{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T18:23:41Z","timestamp":1770834221296,"version":"3.50.1"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":622,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,5,15]]},"abstract":"Abstract<\/jats:title>\n Summary: Functional Gene Networks (FGNet) is an R\/Bioconductor package that generates gene networks derived from the results of functional enrichment analysis (FEA) and annotation clustering. The sets of genes enriched with specific biological terms (obtained from a FEA platform) are transformed into a network by establishing links between genes based on common functional annotations and common clusters. The network provides a new view of FEA results revealing gene modules with similar functions and genes that are related to multiple functions. In addition to building the functional network, FGNet analyses the similarity between the groups of genes and provides a distance heatmap and a bipartite network of functionally overlapping genes. The application includes an interface to directly perform FEA queries using different external tools: DAVID, GeneTerm Linker, TopGO or GAGE; and a graphical interface to facilitate the use.<\/jats:p>\n Availability and implementation: \u00a0FGNet is available in Bioconductor, including a tutorial. URL: http:\/\/bioconductor.org\/packages\/release\/bioc\/html\/FGNet.html<\/jats:p>\n Contact: \u00a0jrivas@usal.es<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu864","type":"journal-article","created":{"date-parts":[[2015,1,20]],"date-time":"2015-01-20T01:59:41Z","timestamp":1421719181000},"page":"1686-1688","source":"Crossref","is-referenced-by-count":57,"title":["Functional Gene Networks: R\/Bioc package to generate and analyse gene networks derived from functional enrichment and clustering"],"prefix":"10.1093","volume":"31","author":[{"given":"Sara","family":"Aibar","sequence":"first","affiliation":[{"name":"Bioinformatics and Functional Genomics Research Group, Cancer Research Center (Consejo Superior de Investigaciones Cient\u00edficas, Universidad de Salamanca and Instituto de Investigaci\u00f3n Biom\u00e9dica de Salamanca, CSIC\/USAL\/IBSAL), Salamanca, Spain"}]},{"given":"Celia","family":"Fontanillo","sequence":"additional","affiliation":[{"name":"Bioinformatics and Functional Genomics Research Group, Cancer Research Center (Consejo Superior de Investigaciones Cient\u00edficas, Universidad de Salamanca and Instituto de Investigaci\u00f3n Biom\u00e9dica de Salamanca, CSIC\/USAL\/IBSAL), Salamanca, Spain"}]},{"given":"Conrad","family":"Droste","sequence":"additional","affiliation":[{"name":"Bioinformatics and Functional Genomics Research Group, Cancer Research Center (Consejo Superior de Investigaciones Cient\u00edficas, Universidad de Salamanca and Instituto de Investigaci\u00f3n Biom\u00e9dica de Salamanca, CSIC\/USAL\/IBSAL), Salamanca, Spain"}]},{"given":"Javier","family":"De Las Rivas","sequence":"additional","affiliation":[{"name":"Bioinformatics and Functional Genomics Research Group, Cancer Research Center (Consejo Superior de Investigaciones Cient\u00edficas, Universidad de Salamanca and Instituto de Investigaci\u00f3n Biom\u00e9dica de Salamanca, CSIC\/USAL\/IBSAL), Salamanca, Spain"}]}],"member":"286","published-online":{"date-parts":[[2015,1,18]]},"reference":[{"key":"2023020115445614400_btu864-B3","article-title":"topGO: Enrichment analysis for Gene Ontology","author":"Alexa","year":"2010"},{"key":"2023020115445614400_btu864-B1","doi-asserted-by":"crossref","first-page":"e24289","DOI":"10.1371\/journal.pone.0024289","article-title":"Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms","volume":"6","author":"Fontanillo","year":"2011","journal-title":"PLoS One"},{"key":"2023020115445614400_btu864-B2","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources","volume":"4","author":"Huang","year":"2009","journal-title":"Nat. Protoc."},{"key":"2023020115445614400_btu864-B4","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1186\/1471-2105-10-161","article-title":"GAGE: generally applicable gene set enrichment for pathway analysis","volume":"10","author":"Luo","year":"2009","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/10\/1686\/49012466\/bioinformatics_31_10_1686.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/10\/1686\/49012466\/bioinformatics_31_10_1686.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:02:24Z","timestamp":1675296144000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/10\/1686\/176902"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,1,18]]},"references-count":4,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2015,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu864","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,5,15]]},"published":{"date-parts":[[2015,1,18]]}}}