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: LAML
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:LAML.final_analysis_set.maf
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Significantly mutated genes (q ≤ 0.1): 29
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: 29. 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 |
|---|---|---|---|---|---|---|---|
| NPM1 | 21731 | 0 | 0 | 47 | 47 | 0 | 0 |
| IDH1 | 32800 | 0 | 0 | 20 | 0 | 0 | 0 |
| NRAS | 14966 | 0 | 0 | 18 | 0 | 0 | 0 |
| FLT3 | 79541 | 0 | 0 | 53 | 35 | 0 | 0 |
| IDH2 | 29521 | 0 | 0 | 20 | 0 | 0 | 0 |
| RUNX1 | 21116 | 0 | 0 | 20 | 11 | 0 | 0 |
| WT1 | 25214 | 0 | 0 | 14 | 12 | 0 | 0 |
| DNMT3A | 58016 | 0 | 0 | 55 | 14 | 0 | 0 |
| TET2 | 84665 | 0 | 0 | 23 | 19 | 0 | 0 |
| CEBPA | 5125 | 0 | 0 | 6 | 5 | 0 | 0 |
| TP53 | 25830 | 0 | 1 | 14 | 5 | 0 | 0 |
| U2AF1 | 18244 | 0 | 0 | 10 | 0 | 0 | 0 |
| KRAS | 21116 | 0 | 0 | 9 | 0 | 7.5e-308 | 1.1e-304 |
| PTPN11 | 45510 | 0 | 0 | 7 | 0 | 1.3e-83 | 1.8e-80 |
| PHF6 | 31981 | 0 | 0 | 6 | 4 | 1.2e-78 | 1.5e-75 |
| ASXL1 | 93480 | 0 | 0 | 5 | 5 | 8.6e-69 | 1e-65 |
| C17orf97 | 19273 | 0 | 1 | 5 | 0 | 2.9e-67 | 3.2e-64 |
| KIT | 77285 | 0 | 0 | 8 | 2 | 8.3e-67 | 8.7e-64 |
| FAM5C | 58221 | 0 | 0 | 6 | 0 | 1.5e-43 | 1.5e-40 |
| ETV6 | 32801 | 0 | 0 | 5 | 3 | 7.7e-40 | 7.3e-37 |
| PRUNE2 | 208881 | 0 | 0 | 7 | 5 | 3.4e-31 | 3.1e-28 |
| OR5H6 | 27676 | 0 | 2 | 4 | 4 | 2e-30 | 1.7e-27 |
| SMC3 | 98399 | 0 | 0 | 6 | 2 | 4.6e-26 | 3.8e-23 |
| RAD21 | 47151 | 0 | 0 | 4 | 4 | 3.5e-18 | 2.8e-15 |
| ZAN | 155607 | 0 | 1 | 6 | 4 | 9.5e-17 | 7.2e-14 |
| SMC1A | 89783 | 0 | 0 | 5 | 1 | 5.1e-15 | 3.7e-12 |
| CYP21A2 | 40299 | 0 | 0 | 4 | 0 | 2.8e-14 | 1.9e-11 |
| CSMD1 | 201675 | 0 | 0 | 6 | 1 | 4.3e-13 | 2.9e-10 |
| STAG2 | 101885 | 0 | 0 | 4 | 4 | 8.2e-09 | 5.3e-06 |
| TTN | 2613354 | 0 | 4 | 9 | 1 | 0.00024 | 0.15 |
| EPPK1 | 110549 | 0 | 0 | 5 | 0 | 0.0048 | 1 |
| QRICH2 | 96150 | 0 | 0 | 4 | 3 | 0.019 | 1 |
| MAP3K4 | 115206 | 0 | 0 | 4 | 3 | 0.036 | 1 |
| SDK1 | 135514 | 0 | 0 | 4 | 1 | 0.059 | 1 |
| PLCE1 | 181221 | 0 | 0 | 4 | 0 | 0.12 | 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. [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.