Rectum 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: READ

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: 204. 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 7519 0 0 39 1 0 0
APC 72124 0 0 94 81 4.2e-161 3.9e-157
POTEB 1387 0 2 6 1 4.8e-98 3e-94
TP53 9198 0 1 47 12 2.4e-72 1.1e-68
LRRC40 16717 0 0 7 1 5.8e-27 2.2e-23
ZNF549 17009 0 0 10 0 4.3e-26 1.3e-22
KIF5B 27083 0 0 13 4 1.3e-25 3.6e-22
YIPF1 8322 0 0 4 0 3.9e-25 9.1e-22
PCCA 18250 0 0 10 2 4.5e-23 9.4e-20
UPF2 35551 0 0 9 0 1.1e-21 2.1e-18
TMPO 23725 0 0 6 5 1.4e-21 2.5e-18
PTPRR 18469 0 0 9 4 6.7e-20 1.1e-16
ZNHIT6 13286 0 0 6 5 2.9e-18 4.2e-15
DGKH 30952 0 0 7 0 2.6e-16 3.5e-13
RTN4 28324 0 0 6 0 3.4e-16 4.2e-13
TGM5 19272 0 0 8 0 3.4e-15 4e-12
CCBP2 10001 0 0 6 0 2.5e-14 2.8e-11
NFKB1 24163 0 0 6 0 1e-13 1.1e-10
KRT84 12483 0 0 7 0 1.1e-13 1.1e-10
CCDC99 17082 0 0 5 0 1.4e-13 1.3e-10
UBOX5 32485 0 0 7 0 1.5e-13 1.4e-10
TP53BP1 47085 0 0 12 3 2.7e-13 2.3e-10
PSMD1 39566 0 0 7 0 3.1e-13 2.6e-10
KBTBD10 16571 0 0 7 2 3.8e-13 2.9e-10
HSPA4 22484 0 0 8 0 4e-13 3e-10
RBPJ 13140 0 0 6 0 8.4e-13 6.1e-10
AKAP3 21827 0 0 9 5 5.2e-12 3.7e-09
PEX3 11461 0 1 6 0 7.4e-12 5e-09
FRMPD1 37303 0 4 10 0 2.2e-11 1.4e-08
ARHGAP12 23579 0 0 7 2 5.9e-11 3.7e-08
ZC3HC1 11680 0 0 7 0 6.4e-11 3.9e-08
TLK1 20805 0 0 7 0 1.3e-10 7.5e-08
NCOA3 35843 0 1 9 2 1.3e-10 7.5e-08
ARID1A 42486 0 0 5 5 2.3e-10 1.3e-07
TTC27 21608 0 0 7 0 2.9e-10 1.6e-07
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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