Ovarian Serous Cystadenocarcinoma: Mutation Analysis (MutSig vS2N)
(primary solid tumor cohort)
Maintained by Dan DiCara (Broad Institute)
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: OV-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: 51. 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 39816 0 2 247 101 0 0
BRCA1 224044 0 0 11 11 9.4e-108 8.9e-104
BRCA2 421544 0 0 11 10 8.3e-40 5.2e-36
CDK12 147256 0 0 8 5 4.6e-23 2.2e-19
CYP11B1 52456 0 0 6 0 2.9e-22 1.1e-18
C9orf171 28440 0 0 5 1 3.6e-21 1.1e-17
PXN 40764 0 0 5 0 5.5e-15 1.5e-11
RB1CC1 194340 0 1 6 5 8.8e-13 2.1e-09
TBP 36024 0 0 4 4 1.6e-12 3.3e-09
OTOF 206348 0 0 8 2 6.1e-12 1.1e-08
ADAMTS14 103964 0 0 6 0 1.4e-11 2.3e-08
NF1 471788 0 0 14 9 2.2e-10 3.5e-07
NBPF16 44240 0 0 4 4 2.4e-10 3.5e-07
KIT 119132 0 1 6 1 3.3e-10 4.4e-07
RASAL1 66044 0 1 6 2 5.7e-10 6.8e-07
ADAMTS16 122292 0 0 6 1 5.8e-10 6.8e-07
SON 252168 0 0 8 4 6.6e-10 7.4e-07
HYDIN 412696 0 2 9 0 7.6e-10 8e-07
CRTAC1 66992 0 1 5 1 2.1e-09 2.1e-06
FAT1 514448 0 1 8 0 2.4e-09 2.3e-06
L3MBTL2 71100 0 0 5 0 6.6e-09 6e-06
GPRIN3 74260 0 0 5 0 1.5e-08 0.000013
DST 777992 0 2 13 2 6.5e-08 0.000053
PLB1 163056 0 0 6 0 1.2e-07 0.000093
GRLF1 167796 0 1 6 3 1.9e-07 0.00014
TOP2A 167480 0 1 6 4 5.1e-07 0.00037
DIDO1 188336 0 1 6 0 1e-06 0.0007
HKDC1 103332 0 0 5 1 2.4e-06 0.0016
SALL4 103648 0 0 5 1 2.4e-06 0.0016
IRS1 106176 0 0 5 1 3.3e-06 0.0021
IRS4 107124 0 0 5 1 3.7e-06 0.0022
HUWE1 427232 0 1 8 2 3.8e-06 0.0022
NCAN 107440 0 0 5 0 3.9e-06 0.0022
SLIT3 155788 0 0 6 1 4.3e-06 0.0024
PLXNA4 223096 0 0 6 1 8.6e-06 0.0047
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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