Mutation Analysis (MutSig vS2N)
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1VX0DSD
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/C1VX0DSD
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: UCEC-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: 54. 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
C14orf38 248 0 2 13 1 0 0
ZNF860 496 0 2 8 0 7.509798e-322 7.000001e-318
PTEN 39928 0 5 255 152 1.7e-267 1e-263
KRAS 25544 0 2 53 0 5.9e-64 2.8e-60
SRRM5 1984 0 2 7 0 8.1e-61 3.1e-57
PIK3R1 73160 0 2 118 96 2.7e-46 8.6e-43
ARID1A 144336 0 5 107 92 2.4e-42 6.6e-39
HMGXB3 1984 0 2 6 0 2.1e-40 5e-37
GOLGA6L1 1240 0 1 5 2 3.9e-33 8.2e-30
LRCH2 27280 0 4 22 3 1e-31 1.9e-28
FAM71E2 3224 0 2 6 0 3.4e-25 5.8e-22
PIK3CA 104408 0 3 172 9 6.5e-24 1e-20
FAM178B 8928 0 1 9 2 8.8e-24 1.3e-20
GOLGA8A 6944 0 1 6 0 2.4e-21 3.2e-18
DPCR1 21576 0 3 14 5 4e-21 5e-18
SLC48A1 1984 0 0 5 1 4.3e-21 5.1e-18
RNPC3 3968 0 1 6 1 1.3e-20 1.4e-17
CTCF 62992 0 1 52 33 1e-19 1e-16
VWA5B2 8928 0 3 8 0 7.1e-19 7e-16
PARG 14880 0 2 10 3 1.4e-17 1.3e-14
DNAH12 43152 0 6 54 9 4.6e-16 4.2e-13
XKR5 14136 0 2 9 2 2.7e-15 2.3e-12
FSIP2 160952 0 5 30 4 4.1e-13 3.3e-10
CTNNB1 62992 0 7 80 0 1e-12 7.9e-10
DNAH6 39928 0 6 42 10 2.3e-12 1.8e-09
TP53 31248 0 2 74 17 1.4e-11 9.9e-09
ATAD3C 3968 0 2 5 0 5.9e-11 4.1e-08
CDR2L 8432 0 1 6 1 4.2e-10 2.8e-07
CYLC1 54312 0 2 27 4 1.2e-09 7.8e-07
NXF2 19344 0 3 8 0 4.1e-09 2.5e-06
NXF2B 19344 0 3 8 0 4.1e-09 2.5e-06
CDHR4 8184 0 4 8 1 3.6e-08 0.000021
FAM200A 5704 0 2 5 0 7.5e-08 0.000043
LRRC8D 83328 0 3 23 2 4.1e-07 0.00023
MRC1 62000 0 0 13 2 4.8e-07 0.00026
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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