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https://github.com/erictleung/gene-fusion-analysis

:stars: Parsing and basic network analysis of fusion genes from the Catalogue of Somatic Mutations in Cancer (COSMIC) database
https://github.com/erictleung/gene-fusion-analysis

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:stars: Parsing and basic network analysis of fusion genes from the Catalogue of Somatic Mutations in Cancer (COSMIC) database

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README 

        
# Gene Fusion Network Analysis



This directory contains the cleaning of gene fusion data from the [Catalogue of

Somatic Mutations in Cancer (COMSIC)][1] and basic statistical and network analysis

on the resulting data.



[1]: http://cancer.sanger.ac.uk/cosmic



## System Specifications



Tested on Mac OS X 10.10.5 Yosemite.



- make

- R 3.2.3

    - [stringr 1.0.0][stringr]

    - [igraph 1.0.1][igraph]

    - [rmarkdown 0.9.2][rmarkdown]

    - [knitr 1.12.3][knitr]



[stringr]: https://cran.r-project.org/web/packages/stringr/index.html

[igraph]: https://cran.r-project.org/web/packages/igraph/index.html

[rmarkdown]: https://cran.r-project.org/web/packages/rmarkdown/index.html

[knitr]: https://cran.r-project.org/web/packages/knitr/



## Download, Run Analysis, and Generate Report



```shell

$ git clone [email protected]: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."][wu] 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."][wang] Nature

  biotechnology 27.11 (2009): 1005-1011.



[wu]: http://www.nature.com/nbt/journal/v27/n11/abs/nbt.1584.html

[wang]: https://bioinformatics.oxfordjournals.org/content/29/9/1174.full



## 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

```