Colon/Rectal Adenocarcinoma: Mutation Analysis (MutSig vS2N)
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: COADREAD-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

- MAF used for this analysis:COADREAD-TP.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 64

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: 64. 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
--- | --- | --- | --- | --- | --- | --- | ---
APC | 225264 | 0 | 4 | 249 | 221 | 9.3e-107 | 1.7e-102
KRAS | 23484 | 0 | 0 | 72 | 1 | 3.9e-103 | 3.7e-99
TP53 | 28728 | 0 | 2 | 109 | 38 | 2.5e-74 | 1.6e-70
NRAS | 16644 | 0 | 0 | 17 | 0 | 1.6e-46 | 7.4e-43
SMAD4 | 41496 | 0 | 0 | 29 | 5 | 1e-31 | 3.9e-28
FAM123B | 70680 | 0 | 3 | 26 | 19 | 4.2e-18 | 1.3e-14
SOX9 | 28500 | 0 | 0 | 11 | 10 | 1.6e-16 | 4.3e-13
ZNF14 | 55404 | 0 | 0 | 10 | 9 | 2e-16 | 4.6e-13
FAM22F | 25308 | 0 | 1 | 10 | 1 | 1.3e-13 | 2.8e-10
POLR3B | 98496 | 0 | 3 | 14 | 2 | 3.6e-13 | 6.7e-10
EYS | 51300 | 0 | 1 | 10 | 3 | 2.9e-12 | 5e-09
TET1 | 171228 | 0 | 4 | 20 | 2 | 3.7e-12 | 5.8e-09
ELF3 | 28272 | 0 | 0 | 8 | 6 | 4.4e-10 | 6.4e-07
RWDD2B | 26676 | 0 | 0 | 8 | 1 | 4.9e-10 | 6.6e-07
TCERG1 | 82764 | 0 | 2 | 19 | 7 | 1.1e-09 | 1.4e-06
PTPN12 | 65208 | 0 | 0 | 11 | 3 | 1.3e-09 | 1.6e-06
PIK3CA | 95988 | 0 | 0 | 33 | 0 | 7.1e-09 | 7.8e-06
PIK3R1 | 67260 | 0 | 0 | 12 | 8 | 1.2e-07 | 0.00012
SMAD2 | 37392 | 0 | 0 | 15 | 5 | 1.6e-07 | 0.00015
ACCN5 | 45144 | 0 | 0 | 8 | 0 | 2.6e-07 | 0.00025
CCBP2 | 31236 | 0 | 0 | 10 | 0 | 4.8e-07 | 0.00043
HLA-B | 21888 | 0 | 0 | 5 | 5 | 7.5e-07 | 0.00064
ARID1A | 132696 | 0 | 2 | 17 | 13 | 9.6e-07 | 0.00078
MBOAT2 | 46056 | 0 | 0 | 10 | 0 | 1.3e-06 | 0.001
COX15 | 32376 | 0 | 0 | 5 | 0 | 1.5e-06 | 0.0012
ZC3H13 | 120384 | 0 | 1 | 23 | 16 | 2.4e-06 | 0.0018
BCL7A | 16416 | 0 | 1 | 8 | 1 | 3.9e-06 | 0.0027
ACVR2A | 43092 | 0 | 0 | 14 | 10 | 5.4e-06 | 0.0036
ZC3HC1 | 36480 | 0 | 2 | 10 | 0 | 7.1e-06 | 0.0046
B2M | 10260 | 0 | 0 | 7 | 4 | 0.000014 | 0.0085
TGM5 | 60192 | 0 | 2 | 11 | 0 | 0.000014 | 0.0085
ATP8A1 | 106248 | 0 | 4 | 11 | 0 | 0.000016 | 0.009
PCOLCE2 | 32832 | 0 | 1 | 9 | 0 | 0.000016 | 0.009
CXCR7 | 32376 | 0 | 2 | 11 | 0 | 0.000018 | 0.0098
NCOA3 | 111948 | 0 | 1 | 15 | 2 | 0.000031 | 0.017

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 - 615 (2011)
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