{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T09:00:40Z","timestamp":1780995640792,"version":"3.54.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2020,1,15]],"date-time":"2020-01-15T00:00:00Z","timestamp":1579046400000},"content-version":"vor","delay-in-days":14,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Research, Development and Innovation Office of Hungary","award":["GINOP-2.3.2-15-2016-00044"],"award-info":[{"award-number":["GINOP-2.3.2-15-2016-00044"]}]},{"name":"National Research, Development and Innovation Office of Hungary","award":["K1328142017-1.3.1-vke-2017-00026"],"award-info":[{"award-number":["K1328142017-1.3.1-vke-2017-00026"]}]},{"name":"Higher Education Institutional Excellence Programme","award":["NKFIH-1150-6\/2019"],"award-info":[{"award-number":["NKFIH-1150-6\/2019"]}]},{"name":"Ministry of Innovation and Technology in Hungary","award":["FIKP_20428-3_2018_FELITSTRAT"],"award-info":[{"award-number":["FIKP_20428-3_2018_FELITSTRAT"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>ChIP-seq reveals genomic regions where proteins, e.g. transcription factors (TFs) interact with DNA. A substantial fraction of these regions, however, do not contain the cognate binding site for the TF of interest. This phenomenon might be explained by protein\u2013protein interactions and co-precipitation of interacting gene regulatory elements. We uniformly processed 3727 human ChIP-seq data sets and determined the cistrome of 292 TFs, as well as the distances between the TF binding motif centers and the ChIP-seq peak summits. ChIPSummitDB enables the analysis of ChIP-seq data using multiple approaches. The 292 cistromes and corresponding ChIP-seq peak sets can be browsed in GenomeView. Overlapping SNPs can be inspected in dbSNPView. Most importantly, the MotifView and PairShiftView pages show the average distance between motif centers and overlapping ChIP-seq peak summits and distance distributions thereof, respectively. In addition to providing a comprehensive human TF binding site collection, the ChIPSummitDB database and web interface allows for the examination of the topological arrangement of TF complexes genome-wide. ChIPSummitDB is freely accessible at http:\/\/summit.med.unideb.hu\/summitdb\/. The database will be regularly updated and extended with the newly available human and mouse ChIP-seq data sets.<\/jats:p>","DOI":"10.1093\/database\/baz141","type":"journal-article","created":{"date-parts":[[2019,11,15]],"date-time":"2019-11-15T07:10:04Z","timestamp":1573801804000},"source":"Crossref","is-referenced-by-count":17,"title":["ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them"],"prefix":"10.1093","volume":"2020","author":[{"given":"Erik","family":"Czipa","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem t\u00e9r 1, Debrecen H-4032, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00e1ty\u00e1s","family":"Schiller","sequence":"additional","affiliation":[{"name":"Agricultural Genomics and Bioinformatics Group, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Gy\u00f6rgyi Albert \u00fat 4, G\u00f6d\u00f6ll\u0151 H-2100, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6753-0714","authenticated-orcid":false,"given":"Tibor","family":"Nagy","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem t\u00e9r 1, Debrecen H-4032, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Levente","family":"Kontra","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem t\u00e9r 1, Debrecen H-4032, Hungary"},{"name":"Agricultural Genomics and Bioinformatics Group, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Gy\u00f6rgyi Albert \u00fat 4, G\u00f6d\u00f6ll\u0151 H-2100, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L\u00e1szl\u00f3","family":"Steiner","sequence":"additional","affiliation":[{"name":"UD-GenoMed Medical Genomic Technologies Research & Development Services Ltd., Nagyerdei krt. 98, Debrecen H-4032, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00falia","family":"Koller","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem t\u00e9r 1, Debrecen H-4032, Hungary"},{"name":"Semmelweis University, Institute of Genomic Medicines and Rare Disorders, \u00dcll\u0151i \u00fat 78\/B, Budapest H-1082, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Orsolya","family":"P\u00e1ln\u00e9-Sz\u00e9n","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem t\u00e9r 1, Debrecen H-4032, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Endre","family":"Barta","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem t\u00e9r 1, Debrecen H-4032, Hungary"},{"name":"Agricultural Genomics and Bioinformatics Group, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Szent-Gy\u00f6rgyi Albert \u00fat 4, G\u00f6d\u00f6ll\u0151 H-2100, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,1,14]]},"reference":[{"key":"2020012105163315100_ref1","first-page":"2306","article-title":"Genome-wide location and function of DNA binding proteins.","volume-title":"Science","author":"Ren","year":"2000"},{"key":"2020012105163315100_ref2","first-page":"533","article-title":"Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.","volume-title":"Nature","author":"Iyer","year":"2001"},{"key":"2020012105163315100_ref3","doi-asserted-by":"crossref","first-page":"2090","DOI":"10.1101\/gr.094144.109","article-title":"Distinguishing direct versus indirect transcription factor-DNA interactions","volume":"19","author":"Gordan","year":"2009","journal-title":"Genome Res."},{"key":"2020012105163315100_ref4","doi-asserted-by":"crossref","first-page":"2174","DOI":"10.1128\/MCB.05093-11","article-title":"Specific sites in the C terminus of CTCF interact with the SA2 subunit of the cohesin complex and are required for cohesin-dependent insulation activity","volume":"31","author":"Xiao","year":"2011","journal-title":"Mol. 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