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 vS2N was used to generate the results found in this report.
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Working with individual set: MOLECULAR_NONSMOKER
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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MAF used for this analysis:MOLECULAR_NONSMOKER.final_analysis_set.maf
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Significantly mutated genes (q ≤ 0.1): 11
Column Descriptions:
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N = number of sequenced bases in this gene across the individual set
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nnon = number of (nonsilent) mutations in this gene across the individual set
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nnull = number of (nonsilent) null mutations in this gene across the individual set
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nflank = number of noncoding mutations from this gene's flanking region, across the individual set
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nsil = number of silent mutations in this gene across the individual set
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p = p-value (overall)
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q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)
Table 1. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 11. 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).
| gene | N | nflank | nsil | nnon | nnull | p | q |
|---|---|---|---|---|---|---|---|
| TP53 | 7056 | 0 | 0 | 21 | 12 | 0 | 0 |
| SETD2 | 41944 | 1 | 0 | 8 | 7 | 5.9e-32 | 5.6e-28 |
| EGFR | 25536 | 3 | 0 | 12 | 4 | 1.7e-27 | 1.1e-23 |
| BRAF | 14616 | 0 | 0 | 7 | 0 | 1.8e-22 | 8.4e-19 |
| EIF5B | 25984 | 0 | 0 | 6 | 3 | 3.3e-19 | 1.2e-15 |
| CDKN2A | 2128 | 0 | 0 | 5 | 3 | 5.9e-17 | 1.8e-13 |
| SMAD4 | 10248 | 1 | 0 | 6 | 3 | 2.9e-10 | 7.8e-07 |
| KEAP1 | 10472 | 0 | 0 | 6 | 1 | 6.3e-10 | 1.5e-06 |
| GLG1 | 23744 | 0 | 0 | 5 | 0 | 1.3e-08 | 0.000028 |
| KRAS | 5824 | 0 | 0 | 4 | 0 | 3.5e-06 | 0.0065 |
| LONP1 | 18424 | 0 | 0 | 5 | 1 | 0.000016 | 0.028 |
| GRM1 | 23128 | 1 | 0 | 6 | 0 | 0.00029 | 0.45 |
| PRB4 | 2632 | 3 | 0 | 4 | 1 | 0.0004 | 0.58 |
| MUC16 | 258272 | 2 | 1 | 14 | 4 | 0.00086 | 1 |
| CASP8 | 13160 | 0 | 0 | 4 | 2 | 0.0038 | 1 |
| FRMD8 | 5544 | 0 | 0 | 4 | 1 | 0.0059 | 1 |
| FMO3 | 11480 | 2 | 0 | 4 | 0 | 0.0089 | 1 |
| ZFHX4 | 61096 | 0 | 1 | 6 | 1 | 0.012 | 1 |
| CSMD3 | 74872 | 3 | 0 | 11 | 0 | 0.013 | 1 |
| OCA2 | 15736 | 0 | 0 | 6 | 0 | 0.017 | 1 |
| PDGFRB | 20272 | 0 | 0 | 5 | 0 | 0.029 | 1 |
| SPTA1 | 49504 | 6 | 1 | 7 | 1 | 0.036 | 1 |
| CNTLN | 29624 | 0 | 0 | 5 | 2 | 0.055 | 1 |
| MAP3K13 | 18480 | 1 | 0 | 4 | 2 | 0.063 | 1 |
| STAG3 | 24808 | 1 | 0 | 5 | 0 | 0.065 | 1 |
| RYR2 | 91280 | 9 | 2 | 10 | 0 | 0.069 | 1 |
| USH2A | 103656 | 3 | 2 | 10 | 2 | 0.076 | 1 |
| CENPF | 66808 | 0 | 1 | 5 | 0 | 0.1 | 1 |
| ABCA12 | 58016 | 0 | 0 | 5 | 0 | 0.12 | 1 |
| PREPL | 19264 | 0 | 0 | 4 | 0 | 0.12 | 1 |
| FAT3 | 86016 | 1 | 0 | 6 | 0 | 0.14 | 1 |
| OR2W5 | 5600 | 0 | 0 | 4 | 0 | 0.17 | 1 |
| XIRP2 | 86968 | 1 | 1 | 7 | 0 | 0.2 | 1 |
| AKAP9 | 83384 | 1 | 2 | 5 | 1 | 0.26 | 1 |
| TTN | 714672 | 8 | 7 | 18 | 2 | 0.27 | 1 |
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. ##REF##38
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.