{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T14:58:43Z","timestamp":1761058723822,"version":"3.33.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The increasing use of microarray technologies brought about a parallel demand in methods for the functional interpretation of the results. Beyond the conventional functional annotations for genes, such as gene ontology, pathways, etc. other sources of information are still to be exploited. Text-mining methods allow extracting informative terms (bioentities) with different functional, chemical, clinical, etc. meanings, that can be associated to genes. We show how to use these associations within an appropriate statistical framework and how to apply them through easy-to-use, web-based environments to the functional interpretation of microarray experiments. Functional enrichment and gene set enrichment tests using bioentities are presented.<\/jats:p><jats:p>Availability: Marmite and MarmiteScan can be found in the Babelomics suite: http:\/\/www.babelomics.org<\/jats:p><jats:p>Contact: \u00a0jdopazo@cipf.es<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm445","type":"journal-article","created":{"date-parts":[[2007,9,14]],"date-time":"2007-09-14T00:23:31Z","timestamp":1189729411000},"page":"3098-3099","source":"Crossref","is-referenced-by-count":18,"title":["Functional profiling of microarray experiments using text-mining derived bioentities"],"prefix":"10.1093","volume":"23","author":[{"given":"Pablo","family":"Minguez","sequence":"first","affiliation":[{"name":"1 Department of Bioinformatics and 2Functional Genomics Node, (INB), Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, E46013, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"F\u00e1tima","family":"Al-Shahrour","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and 2Functional Genomics Node, (INB), Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, E46013, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Montaner","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and 2Functional Genomics Node, (INB), Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, E46013, Spain"},{"name":"1 Department of Bioinformatics and 2Functional Genomics Node, (INB), Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, E46013, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joaqu\u00edn","family":"Dopazo","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and 2Functional Genomics Node, (INB), Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, E46013, Spain"},{"name":"1 Department of Bioinformatics and 2Functional Genomics Node, (INB), Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, E46013, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,9,13]]},"reference":[{"key":"2023041208451902400_","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1093\/bioinformatics\/btg455","article-title":"FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes","volume":"20","author":"Al-Shahrour","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041208451902400_","doi-asserted-by":"crossref","first-page":"2988","DOI":"10.1093\/bioinformatics\/bti457","article-title":"Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information","volume":"21","author":"Al-Shahrour","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041208451902400_","doi-asserted-by":"crossref","first-page":"W472","DOI":"10.1093\/nar\/gkl172","article-title":"BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments","volume":"34","author":"Al-Shahrour","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023041208451902400_","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1093\/bioinformatics\/14.7.600","article-title":"Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families","volume":"14","author":"Andrade","year":"1998","journal-title":"Bioinformatics"},{"key":"2023041208451902400_","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. 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