Mutation Analysis (MutSig vS2N)
Colon Adenocarcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
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/C1765CHG
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: COAD-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: 46. 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 15965 0 0 43 0 5.3e-249 1e-244
APC 153140 0 4 157 140 8.5e-126 8e-122
TP53 19530 0 1 66 26 2.8e-83 1.8e-79
NRAS 11315 0 0 11 0 1.2e-80 5.5e-77
SMAD4 28210 0 0 20 5 3.1e-67 1.2e-63
FAM22F 17205 0 1 9 1 2.3e-29 7.2e-26
FAM123B 48050 0 1 18 14 4.2e-21 1.1e-17
SOX9 19375 0 0 9 8 3.4e-16 8.1e-13
SMAD2 25420 0 0 11 4 4.5e-12 9.5e-09
EYS 34875 0 1 8 3 7.5e-12 1.4e-08
ZNF14 37665 0 0 7 6 1.4e-10 2.5e-07
CDC27 46345 0 4 11 2 3.3e-10 5.3e-07
HLA-B 14880 0 0 5 5 1.6e-09 2.3e-06
ACTBL2 20305 0 1 8 0 4.5e-09 6e-06
HCLS1 24335 0 0 6 3 1.7e-08 0.000021
TCERG1 56265 0 0 11 3 5.4e-08 6e-05
NID2 70370 0 0 10 3 5.4e-08 6e-05
GOLGB1 192200 0 0 15 7 6e-08 0.000063
TBC1D10C 10385 0 0 4 4 8.4e-08 0.000084
FBXW11 30845 0 0 6 0 6.1e-07 0.00058
TGFBR1 26660 0 1 6 0 8.9e-07 0.0008
ZC3H13 81840 0 1 16 12 1.1e-06 0.00098
ACOT4 16430 0 0 6 6 1.6e-06 0.0013
CASP8 36425 0 0 8 4 4.1e-06 0.0032
TXNDC3 35495 0 0 12 5 5.5e-06 0.0042
COL11A2 52235 0 1 8 2 5.8e-06 0.0042
OR2T33 17360 0 1 5 0 6.1e-06 0.0042
VAV3 50840 0 1 8 0 8e-06 0.0054
FAT2 228780 0 4 26 1 9.4e-06 0.0061
PIK3CA 65255 0 0 28 0 1e-05 0.0064
ZMYM6 54560 0 0 10 2 0.000014 0.0081
OR2M4 18910 0 0 8 2 0.000014 0.0081
TM9SF1 36425 0 1 7 0 0.000014 0.0081
SCN11A 111135 0 3 13 0 0.000016 0.009
ZFP3 28520 0 1 7 0 0.000018 0.0099
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)