Mutation Analysis (MutSig v2.0)
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Mutation Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C11C1VG5
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:CESC-TP.final_analysis_set.maf

  • Blacklist used for this analysis: pancan_mutation_blacklist.v14.hg19.txt

  • Significantly mutated genes (q ≤ 0.1): 10

  • Mutations seen in COSMIC: 35

  • Significantly mutated genes in COSMIC territory: 1

  • Significantly mutated genesets: 0

  • Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing
  • Read 39 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 10020

  • After removing 5 mutations outside chr1-24: 10015

  • After removing 474 blacklisted mutations: 9541

  • After removing 599 noncoding mutations: 8942

Mutation Filtering
  • Number of mutations before filtering: 8942

  • After removing 116 mutations outside gene set: 8826

  • After removing 17 mutations outside category set: 8809

- Results
+ Breakdown of Mutations by Type
+ Breakdown of Mutation Rates by Category Type
+ Target Coverage for Each Individual
+ Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples
+ Lego Plots
+ CoMut Plot
+ Significantly Mutated Genes
+ COSMIC analyses
+ Geneset Analyses
+ Methods & Data