(1), FSHR(4), GNAS(3) | 3965423 | 14 | 14 | 13 | 3 | 4 | 0 | 2 | 5 | 3 | 0 | 0.0088 | 0.68 |
| 9 | 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 | 0.014 | 0.96 | |
| 10 | 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 | 0.017 | 1 |
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Methods & Data
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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]
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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.
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References
[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 - 615 (2011)
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Broad Institute TCGA GDAC as part of the TCGA Research Network.
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