R package for Pathway RespOnsive GENe activity inference
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PROGENy: Pathway RespOnsive GENes for activity inference

Aberrant cell signaling is known to cause cancer and many other diseases, as well as a focus of treatment. A common approach is to infer its activity on the level of pathways using gene expression. However, mapping gene expression to pathway components disregards the effect of post-translational modifications, and downstream signatures represent very specific experimental conditions. Here we present PROGENy, a method that overcomes both limitations by leveraging a large compendium of publicly available perturbation experiments to yield a common core of Pathway RespOnsive GENes. Unlike existing methods, PROGENy can (i) recover the effect of known driver mutations, (ii) provide or improve strong markers for drug indications, and (iii) distinguish between oncogenic and tumor suppressor pathways for patient survival. Collectively, these results show that PROGENy more accurately infers pathway activity from gene expression than other methods.

This is an R package for using the method described in Nature Communications.

  doi = {10.1038/s41467-017-02391-6},
  url = {https://doi.org/10.1038/s41467-017-02391-6},
  year  = {2018},
  month = {jan},
  publisher = {Springer Nature},
  volume = {9},
  number = {1},
  author = {Michael Schubert and Bertram Klinger and Martina Kl\"{u}nemann and Anja Sieber and Florian Uhlitz and Sascha Sauer and Mathew J. Garnett and Nils Bl\"{u}thgen and Julio Saez-Rodriguez},
  title = {Perturbation-response genes reveal signaling footprints in cancer gene expression},
  journal = {Nature Communications}