bio2bel/msig

Integration of pathway-related information from MSigDB in BEL

Bio2BEL MSigDB

This package allows the enrichment of BEL networks with MSigDB information. Furthermore, it is integrated in the ComPath environment for pathway database comparison.

If you find this package useful, please consider citing [domingofernandez2018]:

[domingofernandez2018]

Domingo-Fernandez, D., et al (2018). ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases. Npj Systems Biology and Applications, __5__(1), 3.

Warning This package creates partOf relationships in BEL. MSigDB does not contain mechanistic relationships, but it include simplifications of several sources (KEGG, WikiPathways, Reactome, PID) that do have mechanistic relationships. Those sources can be converted to BEL with the PathMe project.

Installation

bio2bel_msig can be installed easily from PyPI with the following code in your favorite terminal:

$ pip install bio2bel_msig

or from the latest code on GitHub in development mode with:

$ git clone https://github.com/bio2bel/msig.git
$ cd msig
$ pip install -e .

Setup

The package expects you have downloaded the gene sets from MSigDB following the instructions and terms stated in their website.

The environment variable BIO2BEL_MSIG_PATH should be set to the directory where the gene set files in the GMT format are stored. Optionally, this can be directly overridden with the keyword argument to populate() in the REPL or as a flag in the command line utility.

Python REPL

>>> import bio2bel_msig
>>> msig_manager = bio2bel_msig.Manager()
>>> msig_manager.populate()

Command Line Utility

bio2bel_msig populate

Other Command Line Utilities

• Run an admin site for simple querying and exploration python3 -m bio2bel_msig web (http://localhost:5000/admin/)
• Export gene sets for programmatic use python3 -m bio2bel_msig export

Citation

• Subramanian, A., et al. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545-15550.
• Liberzon, A., et al (2011). Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27(12), 1739-1740.

msig's Issues

Add tests

Optional parameter in populate for gene set file

Add export function