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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.

SUBMITTER: Soul J 

PROVIDER: S-EPMC5167065 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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

Soul Jamie J   Dunn Sara L SL   Hardingham Tim E TE   Boot-Handford Ray P RP   Schwartz Jean-Marc JM  

Bioinformatics (Oxford, England) 20160824 24


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  ...[more]

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