SKCM-TM: 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: SKCM-TM

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: 231. 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
NRAS 16425 0 1 65 0 2.7e-282 5.1e-278
BRAF 58725 0 2 120 0 1.7e-224 1.6e-220
CDKN2A 13500 0 1 31 21 1.4e-75 9e-72
RTL1 11925 0 3 13 0 2.4e-36 1.1e-32
EYS 50625 0 1 10 0 7.8e-29 2.9e-25
DNAH6 36225 0 1 16 1 1.5e-28 4.8e-25
SPRR3 11250 0 3 12 1 2.3e-23 6.3e-20
SMR3A 6300 0 2 8 0 4e-21 9.4e-18
CCNE2 40275 0 2 12 1 5.6e-20 1.2e-16
NOTCH2 174150 0 9 34 2 4.8e-18 9.1e-15
PPT2 23625 0 2 8 0 2.6e-17 4.4e-14
TAF1A 40950 0 0 14 0 8.2e-17 1.3e-13
LIPF 35775 0 5 14 0 1.3e-16 1.9e-13
ADAM30 65250 0 11 34 3 1.9e-16 2.5e-13
NAP1L4 32625 0 0 13 2 2.6e-16 3.3e-13
DEFB115 7650 0 2 7 1 4.7e-16 5.6e-13
PTEN 36225 0 0 18 11 1.4e-15 1.5e-12
INTS8 83025 0 1 20 2 1.5e-15 1.5e-12
TBC1D3 9675 2 0 7 0 3.8e-14 3.8e-11
TP53 28350 0 1 37 14 7.7e-14 7.3e-11
DISP1 124650 0 9 41 5 1.1e-12 9.8e-10
STK31 91350 0 4 36 2 1.2e-12 1e-09
PRC1 52425 0 2 14 1 1.2e-11 9.5e-09
CDC123 30825 0 0 7 2 1.5e-11 1.2e-08
IVL 19575 0 4 11 0 1.9e-11 1.4e-08
DPY19L4 67275 0 2 18 4 2.2e-11 1.6e-08
CLCC1 49725 0 1 13 2 3.7e-11 2.6e-08
ZNF860 450 0 0 4 0 1.1e-10 7.3e-08
IDH1 36000 0 1 11 0 1.3e-10 8.7e-08
RPTN 58275 0 4 47 0 1.7e-10 1.1e-07
PPP6C 25875 0 2 18 4 8.2e-10 4.9e-07
CECR6 9450 0 1 6 0 8.4e-10 4.9e-07
THADA 141525 0 5 28 4 1.4e-09 7.8e-07
PIK3CB 92925 0 3 21 4 1.6e-09 8.8e-07
ADAM21 58500 0 3 19 1 1.6e-09 8.8e-07
NRAS

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

BRAF

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

CDKN2A

Figure S3.  This figure depicts the distribution of mutations and mutation types across the CDKN2A significant gene.

RTL1

Figure S4.  This figure depicts the distribution of mutations and mutation types across the RTL1 significant gene.

EYS

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

DNAH6

Figure S6.  This figure depicts the distribution of mutations and mutation types across the DNAH6 significant gene.

SPRR3

Figure S7.  This figure depicts the distribution of mutations and mutation types across the SPRR3 significant gene.

SMR3A

Figure S8.  This figure depicts the distribution of mutations and mutation types across the SMR3A significant gene.

CCNE2

Figure S9.  This figure depicts the distribution of mutations and mutation types across the CCNE2 significant gene.

NOTCH2

Figure S10.  This figure depicts the distribution of mutations and mutation types across the NOTCH2 significant gene.

PPT2

Figure S11.  This figure depicts the distribution of mutations and mutation types across the PPT2 significant gene.

TAF1A

Figure S12.  This figure depicts the distribution of mutations and mutation types across the TAF1A significant gene.

LIPF

Figure S13.  This figure depicts the distribution of mutations and mutation types across the LIPF significant gene.

ADAM30

Figure S14.  This figure depicts the distribution of mutations and mutation types across the ADAM30 significant gene.

NAP1L4

Figure S15.  This figure depicts the distribution of mutations and mutation types across the NAP1L4 significant gene.

DEFB115

Figure S16.  This figure depicts the distribution of mutations and mutation types across the DEFB115 significant gene.

PTEN

Figure S17.  This figure depicts the distribution of mutations and mutation types across the PTEN significant gene.

INTS8

Figure S18.  This figure depicts the distribution of mutations and mutation types across the INTS8 significant gene.

TBC1D3

Figure S19.  This figure depicts the distribution of mutations and mutation types across the TBC1D3 significant gene.

TP53

Figure S20.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

DISP1

Figure S21.  This figure depicts the distribution of mutations and mutation types across the DISP1 significant gene.

STK31

Figure S22.  This figure depicts the distribution of mutations and mutation types across the STK31 significant gene.

PRC1

Figure S23.  This figure depicts the distribution of mutations and mutation types across the PRC1 significant gene.

CDC123

Figure S24.  This figure depicts the distribution of mutations and mutation types across the CDC123 significant gene.

IVL

Figure S25.  This figure depicts the distribution of mutations and mutation types across the IVL significant gene.

DPY19L4

Figure S26.  This figure depicts the distribution of mutations and mutation types across the DPY19L4 significant gene.

CLCC1

Figure S27.  This figure depicts the distribution of mutations and mutation types across the CLCC1 significant gene.

ZNF860

Figure S28.  This figure depicts the distribution of mutations and mutation types across the ZNF860 significant gene.

IDH1

Figure S29.  This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

RPTN

Figure S30.  This figure depicts the distribution of mutations and mutation types across the RPTN significant gene.

PPP6C

Figure S31.  This figure depicts the distribution of mutations and mutation types across the PPP6C significant gene.

CECR6

Figure S32.  This figure depicts the distribution of mutations and mutation types across the CECR6 significant gene.

THADA

Figure S33.  This figure depicts the distribution of mutations and mutation types across the THADA significant gene.

PIK3CB

Figure S34.  This figure depicts the distribution of mutations and mutation types across the PIK3CB 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)
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