Mutation Analysis (MutSig vS2N)
Lung Adenocarcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1K072G3
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/C1K072G3
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: LUAD-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: 28. 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 31248 3 2 137 54 8.7e-168 1.7e-163
KRAS 25787 1 0 64 0 1.6e-37 1.5e-33
STK11 21045 2 0 21 11 2.1e-28 1.3e-24
RBM10 49888 4 1 14 11 5.5e-18 2.6e-14
FAM75C1 81405 1 4 22 1 1.5e-11 5.7e-08
U2AF1 21829 2 0 7 0 1.8e-11 5.7e-08
KEAP1 46361 2 0 42 5 1.2e-09 3.2e-06
LOC440563 25272 1 1 7 1 2.2e-09 5.3e-06
DCAF8L2 25758 0 2 7 0 3.3e-09 6.8e-06
NFATC3 88764 4 2 11 0 2.5e-08 0.000048
CDKN2A 9534 4 1 15 5 1.6e-07 0.00027
KRTAP4-11 11178 1 0 5 0 2.3e-07 0.00036
ARID1A 144336 4 1 17 12 1.8e-06 0.0026
AMY1A 13893 1 1 5 2 4.5e-06 0.006
MAP2K1 33480 2 0 7 1 4.8e-06 0.0061
SMARCA4 117477 7 2 20 12 0.000011 0.013
OR2T27 24810 0 2 15 0 0.000014 0.015
CRIPAK 26030 0 4 15 9 0.000024 0.024
MAGEC1 90024 5 3 41 3 0.000026 0.024
CENPF 295854 15 7 32 3 0.000026 0.024
HRNR 135606 3 11 55 14 0.000044 0.039
MGA 242113 5 3 25 14 0.000048 0.042
EGFR 113093 26 7 34 9 0.000063 0.05
SPRR3 12643 1 0 7 5 0.000063 0.05
AGAP6 56619 3 2 7 1 0.000066 0.05
SETD2 185697 2 1 23 12 0.000073 0.053
FAM55B 18225 0 3 5 0 0.000083 0.058
BRAF 64728 11 1 19 2 0.00011 0.073
RIT1 19592 2 1 11 2 0.00019 0.12
OR14I1 29264 0 2 14 0 0.00024 0.15
ANKRD55 52080 8 2 12 1 0.00028 0.17
ZNF770 67178 0 3 6 0 0.00037 0.22
POLR3B 107136 5 0 15 2 0.00039 0.22
MUC17 336774 16 22 89 9 0.00051 0.28
RIF1 234588 11 3 15 2 0.00057 0.31
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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