{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:27Z","timestamp":1740185127662,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,11,16]],"date-time":"2016-11-16T00:00:00Z","timestamp":1479254400000},"content-version":"vor","delay-in-days":84,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000341","name":"Arthritis Research UK","doi-asserted-by":"crossref","award":["20414"],"award-info":[{"award-number":["20414"]}],"id":[{"id":"10.13039\/501100000341","id-type":"DOI","asserted-by":"crossref"}]},{"name":"European Community\u2019s Seventh Framework Programme","award":["602300"],"award-info":[{"award-number":["602300"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,15]]},"abstract":"<jats:p>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.<\/jats:p>\n               <jats:p>Availability and Implementation: Freely available for download at https:\/\/github.com\/soulj\/PhenomeScape<\/jats:p>\n               <jats:p>Contact: \u00a0jamie.soul@postgrad.manchester.ac.uk or jean-marc.schwartz@manchester.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw545","type":"journal-article","created":{"date-parts":[[2016,8,25]],"date-time":"2016-08-25T02:49:07Z","timestamp":1472093347000},"page":"3847-3849","source":"Crossref","is-referenced-by-count":12,"title":["PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations"],"prefix":"10.1093","volume":"32","author":[{"given":"Jamie","family":"Soul","sequence":"first","affiliation":[{"name":"Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK"}]},{"given":"Sara L.","family":"Dunn","sequence":"additional","affiliation":[{"name":"Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK"}]},{"given":"Tim E.","family":"Hardingham","sequence":"additional","affiliation":[{"name":"Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK"}]},{"given":"Ray P.","family":"Boot-Handford","sequence":"additional","affiliation":[{"name":"Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK"}]},{"given":"Jean-Marc","family":"Schwartz","sequence":"additional","affiliation":[{"name":"Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK"}]}],"member":"286","published-online":{"date-parts":[[2016,8,24]]},"reference":[{"key":"2023020114111137600_btw545-B1","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1007\/s00335-012-9422-2","article-title":"The mammalian gene function resource: the International Knockout Mouse Consortium","volume":"23","author":"Bradley","year":"2012","journal-title":"Mamm. 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