Prostate 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: PRAD

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: 8. 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
NKX3-1 4482 0 0 5 1 7.2e-52 1.4e-47
ZMYM3 29005 0 0 5 3 2e-18 1.9e-14
TP53 10458 0 0 5 1 3.7e-12 2.3e-08
MLL3 134697 2 0 10 7 2.7e-11 1.3e-07
SPOP 11452 2 0 4 0 3.9e-07 0.0015
MUC4 53171 0 2 5 0 1.1e-06 0.0033
ATM 99612 0 0 5 0 7e-06 0.019
CNTNAP5 34965 0 0 5 1 0.000039 0.092
TTN 1059218 1 4 18 4 0.002 1
YBX1 6723 0 0 4 0 0.0022 1
AHNAK2 141681 0 2 7 0 0.0074 1
FRG1 8715 1 0 4 1 0.0085 1
PRR21 5229 0 0 4 0 0.099 1
LRP1B 143560 2 1 5 1 0.19 1
MUC16 382810 1 4 9 0 0.21 1
FCGBP 80613 0 1 5 0 0.25 1
TPTE2 18418 1 0 4 1 0.29 1
LPHN3 35599 0 1 4 0 0.35 1
MUC17 112710 0 1 5 0 0.36 1
INADL 52620 3 0 4 1 0.39 1
RP1 67724 0 0 4 1 0.39 1
FAT1 134152 0 1 5 0 0.42 1
SYNE1 272080 6 1 5 0 0.47 1
HSPG2 87788 0 1 4 0 0.53 1
GRID2 30955 0 1 4 0 0.54 1
ASH1L 87644 1 0 4 2 0.58 1
SETD5 35360 0 1 4 0 0.58 1
DMXL2 90047 1 0 4 3 0.58 1
CSMD3 110953 2 1 4 2 0.81 1
FZD2 14278 0 4 4 1 0.84 1
FAT4 142381 0 3 4 1 0.85 1
CROCC 24473 7 1 4 0 0.92 1
AGT 13114 0 0 3 0 1 1
AIM2 11618 0 0 3 1 1 1
ANK2 110058 2 0 3 0 1 1
NKX3-1

Figure S1.  This figure depicts the distribution of mutations and mutation types across the NKX3-1 significant gene.

ZMYM3

Figure S2.  This figure depicts the distribution of mutations and mutation types across the ZMYM3 significant gene.

TP53

Figure S3.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

MLL3

Figure S4.  This figure depicts the distribution of mutations and mutation types across the MLL3 significant gene.

SPOP

Figure S5.  This figure depicts the distribution of mutations and mutation types across the SPOP significant gene.

MUC4

Figure S6.  This figure depicts the distribution of mutations and mutation types across the MUC4 significant gene.

ATM

Figure S7.  This figure depicts the distribution of mutations and mutation types across the ATM significant gene.

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)