{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,25]],"date-time":"2026-07-25T05:36:51Z","timestamp":1784957811249,"version":"3.55.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"15","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["[HG006130]"],"award-info":[{"award-number":["[HG006130]"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["[GM108716]"],"award-info":[{"award-number":["[GM108716]"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["[GM104369]"],"award-info":[{"award-number":["[GM104369]"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The 3D structure of the genome plays a critical role in regulating gene expression. Recent progress in mapping technologies for chromatin interactions has led to a rapid increase in this kind of interaction data. This trend will continue as research in this burgeoning field intensifies.<\/jats:p>\n               <jats:p>Results: We describe the 4DGenome database that stores chromatin interaction data compiled through comprehensive literature curation. The database currently covers both low- and high-throughput assays, including 3C, 4C-Seq, 5C, Hi-C, ChIA-PET and Capture-C. To complement the set of interactions detected by experimental assays, we also include interactions predicted by a recently developed computational method with demonstrated high accuracy. The database currently contains \u223c8 million records, covering 102 cell\/tissue types in five organisms. Records in the database are described using a standardized file format, facilitating data exchange. The vast major of the interactions were assigned a confidence score. Using the web interface, users can query and download database records via a number of annotation dimensions. Query results can be visualized along with other genomics datasets via links to the UCSC genome browser. We anticipate that 4DGenome will be a valuable resource for investigating the spatial structure-and-function relationship of genomes.<\/jats:p>\n               <jats:p>Availability and Implementation: \u00a04Dgenome is freely accessible at http:\/\/4dgenome.int-med.uiowa.edu. The database and web interface are implemented in MySQL, Apache and JavaScript with all major browsers supported.<\/jats:p>\n               <jats:p>Contact: \u00a0kai-tan@uiowa.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary Materials are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv158","type":"journal-article","created":{"date-parts":[[2015,3,19]],"date-time":"2015-03-19T01:13:52Z","timestamp":1426727632000},"page":"2560-2564","source":"Crossref","is-referenced-by-count":108,"title":["4DGenome: a comprehensive database of chromatin interactions"],"prefix":"10.1093","volume":"31","author":[{"given":"Li","family":"Teng","sequence":"first","affiliation":[{"name":"1 Department of Internal Medicine and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bing","family":"He","sequence":"additional","affiliation":[{"name":"2 Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52242, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiahui","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Internal Medicine and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Tan","sequence":"additional","affiliation":[{"name":"1 Department of Internal Medicine and"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,3,18]]},"reference":[{"key":"2023051308493982000_btv158-B1","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":"2023051308493982000_btv158-B2","doi-asserted-by":"crossref","first-page":"D816","DOI":"10.1093\/nar\/gks1158","article-title":"The BioGRID interaction database: 2013 update","volume":"41","author":"Chatr-Aryamontri","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023051308493982000_btv158-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1101\/gr.164079.113","article-title":"Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits","volume":"24","author":"Corradin","year":"2014","journal-title":"Genome Res."},{"key":"2023051308493982000_btv158-B4","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1126\/science.1067799","article-title":"Capturing chromosome conformation","volume":"295","author":"Dekker","year":"2002","journal-title":"Science"},{"key":"2023051308493982000_btv158-B5","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1101\/gr.5571506","article-title":"Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements","volume":"16","author":"Dostie","year":"2006","journal-title":"Genome Res."},{"key":"2023051308493982000_btv158-B6","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1038\/nbt.1662","article-title":"Discovery and characterization of chromatin states for systematic annotation of the human genome","volume":"28","author":"Ernst","year":"2010","journal-title":"Nat. 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