Java Enrichment of Pathways Extended To Topology

JEPETTO is a Cytoscape 3.x plugin which uses our servers: EnrichNet, PathExpand and TopoGSA to analyse a user-submitted human gene set. It identifies associations between genes and pathways using protein interaction network and topological analysis.

JEPETTO performs two types of analysis. It can enrich a gene set with components from the pathways and processes closely connected in the interaction network or compare topological properties of the gene set interactions to properties of known cellular pathways and processes. The plugin allows users to infer information about biological regulatory mechanisms and identify putative new co-factors that would not have been detected using the standard term-based analysis.


The installation process and the plugin features together with several usage examples are described in the tutorial.


You can download the plugin Java source code (GNU GPLv3) or the compiled JAR file.

It is also available directly from the Cytoscape app store.

Project team


If you use JEPETTO, please cite the following publications: