{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T04:31:01Z","timestamp":1785990661860,"version":"3.56.0"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,4,15]]},"abstract":"Abstract<\/jats:title>\n Summary: Precise regulatory control of genes, particularly in eukaryotes, frequently requires the joint action of multiple sequence-specific transcription factors. A cis-regulatory module (CRM) is a genomic locus that is responsible for gene regulation and that contains multiple transcription factor binding sites in close proximity. Given a collection of known transcription factor binding motifs, many bioinformatics methods have been proposed over the past 15 years for identifying within a genomic sequence candidate CRMs consisting of clusters of those motifs.<\/jats:p>\n Results: The MCAST algorithm uses a hidden Markov model with a P-value-based scoring scheme to identify candidate CRMs. Here, we introduce a new version of MCAST that offers improved graphical output, a dynamic background model, statistical confidence estimates based on false discovery rate estimation and, most significantly, the ability to predict CRMs while taking into account epigenomic data such as DNase I sensitivity or histone modification data. We demonstrate the validity of MCAST\u2019s statistical confidence estimates and the utility of epigenomic priors in identifying CRMs.<\/jats:p>\n Availability and implementation: MCAST is part of the MEME Suite software toolkit. A web server and source code are available at http:\/\/meme-suite.org and http:\/\/alternate.meme-suite.org.<\/jats:p>\n Contact: \u00a0t.bailey@imb.uq.edu.au or william-noble@uw.edu<\/jats:p>\n Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv750","type":"journal-article","created":{"date-parts":[[2015,12,25]],"date-time":"2015-12-25T03:13:42Z","timestamp":1451013222000},"page":"1217-1219","source":"Crossref","is-referenced-by-count":13,"title":["MCAST: scanning for cis<\/i>-regulatory motif clusters"],"prefix":"10.1093","volume":"32","author":[{"given":"Charles E.","family":"Grant","sequence":"first","affiliation":[{"name":"1 Department of Genome Sciences, University of Washington, Seattle, WA, USA,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Johnson","sequence":"additional","affiliation":[{"name":"2 Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy L.","family":"Bailey","sequence":"additional","affiliation":[{"name":"2 Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William Stafford","family":"Noble","sequence":"additional","affiliation":[{"name":"1 Department of Genome Sciences, University of Washington, Seattle, WA, USA,"},{"name":"3 Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,12,24]]},"reference":[{"key":"2023020112033498200_btv750-B1","doi-asserted-by":"crossref","first-page":"ii16","DOI":"10.1093\/bioinformatics\/btg1054","article-title":"Searching for statistically significant regulatory modules","volume":"19","author":"Bailey","year":"2003","journal-title":"Bioinformatics"},{"key":"2023020112033498200_btv750-B2","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1093\/bioinformatics\/btr614","article-title":"Epigenetic priors for identifying active transcription factor binding sites","volume":"28","author":"Cuellar-Partida","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020112033498200_btv750-B3","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1111\/1467-9868.00346","article-title":"A direct approach to false discovery rates","volume":"64","author":"Storey","year":"2002","journal-title":"J. R. Stat. Soc. Ser. B"},{"key":"2023020112033498200_btv750-B4","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1006\/jmbi.1998.1700","article-title":"Identification of regulatory regions which confer muscle-specific gene expression","volume":"278","author":"Wasserman","year":"1998","journal-title":"J. Mol. Biol"},{"key":"2023020112033498200_btv750-B5","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.cell.2013.03.035","article-title":"Master transcription factors and mediator establish super-enhancers at key cell identity genes","volume":"153","author":"Whyte","year":"2013","journal-title":"Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/8\/1217\/49018424\/bioinformatics_32_8_1217.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/8\/1217\/49018424\/bioinformatics_32_8_1217.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:16:43Z","timestamp":1675289803000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/8\/1217\/1744747"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,12,24]]},"references-count":5,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2016,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv750","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,4,15]]},"published":{"date-parts":[[2015,12,24]]}}}