Mutation Analysis (MutSig vS2N)
Bladder Urothelial Carcinoma (Primary solid tumor)
22 February 2013 | analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1057D3R
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig vS2N). Broad Institute of MIT and Harvard. doi:10.7908/C1057D3R
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: BLCA-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:BLCA-TP.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 29

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: 29. 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
--- | --- | --- | --- | --- | --- | --- | ---
TP53 | 3528 | 0 | 1 | 14 | 3 | 0 | 0
KDM6A | 12824 | 0 | 2 | 6 | 6 | 1.6e-131 | 1.5e-127
PRX | 9548 | 0 | 0 | 9 | 1 | 5.2e-61 | 3.3e-57
ARID1A | 16296 | 0 | 1 | 8 | 5 | 1e-53 | 4.9e-50
GOLGB1 | 34720 | 0 | 2 | 12 | 3 | 2e-28 | 7.5e-25
ASXL2 | 12600 | 0 | 0 | 6 | 2 | 2.8e-18 | 8.8e-15
FBXW7 | 8036 | 0 | 0 | 6 | 2 | 8.7e-17 | 2.3e-13
MLL | 36344 | 0 | 1 | 9 | 2 | 1.4e-16 | 3.3e-13
FLG | 30520 | 0 | 1 | 8 | 0 | 1.4e-15 | 2.9e-12
HRNR | 15036 | 0 | 0 | 6 | 0 | 1.9e-15 | 3.7e-12
HCN1 | 8148 | 0 | 1 | 5 | 3 | 1.1e-14 | 1.9e-11
TTN | 356944 | 0 | 3 | 34 | 4 | 2.8e-14 | 4.4e-11
BCLAF1 | 9072 | 0 | 0 | 5 | 1 | 2.9e-13 | 4.2e-10
MACF1 | 85736 | 0 | 0 | 9 | 1 | 1.8e-11 | 2.4e-08
RPAP1 | 10640 | 0 | 0 | 5 | 0 | 2e-11 | 2.5e-08
HMCN1 | 55132 | 0 | 0 | 9 | 2 | 3.6e-11 | 4.2e-08
ADAMTS12 | 15260 | 0 | 1 | 4 | 0 | 9.3e-10 | 1e-06
DCC | 13580 | 0 | 1 | 5 | 0 | 4.1e-09 | 4.3e-06
MLL2 | 35028 | 0 | 0 | 6 | 6 | 1.7e-08 | 0.000017
ABCA10 | 17556 | 0 | 0 | 5 | 2 | 3.3e-07 | 0.00031
XPR1 | 7476 | 0 | 1 | 5 | 2 | 9.3e-07 | 0.00084
CREBBP | 20384 | 0 | 1 | 5 | 3 | 2.6e-06 | 0.0022
SETD2 | 20664 | 0 | 0 | 5 | 3 | 3.1e-06 | 0.0025
SACS | 47628 | 0 | 2 | 6 | 2 | 0.000023 | 0.017
DNAH5 | 49336 | 0 | 1 | 7 | 1 | 0.000023 | 0.017
SPTA1 | 24696 | 0 | 0 | 5 | 0 | 0.000024 | 0.018
APOB | 49140 | 0 | 0 | 6 | 0 | 0.000031 | 0.022
GPS2 | 3192 | 0 | 0 | 4 | 3 | 0.000033 | 0.022
TPR | 26152 | 0 | 1 | 5 | 0 | 0.000044 | 0.029
CSMD3 | 37184 | 0 | 1 | 5 | 1 | 0.00019 | 0.12
LAMA3 | 31220 | 0 | 0 | 5 | 2 | 0.00022 | 0.14
SDPR | 4116 | 0 | 0 | 4 | 1 | 0.00031 | 0.18
OTUD7A | 4956 | 0 | 0 | 4 | 0 | 0.0012 | 0.68
SPATS2 | 5376 | 0 | 0 | 4 | 1 | 0.002 | 1
KPNA3 | 5628 | 0 | 0 | 4 | 1 | 0.0026 | 1

TP53

Figure S1. This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

KDM6A

Figure S2. This figure depicts the distribution of mutations and mutation types across the KDM6A significant gene.

PRX

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

ARID1A

Figure S4. This figure depicts the distribution of mutations and mutation types across the ARID1A significant gene.

GOLGB1

Figure S5. This figure depicts the distribution of mutations and mutation types across the GOLGB1 significant gene.

ASXL2

Figure S6. This figure depicts the distribution of mutations and mutation types across the ASXL2 significant gene.

FBXW7

Figure S7. This figure depicts the distribution of mutations and mutation types across the FBXW7 significant gene.

MLL

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

FLG

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

HRNR

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

HCN1

Figure S11. This figure depicts the distribution of mutations and mutation types across the HCN1 significant gene.

TTN

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

BCLAF1

Figure S13. This figure depicts the distribution of mutations and mutation types across the BCLAF1 significant gene.

MACF1

Figure S14. This figure depicts the distribution of mutations and mutation types across the MACF1 significant gene.

RPAP1

Figure S15. This figure depicts the distribution of mutations and mutation types across the RPAP1 significant gene.

HMCN1

Figure S16. This figure depicts the distribution of mutations and mutation types across the HMCN1 significant gene.

ADAMTS12

Figure S17. This figure depicts the distribution of mutations and mutation types across the ADAMTS12 significant gene.

DCC

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

MLL2

Figure S19. This figure depicts the distribution of mutations and mutation types across the MLL2 significant gene.

ABCA10

Figure S20. This figure depicts the distribution of mutations and mutation types across the ABCA10 significant gene.

XPR1

Figure S21. This figure depicts the distribution of mutations and mutation types across the XPR1 significant gene.

CREBBP

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

SETD2

Figure S23. This figure depicts the distribution of mutations and mutation types across the SETD2 significant gene.

SACS

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

DNAH5

Figure S25. This figure depicts the distribution of mutations and mutation types across the DNAH5 significant gene.

SPTA1

Figure S26. This figure depicts the distribution of mutations and mutation types across the SPTA1 significant gene.

APOB

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

GPS2

Figure S28. This figure depicts the distribution of mutations and mutation types across the GPS2 significant gene.

TPR

Figure S29. This figure depicts the distribution of mutations and mutation types across the TPR 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.

- 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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle