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

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 gen...

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Detalles Bibliográficos
Autores principales: Soul, Jamie, Dunn, Sara L., Hardingham, Tim E., Boot-Handford, Ray P., Schwartz, Jean-Marc
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167065/
https://www.ncbi.nlm.nih.gov/pubmed/27559157
http://dx.doi.org/10.1093/bioinformatics/btw545
Descripción
Sumario: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: jamie.soul@postgrad.manchester.ac.uk or jean-marc.schwartz@manchester.ac.uk