title: JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks.
abstract: CONCLUSIONS
  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's disease.
  
  
  BACKGROUND
  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.
authors.affiliation: Institute of Systems & Synthetic Biology, University of Evry Val-d'Essonne, 91000 Evry, France and School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK.
authors.forename: Charles
authors.initials: C
authors.lastname: Winterhalter
authors.forename: Paweł
authors.initials: P
authors.lastname: Widera
authors.forename: Natalio
authors.initials: N
authors.lastname: Krasnogor
mesh_terms: D000544:Alzheimer Disease / Q000235:genetics; D005786:Gene Expression Regulation; D006801:Humans; D060066:Protein Interaction Maps; D012984:Software