Mutation Analysis (MutSig vS2N)
Cervical Squamous Cell Carcinoma (Primary solid tumor)
22 February 2013 | analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1ZW1J32
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/C1ZW1J32
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: CESC-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:CESC-TP.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 41

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: 41. 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
--- | --- | --- | --- | --- | --- | --- | ---
PRSS48 | 4368 | 0 | 3 | 16 | 2 | 0 | 0
PIK3CA | 16419 | 0 | 0 | 11 | 0 | 0 | 0
PRG4 | 17823 | 0 | 0 | 14 | 10 | 0 | 0
UGT2B10 | 16068 | 0 | 3 | 19 | 0 | 5.700001e-318 | 2.7e-314
CRIPAK | 4017 | 0 | 0 | 5 | 5 | 1.2e-251 | 4.4e-248
PRB2 | 2652 | 0 | 0 | 6 | 5 | 8.4e-216 | 2.6e-212
ARID1A | 22698 | 0 | 0 | 9 | 7 | 9.1e-132 | 2.4e-128
IFITM2 | 1872 | 0 | 3 | 9 | 1 | 3.9e-108 | 9.1e-105
C8orf44 | 1950 | 0 | 2 | 5 | 0 | 4.2e-88 | 8.9e-85
NFE2L2 | 8385 | 0 | 0 | 7 | 2 | 5.1e-47 | 9.7e-44
SSX7 | 2886 | 0 | 0 | 5 | 0 | 2.9e-46 | 5e-43
TCHH | 22698 | 0 | 1 | 10 | 3 | 1.4e-36 | 2.1e-33
CDC27 | 11661 | 0 | 0 | 7 | 3 | 5e-34 | 7.3e-31
DNAJB1 | 4329 | 0 | 0 | 5 | 1 | 3.8e-31 | 5.1e-28
MAGEC1 | 14157 | 0 | 0 | 7 | 3 | 3.7e-28 | 4.7e-25
RAET1L | 2925 | 0 | 0 | 5 | 0 | 8.4e-22 | 9.9e-19
SSX3 | 3120 | 1 | 1 | 6 | 0 | 2.8e-19 | 3.1e-16
SIGLEC11 | 6240 | 0 | 2 | 6 | 0 | 2.2e-17 | 2.3e-14
TEX15 | 43329 | 0 | 0 | 6 | 0 | 1.1e-11 | 1.1e-08
TXNDC2 | 7371 | 0 | 0 | 6 | 0 | 3.4e-11 | 3.2e-08
SRRM2 | 28197 | 0 | 0 | 6 | 2 | 7.9e-10 | 7.1e-07
ADAMTS16 | 15093 | 0 | 0 | 5 | 0 | 1.8e-09 | 1.5e-06
MLL2 | 48789 | 0 | 3 | 7 | 5 | 1.9e-09 | 1.6e-06
MYH9 | 27456 | 0 | 1 | 6 | 2 | 1.7e-08 | 0.000013
SYNE2 | 104910 | 0 | 0 | 10 | 2 | 1.7e-08 | 0.000013
TREML4 | 2613 | 0 | 3 | 5 | 1 | 3.6e-08 | 0.000026
CELSR2 | 31278 | 0 | 1 | 6 | 1 | 5.3e-08 | 0.000037
DNMBP | 20631 | 0 | 0 | 5 | 2 | 4e-07 | 0.00027
MKI67 | 42744 | 0 | 0 | 6 | 2 | 9.9e-07 | 0.00064
APOB | 68445 | 0 | 0 | 7 | 0 | 2.1e-06 | 0.0013
PCLO | 63882 | 0 | 0 | 9 | 1 | 1e-05 | 0.0063
MLL3 | 63063 | 0 | 2 | 10 | 7 | 0.000014 | 0.0082
ZSCAN5A | 6591 | 0 | 11 | 39 | 0 | 0.000019 | 0.011
LRP6 | 21723 | 0 | 0 | 5 | 1 | 0.000028 | 0.016
YTHDC1 | 9477 | 0 | 0 | 4 | 0 | 4e-05 | 0.022

PRSS48

Figure S1. This figure depicts the distribution of mutations and mutation types across the PRSS48 significant gene.

PIK3CA

Figure S2. This figure depicts the distribution of mutations and mutation types across the PIK3CA significant gene.

PRG4

Figure S3. This figure depicts the distribution of mutations and mutation types across the PRG4 significant gene.

UGT2B10

Figure S4. This figure depicts the distribution of mutations and mutation types across the UGT2B10 significant gene.

CRIPAK

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

ARID1A

Figure S6. This figure depicts the distribution of mutations and mutation types across the ARID1A significant gene.

IFITM2

Figure S7. This figure depicts the distribution of mutations and mutation types across the IFITM2 significant gene.

C8orf44

Figure S8. This figure depicts the distribution of mutations and mutation types across the C8orf44 significant gene.

NFE2L2

Figure S9. This figure depicts the distribution of mutations and mutation types across the NFE2L2 significant gene.

SSX7

Figure S10. This figure depicts the distribution of mutations and mutation types across the SSX7 significant gene.

TCHH

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

CDC27

Figure S12. This figure depicts the distribution of mutations and mutation types across the CDC27 significant gene.

DNAJB1

Figure S13. This figure depicts the distribution of mutations and mutation types across the DNAJB1 significant gene.

MAGEC1

Figure S14. This figure depicts the distribution of mutations and mutation types across the MAGEC1 significant gene.

RAET1L

Figure S15. This figure depicts the distribution of mutations and mutation types across the RAET1L significant gene.

SSX3

Figure S16. This figure depicts the distribution of mutations and mutation types across the SSX3 significant gene.

SIGLEC11

Figure S17. This figure depicts the distribution of mutations and mutation types across the SIGLEC11 significant gene.

TEX15

Figure S18. This figure depicts the distribution of mutations and mutation types across the TEX15 significant gene.

TXNDC2

Figure S19. This figure depicts the distribution of mutations and mutation types across the TXNDC2 significant gene.

SRRM2

Figure S20. This figure depicts the distribution of mutations and mutation types across the SRRM2 significant gene.

ADAMTS16

Figure S21. This figure depicts the distribution of mutations and mutation types across the ADAMTS16 significant gene.

MLL2

Figure S22. This figure depicts the distribution of mutations and mutation types across the MLL2 significant gene.

MYH9

Figure S23. This figure depicts the distribution of mutations and mutation types across the MYH9 significant gene.

SYNE2

Figure S24. This figure depicts the distribution of mutations and mutation types across the SYNE2 significant gene.

TREML4

Figure S25. This figure depicts the distribution of mutations and mutation types across the TREML4 significant gene.

CELSR2

Figure S26. This figure depicts the distribution of mutations and mutation types across the CELSR2 significant gene.

DNMBP

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

MKI67

Figure S28. This figure depicts the distribution of mutations and mutation types across the MKI67 significant gene.

APOB

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

PCLO

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

MLL3

Figure S31. This figure depicts the distribution of mutations and mutation types across the MLL3 significant gene.

ZSCAN5A

Figure S32. This figure depicts the distribution of mutations and mutation types across the ZSCAN5A significant gene.

LRP6

Figure S33. This figure depicts the distribution of mutations and mutation types across the LRP6 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)
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