PhenomeScape

identify differentially regulated sub-networks from gene expression data using known disease associations
### Overview PhenomeScape is a cytoscape app that enables the identification of active sub-networks, groups of differentially expressed genes that are physically interacting, from human or mouse disease-related expression data. For many diseases, there are genes, which are known through human Mendelian disease and animal models, where perturbation gives rise to observed phenotypes present in the disease being examined through gene expression studies. PhenomeScape is unique in using cross-species phenotype-gene associations, from human, mouse and zebra-fish to guide the identification of differentially regulated modules. ### Tutorial For a tutorial with example data please see: [https://github.com/soulj/PhenomeScape/blob/master/PhenomeScape_Documentation.pdf Documentation] ### For further information: Soul J, Dunn S, Hardingham T, Boot-Handford R, Schwartz J-M: PhenomeScape: a Cytoscape app to identify differentially regulated sub-networks using known disease associations. Bioinformatics 2016 [In Press] Soul J, Hardingham TE, Boot-Handford RP, Schwartz J-M: PhenomeExpress: a refined network analysis of expression datasets by inclusion of known disease phenotypes. Sci Rep 2015, 5:8117.

1.0.3

Works with Cytoscape 3.3

Release Notes

Fixed table export bug occuring on some platforms

1.0.2

Works with Cytoscape 3.3

Release Notes

Improved Human to Mouse known disease gene mapping

1.0.1

Works with Cytoscape 3.3

Release Notes

Fixed bug causing app to fail with network names containing spaces

1.0

Works with Cytoscape 3.3


CYTOSCAPE 3

Version 1.0.3

Released 8 Sep 2016

Works with Cytoscape 3.3

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