Mutation Analysis (MutSig vS2N)
Rectum Adenocarcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1SQ8XN5
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/C1SQ8XN5
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: READ-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: 228. 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
TP53 9198 0 1 43 12 7.3e-132 1.4e-127
KRAS 7519 0 0 29 1 1.5e-99 1.4e-95
APC 72124 0 0 92 81 1.5e-65 9.7e-62
ODF2L 18542 0 0 8 6 4.1e-43 1.9e-39
TGM5 19272 0 0 8 0 3.8e-38 1.4e-34
ZNHIT6 13286 0 0 5 5 6.6e-38 2.1e-34
SEPSECS 12264 0 0 6 0 2.1e-37 5.7e-34
KIF5B 27083 0 0 13 4 8.5e-34 2e-30
NCOA3 35843 0 1 9 2 2e-29 4.3e-26
PTPRR 18469 0 0 9 4 3.2e-26 6e-23
C3orf58 7738 0 0 6 4 4.4e-24 7.5e-21
TMPO 23725 0 0 6 5 1.5e-21 2.3e-18
TET1 54823 0 3 11 1 7.5e-21 1.1e-17
WDR72 30076 0 0 8 2 1.7e-19 2.3e-16
CCBP2 10001 0 0 6 0 8.3e-19 1e-15
KRT84 12483 0 0 5 0 1.6e-18 1.9e-15
MYO1A 28908 0 0 6 0 3e-18 3.4e-15
KBTBD10 16571 0 0 7 2 3e-17 3.1e-14
EXTL2 9417 0 0 5 0 3.2e-17 3.2e-14
ATP8A1 34018 0 2 8 0 7.6e-17 7.2e-14
PEX3 11461 0 1 6 0 1.7e-16 1.5e-13
TMED10 5913 0 0 5 2 1.9e-16 1.6e-13
EDNRB 12264 0 2 7 0 3.7e-16 3e-13
ZNF443 17958 0 0 7 1 5.7e-16 4.4e-13
SYT9 12118 0 0 6 0 1.2e-15 9e-13
MOV10L1 30806 0 3 11 3 1.3e-15 9.5e-13
NDUFS2 12629 0 0 6 2 4.8e-15 3.3e-12
DNAH5 128626 0 2 28 4 1.3e-14 8.8e-12
TCERG1 26499 0 2 8 4 2.5e-14 1.6e-11
MYT1 24528 0 0 6 0 4.8e-14 3e-11
IGF2BP1 14527 0 0 6 0 3.5e-13 2.1e-10
ARHGAP12 23579 0 0 7 2 4.5e-13 2.6e-10
MBOAT2 14746 0 0 6 0 5.4e-13 3.1e-10
KIAA1804 18688 0 0 12 0 5.6e-13 3.1e-10
TP53BP1 47085 0 0 10 3 6.4e-13 3.5e-10
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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