PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations.
Soul, Jamie *; Dunn, Sara L.; Hardingham, Tim E.; Boot-Handford, Ray P.; Schwartz, Jean-Marc *
[Miscellaneous Article]
Bioinformatics.
32(24):3847-3849, December 15, 2016.
(Format: HTML, PDF)
Summary: 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: [email protected] or [email protected]
(C) Copyright Oxford University Press 2016.
