{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T10:02:09Z","timestamp":1769853729858,"version":"3.49.0"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2016,10,4]],"date-time":"2016-10-04T00:00:00Z","timestamp":1475539200000},"content-version":"vor","delay-in-days":1215,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,7,1]]},"DOI":"10.1093\/nar\/gkt448","type":"journal-article","created":{"date-parts":[[2013,6,8]],"date-time":"2013-06-08T02:55:48Z","timestamp":1370660148000},"page":"W535-W543","source":"Crossref","is-referenced-by-count":82,"title":["PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments"],"prefix":"10.1093","volume":"41","author":[{"given":"Federico","family":"Zambelli","sequence":"first","affiliation":[]},{"given":"Graziano","family":"Pesole","sequence":"additional","affiliation":[]},{"given":"Giulio","family":"Pavesi","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2013,6,7]]},"reference":[{"key":"key\n\t\t\t\t20171013130302_gkt448-B1","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1002\/jcb.10286","article-title":"Chromatin remodeling, histone modifications, and DNA methylation-how does it all fit together?","volume":"87","author":"Geiman","year":"2002","journal-title":"J. Cell. Biochem."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B2","doi-asserted-by":"crossref","first-page":"840","DOI":"10.1038\/nrg3306","article-title":"ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions","volume":"13","author":"Furey","year":"2012","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B3","doi-asserted-by":"crossref","first-page":"S22","DOI":"10.1038\/nmeth.1371","article-title":"Computation for ChIP-seq and RNA-seq studies","volume":"6","author":"Pepke","year":"2009","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t20171013130302_gkt448-B4","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1093\/bib\/bbs016","article-title":"Motif discovery and transcription factor binding sites before and after the next-generation sequencing era","volume":"14","author":"Zambelli","year":"2013","journal-title":"Brief. Bioinform."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B5","doi-asserted-by":"crossref","first-page":"W247","DOI":"10.1093\/nar\/gkp464","article-title":"Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes","volume":"37","author":"Zambelli","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B6","doi-asserted-by":"crossref","first-page":"1372","DOI":"10.1093\/nar\/gkh299","article-title":"Detection of functional DNA motifs via statistical over-representation","volume":"32","author":"Frith","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B7","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1186\/1471-2105-9-495","article-title":"CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes","volume":"9","author":"Hestand","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171013130302_gkt448-B8","doi-asserted-by":"crossref","first-page":"W551","DOI":"10.1093\/nar\/gkl322","article-title":"CEAS: cis-regulatory element annotation system","volume":"34","author":"Ji","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B9","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1093\/bioinformatics\/16.1.16","article-title":"DNA binding sites: representation and discovery","volume":"16","author":"Stormo","year":"2000","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013130302_gkt448-B10","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1093\/nar\/gkg108","article-title":"TRANSFAC: transcriptional regulation, from patterns to profiles","volume":"31","author":"Matys","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B11","doi-asserted-by":"crossref","first-page":"D105","DOI":"10.1093\/nar\/gkp950","article-title":"JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles","volume":"38","author":"Portales-Casamar","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B12","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/nature11245","article-title":"Architecture of the human regulatory network derived from ENCODE data","volume":"489","author":"Gerstein","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t20171013130302_gkt448-B13","doi-asserted-by":"crossref","first-page":"1798","DOI":"10.1101\/gr.139105.112","article-title":"Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors","volume":"22","author":"Wang","year":"2012","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B14","doi-asserted-by":"crossref","first-page":"W391","DOI":"10.1093\/nar\/gkr387","article-title":"CENTDIST: discovery of co-associated factors by motif distribution","volume":"39","author":"Zhang","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B15","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":"key\n\t\t\t\t20171013130302_gkt448-B16","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1101\/gr.5533506","article-title":"FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin","volume":"17","author":"Giresi","year":"2007","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B17","doi-asserted-by":"crossref","first-page":"D56","DOI":"10.1093\/nar\/gks1172","article-title":"ENCODE data in the UCSC Genome Browser: year 5 update","volume":"41","author":"Rosenbloom","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B18","doi-asserted-by":"crossref","first-page":"16837","DOI":"10.1073\/pnas.0407387101","article-title":"Discovery of functional noncoding elements by digital analysis of chromatin structure","volume":"101","author":"Sabo","year":"2004","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20171013130302_gkt448-B19","doi-asserted-by":"crossref","first-page":"e98","DOI":"10.1093\/nar\/gkr341","article-title":"Inferring transcription factor complexes from ChIP-seq data","volume":"39","author":"Whitington","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B20","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1016\/j.cell.2008.04.043","article-title":"Integration of external signaling pathways with the core transcriptional network in embryonic stem cells","volume":"133","author":"Chen","year":"2008","journal-title":"Cell"},{"key":"key\n\t\t\t\t20171013130302_gkt448-B21","doi-asserted-by":"crossref","first-page":"4172","DOI":"10.1038\/onc.2008.55","article-title":"A role for Myc in facilitating transcription activation by E2F1","volume":"27","author":"Leung","year":"2008","journal-title":"Oncogene"},{"key":"key\n\t\t\t\t20171013130302_gkt448-B22","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1101\/gr.127597.111","article-title":"Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells","volume":"22","author":"Lee","year":"2012","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B23","doi-asserted-by":"crossref","first-page":"2155","DOI":"10.1093\/nar\/gks1300","article-title":"Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions","volume":"41","author":"Hutchins","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013130302_gkt448-B24","doi-asserted-by":"crossref","DOI":"10.1101\/gr.148080.112","article-title":"NF-Y co-associates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors","author":"Fleming","year":"2013","journal-title":"Genome Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/41\/W1\/W535\/16943601\/gkt448.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T14:41:19Z","timestamp":1522680079000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/41\/W1\/W535\/1105963\/PscanChIP-finding-overrepresented-transcription"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,6,7]]},"references-count":24,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2013,6,7]]},"published-print":{"date-parts":[[2013,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkt448","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,7,1]]},"published":{"date-parts":[[2013,6,7]]}}}