{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T10:50:28Z","timestamp":1771066228839,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Determining genetic factors underlying various phenotypes is hindered by the involvement of multiple genes acting cooperatively. Over the past years, disease\u2013gene prioritization has been central to identify genes implicated in human disorders. Special attention has been paid on using physical interactions between the proteins encoded by the genes to link them with diseases. Such methods exploit the guilt-by-association principle in the protein interaction network to uncover novel disease\u2013gene associations. These methods rely on the proximity of a gene in the network to the genes associated with a phenotype and require a set of initial associations. Here, we present GUILDify, an easy-to-use web server for the phenotypic characterization of genes. GUILDify offers a prioritization approach based on the protein\u2013protein interaction network where the initial phenotype\u2013gene associations are retrieved via free text search on biological databases. GUILDify web server does not restrict the prioritization to any predefined phenotype, supports multiple species and accepts user-specified genes. It also prioritizes drugs based on the ranking of their targets, unleashing opportunities for repurposing drugs for novel therapies.<\/jats:p>\n               <jats:p>Availability and implementation: Available online at http:\/\/sbi.imim.es\/GUILDify.php<\/jats:p>\n               <jats:p>Contact: \u00a0baldo.oliva@upf.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu092","type":"journal-article","created":{"date-parts":[[2014,2,15]],"date-time":"2014-02-15T02:04:22Z","timestamp":1392429862000},"page":"1789-1790","source":"Crossref","is-referenced-by-count":38,"title":["GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms"],"prefix":"10.1093","volume":"30","author":[{"given":"Emre","family":"Guney","sequence":"first","affiliation":[{"name":"Departament de Ciencies Experimentals i de la Salut, Structural Bioinformatics Group (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona, 08003 Catalonia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Javier","family":"Garcia-Garcia","sequence":"additional","affiliation":[{"name":"Departament de Ciencies Experimentals i de la Salut, Structural Bioinformatics Group (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona, 08003 Catalonia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Baldo","family":"Oliva","sequence":"additional","affiliation":[{"name":"Departament de Ciencies Experimentals i de la Salut, Structural Bioinformatics Group (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona, 08003 Catalonia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,2,14]]},"reference":[{"key":"2023012711074164200_btu092-B1","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1038\/nbt1203","article-title":"Gene prioritization through genomic data fusion","volume":"24","author":"Aerts","year":"2006","journal-title":"Nat. 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Genet."},{"key":"2023012711074164200_btu092-B3","doi-asserted-by":"crossref","first-page":"W305","DOI":"10.1093\/nar\/gkp427","article-title":"ToppGene Suite for gene list enrichment analysis and candidate gene prioritization","volume":"37","author":"Chen","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012711074164200_btu092-B4","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1186\/1471-2105-11-56","article-title":"Biana: a software framework for compiling biological interactions and analyzing networks","volume":"11","author":"Garcia-Garcia","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012711074164200_btu092-B5","doi-asserted-by":"crossref","first-page":"3325","DOI":"10.1093\/bioinformatics\/btr584","article-title":"PRINCIPLE: a tool for associating genes with diseases via network propagation","volume":"27","author":"Gottlieb","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012711074164200_btu092-B6","doi-asserted-by":"crossref","first-page":"e43557","DOI":"10.1371\/journal.pone.0043557","article-title":"Exploiting protein-protein interaction networks for genome-wide disease-gene prioritization","volume":"7","author":"Guney","year":"2012","journal-title":"PLoS One"},{"key":"2023012711074164200_btu092-B7","doi-asserted-by":"crossref","first-page":"D514","DOI":"10.1093\/nar\/gki033","article-title":"Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders","volume":"33","author":"Hamosh","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012711074164200_btu092-B8","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1101\/gr.071852.107","article-title":"Protein networks in disease","volume":"18","author":"Ideker","year":"2008","journal-title":"Genome Res."},{"key":"2023012711074164200_btu092-B9","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1093\/bioinformatics\/btt164","article-title":"NetworkPrioritizer: a versatile tool for network-based prioritization of candidate disease genes or other molecules","volume":"29","author":"Kacprowski","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012711074164200_btu092-B10","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1093\/bib\/bbp048","article-title":"Advances in translational bioinformatics: computational approaches for the hunting of disease genes","volume":"11","author":"Kann","year":"2010","journal-title":"Brief. 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