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: LUAD
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:LUAD.final_analysis_set.maf
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Significantly mutated genes (q ≤ 0.1): 36
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: 36. 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 | 31248 | 3 | 2 | 151 | 59 | 1.1e-162 | 2.1e-158 |
| KRAS | 25787 | 1 | 0 | 71 | 0 | 4.1e-40 | 3.8e-36 |
| STK11 | 21045 | 3 | 0 | 24 | 14 | 1.2e-38 | 7.4e-35 |
| PPP2R2A | 45136 | 4 | 0 | 8 | 0 | 2.6e-17 | 1.2e-13 |
| RBM10 | 49888 | 4 | 1 | 14 | 11 | 1e-15 | 3.8e-12 |
| LOC440563 | 25272 | 2 | 1 | 9 | 1 | 1.1e-14 | 3.4e-11 |
| FAM55B | 18225 | 0 | 3 | 7 | 0 | 5.5e-12 | 1.5e-08 |
| U2AF1 | 21829 | 2 | 0 | 7 | 0 | 2.2e-10 | 5.1e-07 |
| MAP2K1 | 33480 | 2 | 0 | 8 | 1 | 2.1e-09 | 4.4e-06 |
| KEAP1 | 46361 | 2 | 0 | 45 | 5 | 5.1e-09 | 9.6e-06 |
| DCAF8L2 | 25758 | 0 | 2 | 7 | 0 | 1.1e-08 | 0.000018 |
| CDKN2A | 9534 | 4 | 1 | 16 | 5 | 9.9e-08 | 0.00016 |
| BRAF | 64728 | 11 | 1 | 21 | 2 | 1.4e-07 | 0.0002 |
| NFATC3 | 88764 | 4 | 2 | 11 | 0 | 1.5e-07 | 0.0002 |
| KRTAP4-11 | 11178 | 1 | 0 | 5 | 0 | 5.7e-07 | 0.00072 |
| CRIPAK | 26030 | 0 | 5 | 17 | 11 | 6.5e-07 | 0.00076 |
| FAM75C1 | 81405 | 1 | 5 | 23 | 1 | 1.2e-06 | 0.0014 |
| ARID1A | 144336 | 5 | 2 | 19 | 13 | 2.3e-06 | 0.0024 |
| PIK3CA | 104894 | 4 | 1 | 15 | 0 | 6.6e-06 | 0.0064 |
| CENPF | 295854 | 17 | 7 | 33 | 3 | 6.8e-06 | 0.0064 |
| OR2T27 | 24810 | 0 | 2 | 16 | 0 | 7.6e-06 | 0.0068 |
| SMARCA4 | 117477 | 9 | 2 | 21 | 13 | 7.9e-06 | 0.0068 |
| AMY1A | 13893 | 1 | 1 | 5 | 2 | 9.5e-06 | 0.0078 |
| BRE | 42403 | 7 | 0 | 10 | 6 | 0.000027 | 0.022 |
| MAGEC1 | 90024 | 6 | 3 | 42 | 3 | 0.000044 | 0.033 |
| AGAP6 | 56619 | 3 | 2 | 7 | 1 | 0.000066 | 0.048 |
| C9orf64 | 30509 | 2 | 0 | 8 | 6 | 8e-05 | 0.055 |
| RUFY1 | 56787 | 10 | 2 | 8 | 0 | 0.000081 | 0.055 |
| RIT1 | 19592 | 2 | 1 | 12 | 3 | 0.000085 | 0.056 |
| SPRR3 | 12643 | 1 | 0 | 8 | 5 | 0.000091 | 0.057 |
| MGA | 242113 | 6 | 3 | 25 | 14 | 0.000099 | 0.061 |
| SETD2 | 185697 | 2 | 1 | 23 | 12 | 0.0001 | 0.062 |
| ZNF681 | 62496 | 8 | 1 | 8 | 1 | 0.00011 | 0.064 |
| OR14I1 | 29264 | 0 | 2 | 15 | 0 | 0.00013 | 0.072 |
| RIF1 | 234588 | 12 | 3 | 16 | 2 | 0.00017 | 0.089 |
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.