Perturbation-response genes reveal signaling footprints in cancer gene expression
European Bioinformatics Institute · Humboldt-Universität zu Berlin · +6 more institutions
Abstract
Aberrant cell signaling can cause cancer and other diseases and is a focal point of drug research. A common approach is to infer signaling activity of pathways from 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 pathway mapping methods, PROGENy can (i) recover the effect of known driver mutations, (ii) provide or improve strong markers for drug…
Citation impact
- FWCI
- 11.10
- Percentile
- 100%
- References
- 53
Authors
9- MSMichaël Schubert
European Bioinformatics Institute
- BKBertram Klinger
Humboldt-Universität zu Berlin, Charité - Universitätsmedizin Berlin
- MKMartina Klünemann
Humboldt-Universität zu Berlin, Charité - Universitätsmedizin Berlin
- ASAnja Sieber
Humboldt-Universität zu Berlin, Charité - Universitätsmedizin Berlin
- FUFlorian Uhlitz
Humboldt-Universität zu Berlin, Charité - Universitätsmedizin Berlin
Topics & keywords
- Gene
- Biology
- Computational biology
- Genetics
- Signal transduction
- Gene expression
- Phenotype
- Biological pathway
- Good health and well-being