(primary solid tumor cohort)
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: GBM-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:GBM-TP.final_analysis_set.maf
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Significantly mutated genes (q ≤ 0.1): 93
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)
gene | N | nflank | nsil | nnon | nnull | p | q |
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PTEN | 46851 | 0 | 0 | 93 | 43 | 0 | 0 |
RB1 | 141717 | 0 | 1 | 24 | 23 | 0 | 0 |
PIK3R1 | 85845 | 0 | 0 | 34 | 20 | 1.1e-205 | 7.2e-202 |
TP53 | 36666 | 0 | 1 | 100 | 19 | 1.9e-194 | 9.1e-191 |
RPL5 | 33756 | 0 | 0 | 8 | 6 | 3.5e-169 | 1.3e-165 |
IDH1 | 46560 | 0 | 0 | 15 | 0 | 1.3e-126 | 4e-123 |
PIK3CA | 122511 | 0 | 0 | 35 | 7 | 5.6e-111 | 1.5e-107 |
STAG2 | 144627 | 0 | 0 | 12 | 10 | 1.3e-95 | 3.1e-92 |
CDC27 | 87009 | 0 | 0 | 7 | 6 | 4.3e-66 | 9e-63 |
C3orf67 | 59073 | 0 | 0 | 6 | 0 | 1.5e-55 | 2.9e-52 |
NF1 | 434463 | 0 | 1 | 34 | 28 | 1.8e-46 | 3.2e-43 |
PRB2 | 19788 | 0 | 0 | 6 | 6 | 1.1e-45 | 1.7e-42 |
SLC22A9 | 59364 | 0 | 0 | 5 | 0 | 2.3e-34 | 3.3e-31 |
LZTR1 | 74787 | 0 | 0 | 10 | 1 | 1.3e-33 | 1.8e-30 |
PDGFRA | 120183 | 0 | 1 | 13 | 2 | 3.7e-33 | 4.6e-30 |
EGFR | 132987 | 0 | 7 | 95 | 5 | 4e-25 | 4.7e-22 |
CHD8 | 213012 | 0 | 0 | 10 | 7 | 7.6e-23 | 8e-20 |
SEMA3C | 82644 | 0 | 1 | 11 | 1 | 7.7e-23 | 8e-20 |
SEMG1 | 48597 | 0 | 0 | 8 | 1 | 6.7e-22 | 6.7e-19 |
DYNC1I1 | 63729 | 0 | 0 | 7 | 1 | 3.9e-19 | 3.7e-16 |
KDR | 145500 | 0 | 0 | 9 | 3 | 1.4e-14 | 1.2e-11 |
ADAM29 | 88173 | 0 | 1 | 9 | 1 | 3.7e-14 | 3.2e-11 |
ATRX | 279942 | 0 | 2 | 17 | 12 | 1.7e-12 | 1.4e-09 |
RBM47 | 48888 | 0 | 3 | 9 | 0 | 3.1e-12 | 2.5e-09 |
CARD6 | 104760 | 0 | 0 | 7 | 1 | 6.3e-12 | 4.8e-09 |
CALCR | 54999 | 0 | 0 | 8 | 0 | 8.4e-12 | 6.1e-09 |
SULT1B1 | 35793 | 0 | 1 | 7 | 1 | 1.1e-11 | 7.6e-09 |
COL4A4 | 107670 | 0 | 1 | 7 | 0 | 1.3e-11 | 8.6e-09 |
KIAA1751 | 72168 | 0 | 1 | 6 | 0 | 1.8e-11 | 1.2e-08 |
QKI | 37248 | 0 | 0 | 5 | 3 | 1.9e-11 | 1.2e-08 |
MYO1B | 131532 | 0 | 0 | 7 | 0 | 8.2e-11 | 5e-08 |
KEL | 78570 | 0 | 2 | 15 | 3 | 8e-10 | 4.7e-07 |
PROKR2 | 42486 | 0 | 0 | 7 | 0 | 8.4e-10 | 4.8e-07 |
BRAF | 75951 | 0 | 1 | 6 | 0 | 1.3e-09 | 7.2e-07 |
F5 | 239784 | 0 | 0 | 9 | 3 | 3.9e-09 | 2.1e-06 |
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.