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: OV-TP
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:OV-TP.final_analysis_set.maf
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Significantly mutated genes (q ≤ 0.1): 51
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: 51. 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 | 39816 | 0 | 2 | 247 | 101 | 0 | 0 |
| BRCA1 | 224044 | 0 | 0 | 11 | 11 | 9.4e-108 | 8.9e-104 |
| BRCA2 | 421544 | 0 | 0 | 11 | 10 | 8.3e-40 | 5.2e-36 |
| CDK12 | 147256 | 0 | 0 | 8 | 5 | 4.6e-23 | 2.2e-19 |
| CYP11B1 | 52456 | 0 | 0 | 6 | 0 | 2.9e-22 | 1.1e-18 |
| C9orf171 | 28440 | 0 | 0 | 5 | 1 | 3.6e-21 | 1.1e-17 |
| PXN | 40764 | 0 | 0 | 5 | 0 | 5.5e-15 | 1.5e-11 |
| RB1CC1 | 194340 | 0 | 1 | 6 | 5 | 8.8e-13 | 2.1e-09 |
| TBP | 36024 | 0 | 0 | 4 | 4 | 1.6e-12 | 3.3e-09 |
| OTOF | 206348 | 0 | 0 | 8 | 2 | 6.1e-12 | 1.1e-08 |
| ADAMTS14 | 103964 | 0 | 0 | 6 | 0 | 1.4e-11 | 2.3e-08 |
| NF1 | 471788 | 0 | 0 | 14 | 9 | 2.2e-10 | 3.5e-07 |
| NBPF16 | 44240 | 0 | 0 | 4 | 4 | 2.4e-10 | 3.5e-07 |
| KIT | 119132 | 0 | 1 | 6 | 1 | 3.3e-10 | 4.4e-07 |
| RASAL1 | 66044 | 0 | 1 | 6 | 2 | 5.7e-10 | 6.8e-07 |
| ADAMTS16 | 122292 | 0 | 0 | 6 | 1 | 5.8e-10 | 6.8e-07 |
| SON | 252168 | 0 | 0 | 8 | 4 | 6.6e-10 | 7.4e-07 |
| HYDIN | 412696 | 0 | 2 | 9 | 0 | 7.6e-10 | 8e-07 |
| CRTAC1 | 66992 | 0 | 1 | 5 | 1 | 2.1e-09 | 2.1e-06 |
| FAT1 | 514448 | 0 | 1 | 8 | 0 | 2.4e-09 | 2.3e-06 |
| L3MBTL2 | 71100 | 0 | 0 | 5 | 0 | 6.6e-09 | 6e-06 |
| GPRIN3 | 74260 | 0 | 0 | 5 | 0 | 1.5e-08 | 0.000013 |
| DST | 777992 | 0 | 2 | 13 | 2 | 6.5e-08 | 0.000053 |
| PLB1 | 163056 | 0 | 0 | 6 | 0 | 1.2e-07 | 0.000093 |
| GRLF1 | 167796 | 0 | 1 | 6 | 3 | 1.9e-07 | 0.00014 |
| TOP2A | 167480 | 0 | 1 | 6 | 4 | 5.1e-07 | 0.00037 |
| DIDO1 | 188336 | 0 | 1 | 6 | 0 | 1e-06 | 0.0007 |
| HKDC1 | 103332 | 0 | 0 | 5 | 1 | 2.4e-06 | 0.0016 |
| SALL4 | 103648 | 0 | 0 | 5 | 1 | 2.4e-06 | 0.0016 |
| IRS1 | 106176 | 0 | 0 | 5 | 1 | 3.3e-06 | 0.0021 |
| IRS4 | 107124 | 0 | 0 | 5 | 1 | 3.7e-06 | 0.0022 |
| HUWE1 | 427232 | 0 | 1 | 8 | 2 | 3.8e-06 | 0.0022 |
| NCAN | 107440 | 0 | 0 | 5 | 0 | 3.9e-06 | 0.0022 |
| SLIT3 | 155788 | 0 | 0 | 6 | 1 | 4.3e-06 | 0.0024 |
| PLXNA4 | 223096 | 0 | 0 | 6 | 1 | 8.6e-06 | 0.0047 |
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]
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.