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
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.final_analysis_set.maf
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Significantly mutated genes (q ≤ 0.1): 54
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: 54. 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 | 3 | 279 | 101 | 0 | 0 |
| BRCA1 | 224044 | 0 | 0 | 12 | 11 | 1.7e-83 | 1.6e-79 |
| KCNJ12 | 45504 | 0 | 2 | 5 | 0 | 4e-34 | 2.5e-30 |
| BRCA2 | 421544 | 0 | 0 | 12 | 10 | 1.5e-27 | 7e-24 |
| CDK12 | 147256 | 0 | 0 | 9 | 5 | 4.6e-23 | 1.7e-19 |
| FAM171B | 93220 | 0 | 0 | 7 | 1 | 6.7e-15 | 2.1e-11 |
| PXN | 40764 | 0 | 0 | 5 | 0 | 9.5e-12 | 2.6e-08 |
| NF1 | 471788 | 0 | 0 | 15 | 9 | 2.7e-11 | 6.4e-08 |
| TRIOBP | 170956 | 0 | 0 | 8 | 1 | 3.5e-11 | 7.2e-08 |
| NBPF16 | 44240 | 0 | 1 | 4 | 4 | 2.4e-10 | 4.2e-07 |
| TFAP2D | 46768 | 0 | 1 | 5 | 0 | 2.5e-10 | 4.2e-07 |
| MGRN1 | 53088 | 0 | 0 | 5 | 1 | 3.4e-09 | 5.4e-06 |
| IRS1 | 106176 | 0 | 0 | 6 | 1 | 6e-09 | 8.2e-06 |
| YSK4 | 160844 | 0 | 0 | 7 | 1 | 6.1e-09 | 8.2e-06 |
| CRB1 | 162108 | 0 | 0 | 7 | 0 | 7.1e-09 | 8.9e-06 |
| CHD4 | 213932 | 0 | 0 | 8 | 0 | 1.1e-08 | 0.000013 |
| HUWE1 | 427232 | 0 | 1 | 11 | 2 | 2.1e-08 | 0.000024 |
| SIGLEC12 | 61620 | 0 | 0 | 5 | 0 | 5.1e-08 | 0.000053 |
| NLRP3 | 120080 | 0 | 0 | 6 | 1 | 5.4e-08 | 0.000053 |
| SON | 252168 | 0 | 0 | 8 | 4 | 8.1e-08 | 0.000076 |
| QSOX2 | 64780 | 0 | 0 | 5 | 1 | 1.2e-07 | 0.0001 |
| CYP11B1 | 52456 | 0 | 0 | 7 | 0 | 1.8e-07 | 0.00015 |
| CRTAC1 | 66992 | 0 | 1 | 5 | 1 | 2e-07 | 0.00016 |
| RB1CC1 | 194340 | 0 | 1 | 7 | 5 | 3e-07 | 0.00024 |
| GPRIN3 | 74260 | 0 | 0 | 5 | 0 | 8.9e-07 | 0.00067 |
| AHNAK | 636108 | 0 | 1 | 12 | 0 | 1.1e-06 | 0.00079 |
| ZNF208 | 147572 | 0 | 0 | 6 | 0 | 1.2e-06 | 0.00085 |
| C9orf171 | 28440 | 0 | 0 | 5 | 1 | 1.4e-06 | 0.00096 |
| DST | 777992 | 0 | 3 | 15 | 2 | 2.4e-06 | 0.0015 |
| PLB1 | 163056 | 0 | 0 | 6 | 0 | 4.4e-06 | 0.0028 |
| KIT | 119132 | 0 | 2 | 7 | 1 | 6e-06 | 0.0036 |
| GRLF1 | 167796 | 0 | 2 | 6 | 3 | 6.3e-06 | 0.0037 |
| SCEL | 88164 | 0 | 0 | 5 | 1 | 8e-06 | 0.0046 |
| RNF213 | 480320 | 0 | 1 | 9 | 1 | 0.000019 | 0.01 |
| NCKAP5 | 186756 | 0 | 1 | 6 | 0 | 0.000021 | 0.011 |
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.