{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T21:48:32Z","timestamp":1782856112345,"version":"3.54.5"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,31]],"date-time":"2022-05-31T00:00:00Z","timestamp":1653955200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001721","name":"University of Groningen","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001721","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Recent advances in the field of high throughput (meta-)transcriptomics and proteomics call for easy and rapid methods enabling to explore not only single genes or proteins but also extended biological systems. Gene set enrichment analysis is commonly used to find relations in a set of genes and helps to uncover the biological meaning in results derived from high-throughput data. The basis for gene set enrichment analysis is a solid functional classification of genes. Here, we describe a comprehensive database containing multiple functional classifications of genes of all (&amp;gt;55 000) publicly available complete bacterial genomes. In addition to the most common functional classes such as COG and GO, also KEGG, InterPro, PFAM, eggnog\u00a0and operon classes are supported. As classification data for features is often not available, we offer fast annotation and classification of proteins in any newly sequenced bacterial genome. The web server FUNAGE-Pro enables fast functional analysis on single gene sets, multiple experiments, time series data, clusters, and gene network modules for any prokaryote species or strain. FUNAGE-Pro is freely available at http:\/\/funagepro.molgenrug.nl.<\/jats:p>","DOI":"10.1093\/nar\/gkac441","type":"journal-article","created":{"date-parts":[[2022,5,10]],"date-time":"2022-05-10T19:19:44Z","timestamp":1652210384000},"page":"W330-W336","source":"Crossref","is-referenced-by-count":62,"title":["FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7024-2334","authenticated-orcid":false,"given":"Anne","family":"de\u00a0Jong","sequence":"first","affiliation":[{"name":"Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute , the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oscar P","family":"Kuipers","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute , the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Kok","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute , the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,5,31]]},"reference":[{"key":"2022070423591413900_B1","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gkaa1113","article-title":"The gene ontology resource: enriching a GOld mine","volume":"49","author":"The Gene Ontology Consortium","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022070423591413900_B2","doi-asserted-by":"crossref","first-page":"D545","DOI":"10.1093\/nar\/gkaa970","article-title":"KEGG: integrating viruses and cellular organisms","volume":"49","author":"Kanehisa","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022070423591413900_B3","doi-asserted-by":"crossref","first-page":"D261","DOI":"10.1093\/nar\/gku1223","article-title":"Expanded microbial genome coverage and improved protein family annotation in the COG database","volume":"43","author":"Galperin","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2022070423591413900_B4","doi-asserted-by":"crossref","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Huerta-Cepas","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022070423591413900_B5","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: the protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022070423591413900_B6","doi-asserted-by":"crossref","first-page":"D344","DOI":"10.1093\/nar\/gkaa977","article-title":"The InterPro protein families and domains database: 20 years on","volume":"49","author":"Blum","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022070423591413900_B7","doi-asserted-by":"crossref","first-page":"W183","DOI":"10.1093\/nar\/gkz347","article-title":"modEnrichr: a suite of gene set enrichment analysis tools for model organisms","volume":"47","author":"Kuleshov","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022070423591413900_B8","doi-asserted-by":"crossref","first-page":"1944","DOI":"10.1093\/bioinformatics\/btx104","article-title":"FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis","volume":"33","author":"Zhang","year":"2017","journal-title":"Bioinformatics"},{"key":"2022070423591413900_B9","doi-asserted-by":"crossref","first-page":"1944","DOI":"10.1093\/bioinformatics\/btz803","article-title":"gep2pep: a bioconductor package for the creation and analysis of pathway-based expression profiles","volume":"36","author":"Napolitano","year":"2020","journal-title":"Bioinformatics"},{"key":"2022070423591413900_B10","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/s12859-017-1482-6","article-title":"GSAR: bioconductor package for gene set analysis in R","volume":"18","author":"Rahmatallah","year":"2017","journal-title":"BMC Bioinf."},{"key":"2022070423591413900_B11","doi-asserted-by":"crossref","first-page":"1805","DOI":"10.1093\/bioinformatics\/bts251","article-title":"DAVID-WS: a stateful web service to facilitate gene\/protein list analysis","volume":"28","author":"Jiao","year":"2012","journal-title":"Bioinformatics"},{"key":"2022070423591413900_B12","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. 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