bio2bel-msig 0.0.3

A wrapper around MSIGDB

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

Installation

This code can be installed with pip3 install git+https://github.com/bio2bel/msig.git

The package expects you have downloaded the gene sets from MSigDB following the instructions and terms stated in their website. The gene sets in gmt format should placed in /resources. However, feel free to change the directory by modifying the constants module.

Functionalities and Commands

Following, the main functionalities and commands to work with this package:

• Populate local database with MSigDB python3 -m bio2bel_msig populate --path='/my/path/to/genesets/msigdb.v6.1.symbols.gmt'

• 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., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., … & Mesirov, J. P. (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., Subramanian, A., Pinchback, R., Thorvaldsdóttir, H., Tamayo, P., & Mesirov, J. P. (2011). Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27(12), 1739-1740.