PANCANCER subset with 8 initial disease types: Mutation Analysis (MutSig vS2N)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

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.

  • Working with individual set: PANCAN8

Input

The input for this pipeline is a set of individuals with the following files associated for each:

  1. An annotated .maf file describing the mutations called for the respective individual, and their properties.

  2. A .wig file that contains information about the coverage of the sample.

Summary
Results
Significantly Mutated Genes

Column Descriptions:

  • N = number of sequenced bases in this gene across the individual set

  • nnon = number of (nonsilent) mutations in this gene across the individual set

  • nnull = number of (nonsilent) null mutations in this gene across the individual set

  • nflank = number of noncoding mutations from this gene's flanking region, across the individual set

  • nsil = number of silent mutations in this gene across the individual set

  • p = p-value (overall)

  • 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: 103. 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
ZNF717 314 2 4 9 5 0 0
C14orf38 2165 0 3 16 1 0 0
GOLGA6L6 628 0 0 9 1 0 0
ZFP92 628 0 8 9 1 0 0
PABPC4L 314 0 2 6 1 0 0
OR4C45 1256 2 1 7 0 0 0
ELFN1 1570 3 4 7 1 5.4e-285 1.5e-281
C1orf212 1884 1 2 7 3 7.2e-238 1.7e-234
FAM86B2 10048 2 1 10 6 8.5e-202 1.8e-198
ZNF732 53066 1 3 24 5 6.8e-181 1.3e-177
ZFP62 2512 0 0 6 0 2.5e-118 4.3e-115
PTEN 346681 4 10 394 226 2.5e-102 3.9e-99
SPDYE4 13816 1 2 11 2 2.7e-81 3.9e-78
ZNF879 6594 3 1 21 2 1.6e-77 2.1e-74
VHL 93409 1 8 186 102 9.7e-65 1.2e-61
SLFN12L 58718 1 4 25 3 2.9e-61 3.4e-58
GOLGA6L1 10511 1 2 8 2 1.6e-58 1.7e-55
ZNF90 65312 1 2 19 2 1e-50 1.1e-47
TP53 272790 1 20 869 307 2.4e-49 2.4e-46
KDM4DL 21038 1 1 10 2 1.9e-45 1.8e-42
HMGXB3 17320 0 3 9 0 2.7e-45 2.4e-42
KRTAP4-9 13816 0 1 8 2 1e-44 8.9e-42
ZNF853 314 0 1 4 1 3.5e-44 2.9e-41
ANKRD18A 11618 0 4 18 3 2.2e-43 1.7e-40
OR56A5 25748 0 0 10 0 2.9e-37 2.2e-34
PIK3CA 912093 4 13 467 20 1.2e-35 8.6e-33
SLC22A24 12874 1 1 7 1 1.4e-35 9.6e-33
KRAS 223309 1 5 136 2 1.3e-34 8.6e-32
CTAGE9 59660 0 0 15 0 1.8e-31 1.2e-28
FAM200A 50109 0 3 13 1 4.9e-30 3.1e-27
ZNF736 21980 0 2 8 0 2.2e-28 1.4e-25
TCP10L2 22608 0 2 8 0 1.3e-27 7.7e-25
ZSCAN12 17898 1 3 13 3 4.1e-24 2.4e-21
PIK3R1 638989 4 6 164 122 6.2e-22 3.4e-19
RGPD8 102050 0 3 16 0 5.3e-21 2.9e-18
Methods & Data
Methods

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]

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 - 615 (2011)
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