{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T11:40:05Z","timestamp":1783597205807,"version":"3.55.0"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,11,27]],"date-time":"2020-11-27T00:00:00Z","timestamp":1606435200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Research Foundation in the Republic of Korea","award":["NRF-2020M3C9A5085887"],"award-info":[{"award-number":["NRF-2020M3C9A5085887"]}]},{"name":"National Research Foundation in the Republic of Korea","award":["NRF-2020R1A2C4001464"],"award-info":[{"award-number":["NRF-2020R1A2C4001464"]}]},{"name":"National Research Foundation in the Republic of Korea","award":["NRF-2018M3C9A5064704"],"award-info":[{"award-number":["NRF-2018M3C9A5064704"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Three-dimensional (3D) genome organization is tightly coupled with gene regulation in various biological processes and diseases. In cancer, various types of large-scale genomic rearrangements can disrupt the 3D genome, leading to oncogenic gene expression. However, unraveling the pathogenicity of the 3D cancer genome remains a challenge since closer examinations have been greatly limited due to the lack of appropriate tools specialized for disorganized higher-order chromatin structure. Here, we updated a 3D-genome Interaction Viewer and database named 3DIV by uniformly processing \u223c230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows:\u00a0(i) the collection of 401 samples including 220 cancer cell line\/tumor Hi-C data, 153 normal cell line\/tissue Hi-C data, and 28 promoter capture Hi-C data, (ii) the live interactive manipulation of the 3D cancer genome to simulate the impact of structural variations and (iii) the reconstruction of Hi-C contact maps by user-defined chromosome order to investigate the 3D genome of the complex genomic rearrangement. In summary, the updated 3DIV will be the most comprehensive resource to explore the gene regulatory effects of both the normal and cancer 3D genome. \u20183DIV\u2019 is freely available at http:\/\/3div.kr.<\/jats:p>","DOI":"10.1093\/nar\/gkaa1078","type":"journal-article","created":{"date-parts":[[2020,10,26]],"date-time":"2020-10-26T12:10:39Z","timestamp":1603714239000},"page":"D38-D46","source":"Crossref","is-referenced-by-count":40,"title":["3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome"],"prefix":"10.1093","volume":"49","author":[{"given":"Kyukwang","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Insu","family":"Jang","sequence":"additional","affiliation":[{"name":"Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mooyoung","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinhyuk","family":"Choi","sequence":"additional","affiliation":[{"name":"Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min-Seo","family":"Kim","sequence":"additional","affiliation":[{"name":"Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Byungwook","family":"Lee","sequence":"additional","affiliation":[{"name":"Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5885-2754","authenticated-orcid":false,"given":"Inkyung","family":"Jung","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,11,27]]},"reference":[{"key":"2021010313115597300_B1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long-range interactions reveals folding principles of the human genome","volume":"326","author":"Lieberman-Aiden","year":"2009","journal-title":"Science"},{"key":"2021010313115597300_B2","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature11082","article-title":"Topological domains in mammalian genomes identified by analysis of chromatin interactions","volume":"485","author":"Dixon","year":"2012","journal-title":"Nature"},{"key":"2021010313115597300_B3","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"Rao","year":"2014","journal-title":"Cell"},{"key":"2021010313115597300_B4","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1038\/nature14450","article-title":"Condensin-driven remodelling of X chromosome topology during dosage compensation","volume":"523","author":"Crane","year":"2015","journal-title":"Nature"},{"key":"2021010313115597300_B5","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/nature14222","article-title":"Chromatin architecture reorganization during stem cell differentiation","volume":"518","author":"Dixon","year":"2015","journal-title":"Nature"},{"key":"2021010313115597300_B6","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1038\/nature13986","article-title":"Topologically associating domains are stable units of replication-timing regulation","volume":"515","author":"Pope","year":"2014","journal-title":"Nature"},{"key":"2021010313115597300_B7","doi-asserted-by":"crossref","first-page":"eaar2555","DOI":"10.1126\/science.aar2555","article-title":"Imaging dynamic and selective low-complexity domain interactions that control gene transcription","volume":"361","author":"Chong","year":"2018","journal-title":"Science"},{"key":"2021010313115597300_B8","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1038\/s41588-017-0030-7","article-title":"Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming","volume":"50","author":"Stadhouders","year":"2018","journal-title":"Nat. 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