Kidney Renal Clear Cell Carcinoma: 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: KIRC

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: 24. 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
KIAA1731 2529 2 1 6 0 0 0
PBRM1 254039 7 3 154 123 1.6e-289 1.6e-285
FAM200A 9688 0 0 10 0 1.8e-237 1.1e-233
VHL 17868 2 7 198 118 5.3e-130 2.5e-126
ZNF717 281 2 2 4 3 6.9e-113 2.6e-109
BAP1 94426 2 1 43 25 5.9e-112 1.9e-108
SETD2 304933 4 2 60 38 8.2e-62 2.2e-58
POTED 20731 0 0 6 0 1.5e-61 3.5e-58
KDM5C 169432 1 1 27 16 4.1e-27 8.5e-24
PTEN 64163 3 4 25 13 3.9e-24 7.4e-21
CT47B1 19951 0 1 5 0 2.2e-19 3.7e-16
ZNF844 45241 2 0 6 0 1e-16 1.6e-13
ANKRD30B 67721 4 1 7 0 4.8e-10 7e-07
TP53 51534 1 5 23 3 2.8e-08 0.000038
ETF1 69274 1 0 6 5 2.8e-07 0.00035
PIK3CA 172751 3 2 19 1 3.2e-06 0.0037
STAU2 71447 5 0 7 0 3.5e-06 0.0039
VCX2 6416 0 0 5 2 0.000013 0.014
EBPL 24540 0 0 8 0 0.000018 0.018
WDR52 164571 6 1 11 0 0.000021 0.02
GPR112 462604 2 2 11 1 0.000031 0.027
MUC17 555166 0 3 22 0 0.000064 0.052
MTOR 418151 6 3 32 0 0.000064 0.052
CR1 213857 2 0 13 6 0.00012 0.095
NF2 83308 7 3 7 5 0.0002 0.15
KBTBD8 91794 0 0 9 0 0.00028 0.2
UPF2 199464 6 3 9 0 0.00037 0.26
MAN2C1 116921 0 1 9 0 0.00043 0.29
UNC80 39545 4 2 6 0 0.00063 0.4
C22orf42 33538 3 0 5 0 0.00064 0.4
ACSBG2 104857 2 1 6 0 0.00072 0.44
DNAH6 68378 4 2 6 0 0.00075 0.44
SMCR8 144377 0 0 6 0 0.00079 0.45
MUC16 1887204 8 21 49 1 0.00098 0.55
COL11A1 199642 6 1 11 7 0.001 0.55
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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