3DIV


33245777	3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome. [PMID: 33245777] Kim K, Jang I, Kim M, Choi J, Kim MS, Lee B, Jung I. Abstract 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 ∼230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows: (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. '3DIV' is freely available at http://3div.kr. Nucleic Acids Res. 2021:49(D1) \| 15 Citations (from Europe PMC, 2025-03-29)
29106613	3DIV: A 3D-genome Interaction Viewer and database. [PMID: 29106613] Yang D, Jang I, Choi J, Kim MS, Lee AJ, Kim H, Eom J, Kim D, Jung I, Lee B. Abstract Three-dimensional (3D) chromatin structure is an emerging paradigm for understanding gene regulation mechanisms. Hi-C (high-throughput chromatin conformation capture), a method to detect long-range chromatin interactions, allows extensive genome-wide investigation of 3D chromatin structure. However, broad application of Hi-C data have been hindered by the level of complexity in processing Hi-C data and the large size of raw sequencing data. In order to overcome these limitations, we constructed a database named 3DIV (a 3D-genome Interaction Viewer and database) that provides a list of long-range chromatin interaction partners for the queried locus with genomic and epigenomic annotations. 3DIV is the first of its kind to collect all publicly available human Hi-C data to provide 66 billion uniformly processed raw Hi-C read pairs obtained from 80 different human cell/tissue types. In contrast to other databases, 3DIV uniquely provides normalized chromatin interaction frequencies against genomic distance dependent background signals and a dynamic browsing visualization tool for the listed interactions, which could greatly advance the interpretation of chromatin interactions. '3DIV' is available at http://kobic.kr/3div. Nucleic Acids Res. 2018:46(D1) \| 65 Citations (from Europe PMC, 2025-03-29)

3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome. [PMID: 33245777]

Kim K, Jang I, Kim M, Choi J, Kim MS, Lee B, Jung I.

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 ∼230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows: (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. '3DIV' is freely available at http://3div.kr.

Nucleic Acids Res. 2021:49(D1) | 15 Citations (from Europe PMC, 2025-03-29)

3DIV: A 3D-genome Interaction Viewer and database. [PMID: 29106613]

Yang D, Jang I, Choi J, Kim MS, Lee AJ, Kim H, Eom J, Kim D, Jung I, Lee B.

Abstract

Three-dimensional (3D) chromatin structure is an emerging paradigm for understanding gene regulation mechanisms. Hi-C (high-throughput chromatin conformation capture), a method to detect long-range chromatin interactions, allows extensive genome-wide investigation of 3D chromatin structure. However, broad application of Hi-C data have been hindered by the level of complexity in processing Hi-C data and the large size of raw sequencing data. In order to overcome these limitations, we constructed a database named 3DIV (a 3D-genome Interaction Viewer and database) that provides a list of long-range chromatin interaction partners for the queried locus with genomic and epigenomic annotations. 3DIV is the first of its kind to collect all publicly available human Hi-C data to provide 66 billion uniformly processed raw Hi-C read pairs obtained from 80 different human cell/tissue types. In contrast to other databases, 3DIV uniquely provides normalized chromatin interaction frequencies against genomic distance dependent background signals and a dynamic browsing visualization tool for the listed interactions, which could greatly advance the interpretation of chromatin interactions. '3DIV' is available at http://kobic.kr/3div.

Nucleic Acids Res. 2018:46(D1) | 65 Citations (from Europe PMC, 2025-03-29)

URL:	http://kobic.kr/3div
Full name:	A 3D-genome Interaction Viewer and database
Description:	3D Interaction Viewer and Database (3DIV) is an easy-to-use database providing epigenetic annotation, one-to-all chromatin interaction visualization in a variety of options. Spatial chromatin interaction has a significant role in gene regulation, and visualization and annotation of these interactions is key to connect between genetic/epigenetic variation and phenotypical polymorphism.
Year founded:	2018
Last update:
Version:
Accessibility:	Accessible
Country/Region:	Korea, Republic of

Data type:	DNA
Data object:	Animal
Database category:	Interaction Modification
Major species:	Homo sapiens
Keywords:	3D-genome Hi-C epigenetic annotation

University/Institution:	Korea Advanced Institute of Science and Technology
Address:	Department of Biological Sciences, KAIST, Daejeon 34141, Korea
City:
Province/State:
Country/Region:	Korea, Republic of
Contact name (PI/Team):	Inkyung Jung
Contact email (PI/Helpdesk):	ijung@kaist.ac.kr

Database Commons
a catalog of worldwide biological databases

a catalog of worldwide biological databases

Database Profile

General information

Classification & Tag

Contact information

Publications

Ranking

Community reviews

Word cloud

Tags

Related Databases

Record metadata

Research & Resources

Featured

Alliance & Collaboration

Conference & Outreach

About

Database Commons a catalog of worldwide biological databases