{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:51:03Z","timestamp":1773276663517,"version":"3.50.1"},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"suppl_2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2003,9,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The transcriptional regulation of a metazoan gene depends on the cooperative action of multiple transcription factors that bind to cis-regulatory modules (CRMs) located in the neighborhood of the gene. By integrating multiple signals, CRMs confer an organism specific spatial and temporal rate of transcription.<\/jats:p>\n               <jats:p>Results: Based on the hypothesis that genes that are needed in exactly the same conditions might share similar regulatory switches, we have developed a novel methodology to find CRMs in a set of coexpressed or coregulated genes. The ModuleSearcher algorithm finds for a given gene set the best scoring combination of transcription factor binding sites within a sequence window using an A*procedure for tree searching. To keep the level of noise low, we use DNA sequences that are most likely to contain functional cis-regulatory information, namely conserved regions between human and mouse orthologous genes. The ModuleScanner performs genomic searches with a predicted CRM or with a user-defined CRM known from the literature to find possible target genes. The validity of a set of putative targets is checked using Gene Ontology annotations. We demonstrate the use and effectiveness of the ModuleSearcher and ModuleScanner algorithms and test their specificity and sensitivity on semi-artificial data. Next, we search for a module in a cluster of gene expression profiles of human cell cycle genes.<\/jats:p>\n               <jats:p>Availability: The ModuleSearcher is available as a web service within the TOUCAN workbench for regulatory sequence analysis, which can be downloaded from http:\/\/www.esat.kuleuven.ac.be\/~dna\/BioI.<\/jats:p>\n               <jats:p>Contact: stein.aerts@esat.kuleuven.ac.be<\/jats:p>\n               <jats:p>*To whom correspondence should be addressed.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btg1052","type":"journal-article","created":{"date-parts":[[2003,10,9]],"date-time":"2003-10-09T01:10:44Z","timestamp":1065661844000},"page":"ii5-ii14","source":"Crossref","is-referenced-by-count":75,"title":["Computational detection of <i>cis<\/i> -regulatory modules"],"prefix":"10.1093","volume":"19","author":[{"given":"Stein","family":"Aerts","sequence":"first","affiliation":[{"name":"1Department of Electrical Engineering ESAT-SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, Leuven, 3001, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Van Loo","sequence":"additional","affiliation":[{"name":"1Department of Electrical Engineering ESAT-SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, Leuven, 3001, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gert","family":"Thijs","sequence":"additional","affiliation":[{"name":"1Department of Electrical Engineering ESAT-SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, Leuven, 3001, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yves","family":"Moreau","sequence":"additional","affiliation":[{"name":"1Department of Electrical Engineering ESAT-SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, Leuven, 3001, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bart","family":"De Moor","sequence":"additional","affiliation":[{"name":"1Department of Electrical Engineering ESAT-SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, Leuven, 3001, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2003,9,27]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_2\/ii5\/180082","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_2\/ii5\/180082","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T18:45:19Z","timestamp":1674672319000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_2\/ii5\/180082"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2003,9,27]]},"references-count":0,"journal-issue":{"issue":"suppl_2","published-print":{"date-parts":[[2003,9,27]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btg1052","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2003,9,27]]},"published":{"date-parts":[[2003,9,27]]}}}