Colon/Rectal Adenocarcinoma: Mutation Analysis (MutSig)
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: COADREAD

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: 49. 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
KRAS 23484 0 0 98 1 0 0
APC 225264 0 4 257 221 2.1e-83 1.9e-79
TP53 28728 0 2 124 38 9.9e-74 6.2e-70
BRAF 59508 0 0 23 0 9.6e-46 4.5e-42
POTED 11400 0 1 9 0 8.1e-33 3.1e-29
NRAS 16644 0 0 21 0 2.2e-27 6.9e-24
PIK3CA 95988 0 2 40 0 4.2e-20 1.1e-16
SOX9 28500 0 0 11 10 7e-15 1.7e-11
FAM123B 70680 0 3 27 19 3.4e-11 7.2e-08
EYS 51300 1 1 11 3 5.1e-11 9.7e-08
FAM22F 25308 0 1 10 1 1.1e-09 1.9e-06
PCBP1 26220 0 0 6 0 4.2e-09 6.6e-06
FBXW7 65436 1 2 48 10 8.7e-08 0.00013
ELF3 28272 0 0 8 6 1.6e-07 0.0002
ANKRD20A3 50616 0 0 7 1 1.6e-07 0.0002
ARID1A 132696 0 3 22 13 1.8e-07 0.00021
ACOT4 24168 0 1 6 6 4.9e-07 0.00055
ZNF14 55404 0 0 10 9 5.3e-07 0.00056
RBBP7 35112 0 0 8 0 2.6e-06 0.0025
ZC3H13 120384 0 1 30 16 2.6e-06 0.0025
LGR4 76380 0 2 11 2 5.3e-06 0.0047
ACVR2A 43092 0 1 14 10 5.8e-06 0.0049
NCOA3 111948 0 1 15 2 6.7e-06 0.0053
SMAD4 41496 0 0 31 5 6.8e-06 0.0053
PCDHGC4 120384 0 3 13 0 7.5e-06 0.0057
KPNA1 45828 1 0 8 0 7.9e-06 0.0057
RUVBL1 38532 0 2 9 0 9.9e-06 0.0069
PIK3R1 67260 0 0 13 8 0.000012 0.008
HLA-B 21888 0 0 5 5 0.000021 0.014
USP40 80028 0 0 9 1 0.000027 0.017
TAT 35112 0 1 7 0 0.000037 0.023
ZNF439 42864 0 1 9 0 0.000044 0.026
UPF2 111036 1 1 16 0 0.000046 0.026
TLK1 64980 0 0 11 0 0.000051 0.028
SCAND3 113316 0 4 13 9 0.000051 0.028
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)
Copyright © 2012 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
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