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For assessing the overrepresentation and underrepresentation of pathway genes in a given expression table

Project description



Boris Reva1, Anna Calinawan1

1Icahn School of Medicine at Mount Sinai (USA)


Comparison of tumors by activities of molecular pathways can help nominate disease driver pathways, identify targets for therapeutic intervention, and determine clinically relevant subtypes and diagnostic biomarkers. We introduce a new method for calculating overrepresentation and underrepresentation scores to assess a pathway’s activation and suppression, respectively. The novelty of this approach is in independent assessment of overrepresentation and underrepresentation of pathway’s genes from both top and bottom of the ranked gene list of a given sample.


Requires: Python >= 3.6

To install the latest version of PathwayAssessor, run:

pip install pathway-assessor


To see more information about the main functions, visit the ReadMe included with the package code.

import pathway_assessor as pa



  1. Barbie, D.A. , et al. “Systematic RNA interference reveals…”, Nature. 2009 Nov 5;462(7269):108-12.
  2. Abril-Rodrigues, G., Ribas A., “SnapShot: Immune Checkpoint Inhibitors”, Cancer Cell 31, June 12, 2017.
  3. Aran, D., Hu Z., Butte, A. “xCell: digitally portraying the tissue…”, Genome Biology. (2017) 18:220.


If you find small bugs, larger issues, or have suggestions, please email the maintainer at Contributions (via pull requests or otherwise) are welcome.

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