Mutation Analysis (MutSig vS2N)
Colon/Rectal Adenocarcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1K935Q2
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig vS2N). Broad Institute of MIT and Harvard. doi:10.7908/C1K935Q2
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: COADREAD-TP

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: 64. 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
APC 225264 0 4 249 221 9.3e-107 1.7e-102
KRAS 23484 0 0 72 1 3.9e-103 3.7e-99
TP53 28728 0 2 109 38 2.5e-74 1.6e-70
NRAS 16644 0 0 17 0 1.6e-46 7.4e-43
SMAD4 41496 0 0 29 5 1e-31 3.9e-28
FAM123B 70680 0 3 26 19 4.2e-18 1.3e-14
SOX9 28500 0 0 11 10 1.6e-16 4.3e-13
ZNF14 55404 0 0 10 9 2e-16 4.6e-13
FAM22F 25308 0 1 10 1 1.3e-13 2.8e-10
POLR3B 98496 0 3 14 2 3.6e-13 6.7e-10
EYS 51300 0 1 10 3 2.9e-12 5e-09
TET1 171228 0 4 20 2 3.7e-12 5.8e-09
ELF3 28272 0 0 8 6 4.4e-10 6.4e-07
RWDD2B 26676 0 0 8 1 4.9e-10 6.6e-07
TCERG1 82764 0 2 19 7 1.1e-09 1.4e-06
PTPN12 65208 0 0 11 3 1.3e-09 1.6e-06
PIK3CA 95988 0 0 33 0 7.1e-09 7.8e-06
PIK3R1 67260 0 0 12 8 1.2e-07 0.00012
SMAD2 37392 0 0 15 5 1.6e-07 0.00015
ACCN5 45144 0 0 8 0 2.6e-07 0.00025
CCBP2 31236 0 0 10 0 4.8e-07 0.00043
HLA-B 21888 0 0 5 5 7.5e-07 0.00064
ARID1A 132696 0 2 17 13 9.6e-07 0.00078
MBOAT2 46056 0 0 10 0 1.3e-06 0.001
COX15 32376 0 0 5 0 1.5e-06 0.0012
ZC3H13 120384 0 1 23 16 2.4e-06 0.0018
BCL7A 16416 0 1 8 1 3.9e-06 0.0027
ACVR2A 43092 0 0 14 10 5.4e-06 0.0036
ZC3HC1 36480 0 2 10 0 7.1e-06 0.0046
B2M 10260 0 0 7 4 0.000014 0.0085
TGM5 60192 0 2 11 0 0.000014 0.0085
ATP8A1 106248 0 4 11 0 0.000016 0.009
PCOLCE2 32832 0 1 9 0 0.000016 0.009
CXCR7 32376 0 2 11 0 0.000018 0.0098
NCOA3 111948 0 1 15 2 0.000031 0.017
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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