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 SL, Hardingham TE, Boot-Handford RP, Schwartz JM. PhenomeScape: a
cytoscape app to identify differentially regulated sub-networks using known
disease associations. Bioinformatics. 2016 Dec 15;32(24):3847-3849. Epub 2016 Aug
24. PubMed PMID: 27559157; PubMed Central PMCID: PMC5167065.
Soul J, Hardingham TE, Boot-Handford RP, Schwartz JM. PhenomeExpress: a
refined network analysis of expression datasets by inclusion of known disease
phenotypes. Sci Rep. 2015 Jan 29;5:8117. doi: 10.1038/srep08117. PubMed PMID:
25631385; PubMed Central PMCID: PMC4822650.