{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T12:59:29Z","timestamp":1775134769880,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2018,3,28]],"date-time":"2018-03-28T00:00:00Z","timestamp":1522195200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["K22CA204439"],"award-info":[{"award-number":["K22CA204439"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000048","name":"American Cancer Society","doi-asserted-by":"publisher","award":["IRG 81-001-26"],"award-info":[{"award-number":["IRG 81-001-26"]}],"id":[{"id":"10.13039\/100000048","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Identification of functional transcription factors that regulate a given gene set is an important problem in gene regulation studies. Conventional approaches for identifying transcription factors, such as DNA sequence motif analysis, are unable to predict functional binding of specific factors and not sensitive enough to detect factors binding at distal enhancers. Here, we present binding analysis for regulation of transcription (BART), a novel computational method and software package for predicting functional transcription factors that regulate a query gene set or associate with a query genomic profile, based on more than 6000 existing ChIP-seq datasets for over 400 factors in human or mouse. This method demonstrates the advantage of utilizing publicly available data for functional genomics research.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>BART is implemented in Python and available at http:\/\/faculty.virginia.edu\/zanglab\/bart.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty194","type":"journal-article","created":{"date-parts":[[2018,3,27]],"date-time":"2018-03-27T23:12:03Z","timestamp":1522192323000},"page":"2867-2869","source":"Crossref","is-referenced-by-count":129,"title":["BART: a transcription factor prediction tool with query gene sets or epigenomic profiles"],"prefix":"10.1093","volume":"34","author":[{"given":"Zhenjia","family":"Wang","sequence":"first","affiliation":[{"name":"Center for Public Health Genomics, Charlottesville, VA, USA"}]},{"given":"Mete","family":"Civelek","sequence":"additional","affiliation":[{"name":"Center for Public Health Genomics, Charlottesville, VA, USA"},{"name":"Department of Biomedical Engineering, Charlottesville, VA, USA"}]},{"given":"Clint L","family":"Miller","sequence":"additional","affiliation":[{"name":"Center for Public Health Genomics, Charlottesville, VA, USA"},{"name":"Department of Biomedical Engineering, Charlottesville, VA, USA"},{"name":"Department of Public Health Sciences, Charlottesville, VA, USA"},{"name":"Department of Biochemistry and Molecular Genetics, Charlottesville, VA, USA"}]},{"given":"Nathan C","family":"Sheffield","sequence":"additional","affiliation":[{"name":"Center for Public Health Genomics, Charlottesville, VA, USA"},{"name":"Department of Biomedical Engineering, Charlottesville, VA, USA"},{"name":"Department of Public Health Sciences, Charlottesville, VA, USA"},{"name":"Department of Biochemistry and Molecular Genetics, Charlottesville, VA, USA"}]},{"given":"Michael J","family":"Guertin","sequence":"additional","affiliation":[{"name":"Center for Public Health Genomics, Charlottesville, VA, USA"},{"name":"Department of Biochemistry and Molecular Genetics, Charlottesville, VA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4812-3627","authenticated-orcid":false,"given":"Chongzhi","family":"Zang","sequence":"additional","affiliation":[{"name":"Center for Public Health Genomics, Charlottesville, VA, USA"},{"name":"Department of Biomedical Engineering, Charlottesville, VA, USA"},{"name":"Department of Public Health Sciences, Charlottesville, VA, USA"},{"name":"Department of Biochemistry and Molecular Genetics, Charlottesville, VA, USA"},{"name":"Cancer Center, University of Virginia, Charlottesville, VA, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,3,28]]},"reference":[{"key":"2023012712592431900_bty194-B1","doi-asserted-by":"crossref","first-page":"1922","DOI":"10.1093\/bioinformatics\/btt316","article-title":"Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool","volume":"29","author":"Auerbach","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012712592431900_bty194-B2","doi-asserted-by":"crossref","first-page":"24.","DOI":"10.3389\/fgene.2016.00024","article-title":"Analysis of genomic sequence motifs for deciphering transcription factor binding and transcriptional regulation in eukaryotic cells","volume":"7","author":"Boeva","year":"2016","journal-title":"Front. 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