Mutation Analysis (MutSig vS2N)
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1571978
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/C1571978
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: LAML-TB

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: 0. 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
A1BG 20882 0 0 0 0 1 1
A1CF 42946 0 0 0 0 1 1
A2BP1 28762 0 0 0 0 1 1
A2LD1 0 0 0 0 0 1 1
A2M 93969 0 0 0 0 1 1
A2ML1 104804 0 0 0 0 1 1
A4GALT 19306 0 0 0 0 1 1
A4GNT 24822 0 0 0 0 1 1
AAAS 39400 0 0 0 0 1 1
AACS 45901 0 0 0 0 1 1
AADAC 29747 0 0 0 0 1 1
AADACL2 29747 0 0 0 0 1 1
AADACL3 25216 0 0 0 0 1 1
AADACL4 28762 0 0 0 0 1 1
AADAT 31520 0 0 0 0 1 1
AAGAB 22655 0 0 0 0 1 1
AAK1 48462 0 0 0 0 1 1
AAMP 31914 0 0 0 0 1 1
AANAT 8274 0 0 0 0 1 1
AARS 65207 0 0 0 0 1 1
AARS2 54175 0 0 0 0 1 1
AARSD1 38809 0 0 0 0 1 1
AASDH 81558 0 0 0 0 1 1
AASDHPPT 22458 0 0 0 0 1 1
AASS 66980 0 0 0 0 1 1
AATF 36642 0 0 0 0 1 1
AATK 22458 0 0 0 0 1 1
ABAT 35854 0 0 0 0 1 1
ABCA1 164889 0 0 0 0 1 1
ABCA10 124307 1 0 0 0 1 1
ABCA12 204092 0 0 0 0 1 1
ABCA13 363662 0 0 0 0 1 1
ABCA2 114260 0 0 0 0 1 1
ABCA3 106183 0 0 0 0 1 1
ABCA4 158388 0 0 0 0 1 1
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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