Mutation Analysis (MutSig vS2N)
Stomach Adenocarcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C10Z71JZ
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/C10Z71JZ
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: STAD-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: 11. 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 14616 1 1 57 19 1.1e-59 2.1e-55
KRAS 12004 0 0 14 0 9.3e-56 8.7e-52
CBWD1 13232 3 0 15 14 8.9e-42 5.6e-38
RPL22 5800 1 0 9 9 3e-36 1.4e-32
ARID1A 67512 5 1 26 17 1.4e-16 5.3e-13
RNF43 23260 4 2 14 9 9.5e-12 3e-08
PIK3CA 48948 10 2 32 1 1.6e-11 4.3e-08
PHF2 33056 6 4 13 9 4.3e-10 1e-06
PGM5 18160 4 0 19 2 6.7e-10 1.4e-06
ACVR2A 22036 7 0 14 10 1.3e-09 2.4e-06
MLL2 143772 3 6 29 10 0.000011 0.02
HLA-B 11080 6 0 10 5 0.000091 0.14
RHOA 11136 5 0 8 0 0.00016 0.22
UPF3A 13976 4 1 6 5 0.00017 0.22
ERBB3 51192 5 3 16 0 0.00036 0.45
HNF1A 19780 1 0 6 5 0.00071 0.84
IRF2 15024 2 1 11 3 0.00076 0.84
OR8H3 14672 0 1 10 0 0.0011 1
DRD3 15660 3 2 6 0 0.0011 1
NCOA2 55744 14 2 12 1 0.0015 1
LRRN3 32132 2 3 11 2 0.0016 1
BMPR2 42456 6 0 12 6 0.0016 1
MLL4 56872 2 3 17 7 0.0017 1
DOCK3 76004 18 5 23 9 0.0017 1
BCOR 56996 9 2 14 8 0.0019 1
MAP2K7 12444 4 0 12 1 0.0026 1
SAFB2 25576 4 2 6 5 0.003 1
MUC17 157408 3 11 24 0 0.0032 1
SPERT 12352 0 2 7 2 0.0034 1
CRYGC 6960 0 0 5 0 0.0044 1
TPTE 26736 15 3 15 1 0.0051 1
TLR4 37584 0 2 11 0 0.0064 1
XRN2 38684 11 0 10 1 0.0074 1
RP1 94536 4 7 16 1 0.0078 1
CNGA4 22736 0 2 9 0 0.008 1
TP53

Figure S1.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

KRAS

Figure S2.  This figure depicts the distribution of mutations and mutation types across the KRAS significant gene.

RPL22

Figure S3.  This figure depicts the distribution of mutations and mutation types across the RPL22 significant gene.

ARID1A

Figure S4.  This figure depicts the distribution of mutations and mutation types across the ARID1A significant gene.

RNF43

Figure S5.  This figure depicts the distribution of mutations and mutation types across the RNF43 significant gene.

PIK3CA

Figure S6.  This figure depicts the distribution of mutations and mutation types across the PIK3CA significant gene.

PHF2

Figure S7.  This figure depicts the distribution of mutations and mutation types across the PHF2 significant gene.

PGM5

Figure S8.  This figure depicts the distribution of mutations and mutation types across the PGM5 significant gene.

ACVR2A

Figure S9.  This figure depicts the distribution of mutations and mutation types across the ACVR2A significant gene.

MLL2

Figure S10.  This figure depicts the distribution of mutations and mutation types across the MLL2 significant gene.

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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