{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T14:21:21Z","timestamp":1770992481175,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1018,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: JEPETTO (Java Enrichment of Pathways Extended To TOpology) is a Cytoscape 3.x plugin performing integrative human gene set analysis. It identifies functional associations between genes and known cellular pathways, and processes using protein interaction networks and topological analysis. The plugin integrates information from three separate web servers we published previously, specializing in enrichment analysis, pathways expansion and topological matching. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results. We demonstrate the utility of the JEPETTO plugin on a set of misregulated genes associated with Alzheimer\u2019s disease.<\/jats:p>\n               <jats:p>Availability: Source code and binaries are freely available for download at http:\/\/apps.cytoscape.org\/apps\/jepetto, implemented in Java and multi-platform. Installable directly via Cytoscape plugin manager. Released under the GNU General Public Licence.<\/jats:p>\n               <jats:p>Contact: \u00a0jepetto.plugin@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt732","type":"journal-article","created":{"date-parts":[[2013,12,21]],"date-time":"2013-12-21T03:17:47Z","timestamp":1387595867000},"page":"1029-1030","source":"Crossref","is-referenced-by-count":43,"title":["JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks"],"prefix":"10.1093","volume":"30","author":[{"given":"Charles","family":"Winterhalter","sequence":"first","affiliation":[{"name":"1 Institute of Systems & Synthetic Biology, University of Evry Val-d\u2019Essonne, 91000 Evry, France and 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pawe\u0142","family":"Widera","sequence":"additional","affiliation":[{"name":"1 Institute of Systems & Synthetic Biology, University of Evry Val-d\u2019Essonne, 91000 Evry, France and 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natalio","family":"Krasnogor","sequence":"additional","affiliation":[{"name":"1 Institute of Systems & Synthetic Biology, University of Evry Val-d\u2019Essonne, 91000 Evry, France and 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,12,19]]},"reference":[{"key":"2023012710445529700_btt732-B1","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1186\/1471-2105-11-597","article-title":"Extending pathways and processes using molecular interaction networks to analyse cancer genome data","volume":"11","author":"Glaab","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012710445529700_btt732-B2","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1093\/bioinformatics\/btq131","article-title":"TopoGSA: network topological gene set analysis","volume":"26","author":"Glaab","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012710445529700_btt732-B3","doi-asserted-by":"crossref","first-page":"i451","DOI":"10.1093\/bioinformatics\/bts389","article-title":"EnrichNet: network-based gene set enrichment analysis","volume":"28","author":"Glaab","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012710445529700_btt732-B4","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2023012710445529700_btt732-B5","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1111\/j.1365-2990.2010.01076.x","article-title":"Aberrant microRNA expression in the brains of neurodegenerative diseases: miR-29a decreased in Alzheimer disease brains targets neurone navigator 3","volume":"36","author":"Shioya","year":"2010","journal-title":"Neuropath. 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