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.
For a tutorial with example data please see:
### 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.