{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T17:11:12Z","timestamp":1722877872789},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The protein\u2013DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human.<\/jats:p>\n               <jats:p>Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions.<\/jats:p>\n               <jats:p>Availability and implementation: The identified motif pair data is compressed and available in the supplementary materials associated with this manuscript.<\/jats:p>\n               <jats:p>Contact: \u00a0kc.w@cityu.edu.hk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv555","type":"journal-article","created":{"date-parts":[[2015,9,27]],"date-time":"2015-09-27T23:57:20Z","timestamp":1443398240000},"page":"321-324","source":"Crossref","is-referenced-by-count":10,"title":["Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells"],"prefix":"10.1093","volume":"32","author":[{"given":"Ka-Chun","family":"Wong","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong,"}]},{"given":"Yue","family":"Li","sequence":"additional","affiliation":[{"name":"2 CSAIL, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA and"}]},{"given":"Chengbin","family":"Peng","sequence":"additional","affiliation":[{"name":"3 CEMSE Division, King Abdullah University of Science and Technology, Thuwal, Jeddah, Kingdom of Saudi Arabia"}]}],"member":"286","published-online":{"date-parts":[[2015,9,26]]},"reference":[{"key":"2023020110304335100_btv555-B1","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature11632","article-title":"An integrated map of genetic variation from 1\u2009092 human genomes","volume":"491","author":"Abecasis","year":"2012","journal-title":"Nature"},{"key":"2023020110304335100_btv555-B2","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1101\/gr.160374.113","article-title":"Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts","volume":"24","author":"Ay","year":"2014","journal-title":"Genome Res."},{"key":"2023020110304335100_btv555-B3","doi-asserted-by":"crossref","first-page":"e1004221","DOI":"10.1371\/journal.pcbi.1004221","article-title":"Hi-C chromatin interaction networks predict co-expression in the mouse cortex","volume":"11","author":"Babaei","year":"2015","journal-title":"PLoS Comput. 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