PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations.

ABSTRACT

PhenomeScape is a Cytoscape app which provides easy access to the PhenomeExpress algorithm to interpret gene expression data. PhenomeExpress integrates protein interaction networks with known phenotype to gene associations to find active sub-networks enriched in differentially expressed genes. It also incorporates cross-species phenotypes and associations to include results from animal models of disease. With expression data imported into PhenomeScape, the user can quickly generate and visualise interactive sub-networks. PhenomeScape thus enables researchers to use prior knowledge of a disease to identify differentially regulated sub-networks and to generate an overview of altered biologically processes specific to that disease. AVAILABILITY AND IMPLEMENTATION Freely available for download at https//github.com/soulj/PhenomeScape CONTACT jamie.soul@postgrad.manchester.ac.uk or jean-marc.schwartz@manchester.ac.uk.