Mutation Analysis (MutSig vS2N)
Breast Invasive Carcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C17H1GRF
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/C17H1GRF
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: BRCA-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: 125. 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
KRTAP4-7 36 0 1 7 0 0 0
LOC100132247 67 0 1 8 1 0 0
NBPF10 377 0 0 13 1 0 0
ZNF841 266 0 0 8 2 0 0
ZSCAN12 57 0 2 5 1 0 0
PRAMEF11 156 0 0 6 0 0 0
ANKRD30B 241 0 3 6 1 0 0
RGPD3 419 0 3 7 1 0 0
NBPF9 302 0 0 6 0 0 0
FAM75C1 335 0 3 6 0 0 0
ZNF90 208 0 0 5 1 0 0
RGPD4 446 0 2 5 1 0 0
PIK3CA 325014 0 4 287 16 0 0
GATA3 88779 0 1 85 79 0 0
TP53 97272 0 3 261 104 3.6e-315 4.5e-312
PTEN 124286 0 0 30 22 2.6e-269 3e-266
NCOR2 405321 0 1 29 26 3e-179 3.3e-176
ZNF814 212 0 0 4 0 9.3e-169 9.7e-166
RUNX1 79517 0 3 26 19 3.5e-153 3.4e-150
MAP2K4 108081 0 0 32 20 2.5e-97 2.3e-94
CDH1 225424 0 2 56 47 1.6e-92 1.4e-89
HLA-DRB1 61758 0 2 10 8 9.3e-83 8e-80
DSPP 155170 0 0 30 7 5.6e-82 4.6e-79
C14orf38 772 0 0 4 0 2.3e-75 1.8e-72
RBMX 105765 0 1 13 13 2.7e-64 2e-61
MAP3K1 358210 0 3 85 69 9.4e-63 6.8e-60
AKD1 310363 0 0 19 13 4.6e-58 3.2e-55
TBL1XR1 120429 0 0 11 9 4e-57 2.7e-54
DNAH14 70252 0 1 11 3 1.5e-56 9.8e-54
MEF2A 110392 0 0 14 13 1.4e-48 9e-46
HNF1A 132011 0 0 9 6 8.8e-42 5.3e-39
CDKN1B 46321 0 0 7 7 1.3e-35 7.8e-33
CCDC144NL 41688 0 0 8 7 2.3e-35 1.3e-32
ZNF384 143591 0 1 14 14 1.6e-34 9.1e-32
KRTAP9-9 20096 0 0 6 5 2.5e-34 1.3e-31
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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