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Yet, despite this progress, many of the identified signatures are not robust enough to be clinically used and not consistent enough to provide a follow-up on molecular mechanisms.<\/jats:p><jats:p>Results: To address these issues, we introduce PhenoNet, a novel algorithm for the identification of pathways and networks associated with different phenotypes. PhenoNet uses two types of input data: gene expression data (RMA, RPKM, FPKM, etc.) and phenotypic information, and integrates these data with curated pathways and protein\u2013protein interaction information. Comprehensive iterations across all possible pathways and subnetworks result in the identification of key pathways or subnetworks that distinguish between the two phenotypes.<\/jats:p><jats:p>Availability and implementation: Matlab code is available upon request.<\/jats:p><jats:p>Contact: \u00a0sol.efroni@biu.ac.il<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu199","type":"journal-article","created":{"date-parts":[[2014,5,9]],"date-time":"2014-05-09T04:37:58Z","timestamp":1399610278000},"page":"2399-2405","source":"Crossref","is-referenced-by-count":17,"title":["PhenoNet: identification of key networks associated with disease phenotype"],"prefix":"10.1093","volume":"30","author":[{"given":"Rotem","family":"Ben-Hamo","sequence":"first","affiliation":[{"name":"1The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Moriah","family":"Gidoni","sequence":"additional","affiliation":[{"name":"1The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sol","family":"Efroni","sequence":"additional","affiliation":[{"name":"1The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,5,7]]},"reference":[{"key":"2023012711524905700_btu199-B1","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/1745-6150-6-31","article-title":"Structural influence of gene networks on their inference: analysis of C3NET","volume":"6","author":"Altay","year":"2011","journal-title":"Biol. 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