(classical 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: THCA-classical
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:THCA-classical.final_analysis_set.maf
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Significantly mutated genes (q ≤ 0.1): 6
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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BRAF | 33408 | 0 | 0 | 98 | 0 | 0 | 0 |
CCDC15 | 34077 | 0 | 1 | 5 | 0 | 2e-181 | 1.9e-177 |
ZNF845 | 32752 | 0 | 0 | 5 | 0 | 6.8e-47 | 4.3e-43 |
PPM1D | 22528 | 0 | 0 | 4 | 4 | 7.7e-43 | 3.6e-39 |
MLL3 | 207510 | 0 | 0 | 5 | 2 | 5.1e-08 | 0.00018 |
MUC17 | 173746 | 0 | 2 | 5 | 0 | 5.7e-08 | 0.00018 |
ZFHX3 | 150567 | 0 | 0 | 4 | 0 | 0.05 | 1 |
LRP1 | 188956 | 0 | 0 | 4 | 2 | 0.099 | 1 |
TTN | 1632990 | 0 | 2 | 5 | 1 | 0.12 | 1 |
MUC16 | 590609 | 0 | 4 | 5 | 1 | 0.35 | 1 |
ASH1L | 135090 | 0 | 0 | 3 | 0 | 1 | 1 |
ATM | 153834 | 0 | 0 | 3 | 1 | 1 | 1 |
CCDC39 | 34883 | 0 | 1 | 3 | 1 | 1 | 1 |
COL5A3 | 46319 | 0 | 0 | 3 | 1 | 1 | 1 |
CSMD3 | 170785 | 0 | 0 | 3 | 0 | 1 | 1 |
CTTNBP2 | 71602 | 0 | 0 | 3 | 0 | 1 | 1 |
DNAH9 | 204672 | 0 | 0 | 3 | 0 | 1 | 1 |
FLG | 139965 | 0 | 0 | 3 | 0 | 1 | 1 |
MYH6 | 92110 | 0 | 0 | 3 | 0 | 1 | 1 |
NBPF10 | 33553 | 0 | 0 | 3 | 0 | 1 | 1 |
NISCH | 60354 | 0 | 1 | 3 | 0 | 1 | 1 |
OBSCN | 218568 | 0 | 0 | 3 | 0 | 1 | 1 |
PKHD1L1 | 180085 | 0 | 0 | 3 | 2 | 1 | 1 |
PLXNB1 | 67889 | 0 | 0 | 3 | 0 | 1 | 1 |
PRDM9 | 39168 | 0 | 1 | 3 | 0 | 1 | 1 |
PRG4 | 58852 | 0 | 1 | 3 | 0 | 1 | 1 |
PTPRZ1 | 108388 | 0 | 0 | 3 | 0 | 1 | 1 |
STXBP5L | 55602 | 0 | 0 | 3 | 0 | 1 | 1 |
VWA3B | 59637 | 0 | 0 | 3 | 0 | 1 | 1 |
ZNF185 | 17052 | 0 | 0 | 3 | 1 | 1 | 1 |
ZNF799 | 29095 | 0 | 1 | 3 | 0 | 1 | 1 |
ABL2 | 49152 | 0 | 0 | 2 | 2 | 1 | 1 |
ACD | 22845 | 0 | 0 | 2 | 1 | 1 | 1 |
ACRC | 26040 | 0 | 0 | 2 | 0 | 1 | 1 |
ADAMTS19 | 47154 | 0 | 0 | 2 | 0 | 1 | 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.