{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,18]],"date-time":"2026-01-18T05:29:22Z","timestamp":1768714162306,"version":"3.49.0"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":515,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,9,1]]},"abstract":"Abstract<\/jats:title>\n Summary: Current methods for motif discovery from chromatin immunoprecipitation followed by sequencing (ChIP-seq) data often identify non-targeted transcription factor (TF) motifs, and are even further limited when peak sequences are similar due to common ancestry rather than common binding factors. The latter aspect particularly affects a large number of proteins from the Cys2His2 zinc finger (C2H2-ZF) class of TFs, as their binding sites are often dominated by endogenous retroelements that have highly similar sequences. Here, we present recognition code-assisted discovery of regulatory elements (RCADE) for motif discovery from C2H2-ZF ChIP-seq data. RCADE combines predictions from a DNA recognition code of C2H2-ZFs with ChIP-seq data to identify models that represent the genuine DNA binding preferences of C2H2-ZF proteins. We show that RCADE is able to identify generalizable binding models even from peaks that are exclusively located within the repeat regions of the genome, where state-of-the-art motif finding approaches largely fail.<\/jats:p>\n Availability and implementation: RCADE is available as a webserver and also for download at http:\/\/rcade.ccbr.utoronto.ca\/.<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>\n Contact: \u00a0t.hughes@utoronto.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv284","type":"journal-article","created":{"date-parts":[[2015,5,8]],"date-time":"2015-05-08T00:12:11Z","timestamp":1431043931000},"page":"2879-2881","source":"Crossref","is-referenced-by-count":28,"title":["Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE"],"prefix":"10.1093","volume":"31","author":[{"given":"Hamed S.","family":"Najafabadi","sequence":"first","affiliation":[{"name":"1 Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada,"}]},{"given":"Mihai","family":"Albu","sequence":"additional","affiliation":[{"name":"1 Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada,"}]},{"given":"Timothy R.","family":"Hughes","sequence":"additional","affiliation":[{"name":"1 Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada,"},{"name":"2 Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada and"},{"name":"3 Canadian Institute for Advanced Research, Toronto, ON, Canada"}]}],"member":"286","published-online":{"date-parts":[[2015,5,6]]},"reference":[{"key":"2023020202234537600_btv284-B1","first-page":"28","article-title":"Fitting a mixture model by expectation maximization to discover motifs in biopolymers","volume":"2","author":"Bailey","year":"1994","journal-title":"Proc. Int. Conf. Intell. Syst. Mol. Biol."},{"key":"2023020202234537600_btv284-B2","doi-asserted-by":"crossref","first-page":"e128","DOI":"10.1093\/nar\/gks433","article-title":"Inferring direct DNA binding from ChIP-seq","volume":"40","author":"Bailey","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023020202234537600_btv284-B3","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"ENCODE Project Consortium","year":"2012","journal-title":"Nature"},{"key":"2023020202234537600_btv284-B4","doi-asserted-by":"crossref","first-page":"4800","DOI":"10.1093\/nar\/gku132","article-title":"An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins","volume":"42","author":"Gupta","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023020202234537600_btv284-B5","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/nbt.3128","article-title":"C2H2 zinc finger proteins greatly expand the human regulatory lexicon","volume":"33","author":"Najafabadi","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"2023020202234537600_btv284-B6","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1093\/nar\/gkt890","article-title":"De\u00a0novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins","volume":"42","author":"Persikov","year":"2014","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/17\/2879\/49035256\/bioinformatics_31_17_2879.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/17\/2879\/49035256\/bioinformatics_31_17_2879.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:42:39Z","timestamp":1675309359000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/17\/2879\/183644"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,5,6]]},"references-count":6,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2015,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv284","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,9,1]]},"published":{"date-parts":[[2015,5,6]]}}}