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

- MAF used for this analysis:READ-TP.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 228

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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