Gene Fusion Network Analysis

This directory contains the cleaning of gene fusion data from the Catalogue of Somatic Mutations in Cancer (COMSIC) and basic statistical and network analysis on the resulting data.

System Specifications

Tested on Mac OS X 10.10.5 Yosemite.

• make
• R 3.2.3
  • stringr 1.0.0
  • igraph 1.0.1
  • rmarkdown 0.9.2
  • knitr 1.12.3

Download, Run Analysis, and Generate Report

$ git clone git@github.com:erictleung/gene-fusion-analysis.git
$ cd gene-fusion-analysis
$ make

Written Scripts

• report/cosmic_fusion_extraction.Rmd
  • Cleans COSMIC data
  • Writes file results/newDescription.txt with the gene fusion data
  • Takes in Ensembl and functional interaction network data for analysis
  • Performs simple statistics and basic network statistics

Notes on Downloaded Files

• raw-data/FIsInGene_121013_with_annotations.txt
  • Description:
    • This is the functional interaction network file from the Reactome website. The file will be used so that the gene fusions can be overlaid on top to calculate metrics that will categorize the cancerous gene fusions.
    • “Functional interactions (FIs) derived from Reactome, and other pathway and interaction databases.” We downloaded the Version 2013.
  • Source: http://www.reactome.org/pages/download-data/
• bin/ensembl_GRCh37_BioMart_2014.08.29.pl
  • Description:
    • This is a Perl script that Ensembl automatically generated, based on the parameters I set:
      • Associated Gene name
      • Ensembl Transcript ID
      • 5' UTR Start
      • 5' UTR End
      • Exon Chr Start (bp)
      • Exon Chr End (bp)
      • 3' UTR Start
      • 3' UTR End
      • Strand (directionality)
      • Exon Rank in Transcript (which exon number it is)
  • Downloads: raw-data/ensembl_GRCh37_BioMart_2014.08.29.csv
  • Source: http://grch37.ensembl.org/biomart/martview/
• raw-data/CosmicFusionExport_v69_310514.tsv
  • Description:
    • "All gene fusion mutation data from the current release in a tab separated file."
  • Source: cancer.sanger.ac.uk/cancergenome/projects/cosmic/download

NOTE: Error in COSMIC Data

If you try and compile and run the cosmic_fusion_extraction.Rmd analysis, it will not fail but it will if you start with the raw data. The reason being is that the COSMIC gene fusion data set (CosmicFusionExport_v69_310514.tsv) is missing an open bracket on Line 11620.

The converted .csv version of the data (CosmicFusionExport_v69_310514.csv) included in this analysis is manually edited so that the .Rmd analysis file will run correctly.

Related Literature

• Wu, Chia-Chin, et al. "Identification of cancer fusion drivers using network fusion centrality." Bioinformatics 29.9 (2013): 1174-1181.
• Wang, Xiao-Song, et al. "An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer." Nature biotechnology 27.11 (2009): 1005-1011.

Analysis Directory Structure

.
├── Makefile
├── README.md
├── bin
│   └── ensembl_GRCh37_BioMart_2014.08.29.pl
├── data
│   └── CosmicFusionExport_v69_310514.csv
├── raw-data
│   ├── CosmicFusionExport_v69_310514.tsv
│   ├── FIsInGene_121013_with_annotations.txt
│   └── ensembl_GRCh37_2014.08.29.csv
├── report
│   ├── cosmic_fusion_extraction.Rmd
│   └── cosmic_fusion_extraction.html
└── results
    └── newDescription.txt

5 directories, 10 files