title: 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.
  
  
  
  Freely available for download at https://github.com/soulj/PhenomeScape CONTACT: jamie.soul@postgrad.manchester.ac.uk or jean-marc.schwartz@manchester.ac.uk.
authors: Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
authors: Jamie
authors: J
authors: Soul
authors: Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
authors: Sara L
authors: SL
authors: Dunn
authors: Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
authors: Tim E
authors: TE
authors: Hardingham
authors: Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
authors: Ray P
authors: RP
authors: Boot-Handford
authors: Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
authors: Jean-Marc
authors: JM
authors: Schwartz
mesh_terms: D000465:Algorithms; D000818:Animals; D004195:Disease Models, Animal; D015870:Gene Expression; D006801:Humans; D010641:Phenotype; D060066:Protein Interaction Maps; D012984:Software