Skip to main content

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. Similarly to the ssGSEA method, we assume that pathway activity can be compared across different samples based on ranking the expression of pathway genes.
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.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for pathway-assessor, version 0.0.3
Filename, size & hash File type Python version Upload date
pathway_assessor-0.0.3-py3-none-any.whl (1.0 MB) View hashes Wheel py3
pathway-assessor-0.0.3.tar.gz (973.3 kB) View hashes Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page