{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,13]],"date-time":"2023-09-13T12:43:37Z","timestamp":1694609017451},"reference-count":21,"publisher":"World Scientific Pub Co Pte Ltd","issue":"08","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Found. Comput. Sci."],"published-print":{"date-parts":[[2018,12]]},"abstract":"<jats:p>Identification and functional characterization of regulatory elements in the human genome is a challenging task. A sequence feature commonly used to predict regulatory activity is the co-occurrence of transcription factor binding sites (TFBSs) in regulatory regions. In this work, we present a graph-based approach to detect frequently co-occurring TFBSs in evolutionarily conserved non-coding elements (CNEs). We introduce a graph representation of the sequence of TFBSs identified in a CNE that allows us to handle overlapping binding sites. We use a dynamic programming algorithm to align such graphs and determine the relative enrichment of short sequences of TFBSs in the alignments. We evaluate our approach on a set of functionally validated CNEs. Our findings include a regulatory signature composed of co-occurring Pbx-Hox and Meis binding motifs associated with hindbrain enhancer activity.<\/jats:p>","DOI":"10.1142\/s0129054118430074","type":"journal-article","created":{"date-parts":[[2018,12,27]],"date-time":"2018-12-27T07:58:46Z","timestamp":1545897526000},"page":"1345-1354","source":"Crossref","is-referenced-by-count":1,"title":["Identifying Potential Regulatory Elements by Transcription Factor Binding Site Alignment Using Partial Order Graphs"],"prefix":"10.1142","volume":"29","author":[{"given":"Maryam","family":"Abdollahyan","sequence":"first","affiliation":[{"name":"School of Electronic Engineering and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom"}]},{"given":"Greg","family":"Elgar","sequence":"additional","affiliation":[{"name":"Regulatory Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom"}]},{"given":"Fabrizio","family":"Smeraldi","sequence":"additional","affiliation":[{"name":"School of Electronic Engineering and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom"}]}],"member":"219","published-online":{"date-parts":[[2018,12,26]]},"reference":[{"issue":"2","key":"S0129054118430074BIB002","doi-asserted-by":"crossref","first-page":"ii16","DOI":"10.1093\/bioinformatics\/btg1054","volume":"19","author":"Bailey T. L.","year":"2003","journal-title":"Bioinformatics"},{"key":"S0129054118430074BIB003","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.231608898"},{"key":"S0129054118430074BIB004","doi-asserted-by":"publisher","DOI":"10.1016\/S0925-4773(01)00554-8"},{"key":"S0129054118430074BIB005","doi-asserted-by":"publisher","DOI":"10.1186\/1471-213X-13-31"},{"key":"S0129054118430074BIB006","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg540"},{"key":"S0129054118430074BIB007","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr064"},{"key":"S0129054118430074BIB008","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bth126"},{"key":"S0129054118430074BIB009","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0130413"},{"key":"S0129054118430074BIB010","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2005.10.042"},{"key":"S0129054118430074BIB011","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.19.7.5134"},{"key":"S0129054118430074BIB012","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg1021"},{"key":"S0129054118430074BIB013","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.3.452"},{"key":"S0129054118430074BIB014","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt997"},{"key":"S0129054118430074BIB015","doi-asserted-by":"publisher","DOI":"10.1006\/dbio.1996.8449"},{"key":"S0129054118430074BIB016","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt578"},{"key":"S0129054118430074BIB017","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(70)90057-4"},{"key":"S0129054118430074BIB018","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-3-30"},{"issue":"1","key":"S0129054118430074BIB019","first-page":"D124","volume":"39","author":"Robasky K.","year":"2010","journal-title":"Nucleic Acids Research"},{"key":"S0129054118430074BIB020","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(81)90087-5"},{"key":"S0129054118430074BIB021","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-13-S7-S11"},{"key":"S0129054118430074BIB022","doi-asserted-by":"publisher","DOI":"10.1186\/1471-213X-7-100"}],"container-title":["International Journal of Foundations of Computer Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0129054118430074","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,12]],"date-time":"2023-09-12T13:17:44Z","timestamp":1694524664000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0129054118430074"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,12]]},"references-count":21,"journal-issue":{"issue":"08","published-online":{"date-parts":[[2018,12,26]]},"published-print":{"date-parts":[[2018,12]]}},"alternative-id":["10.1142\/S0129054118430074"],"URL":"https:\/\/doi.org\/10.1142\/s0129054118430074","relation":{},"ISSN":["0129-0541","1793-6373"],"issn-type":[{"value":"0129-0541","type":"print"},{"value":"1793-6373","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,12]]}}}