3DIV: A 3D-genome Interaction Viewer and database

Cited 47 time in scopus
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Title
3DIV: A 3D-genome Interaction Viewer and database
Author(s)
D Yang; Insu Jang; Jinhyuk Choi; Min-Seo Kim; A J Lee; H Kim; J Eom; D Kim; I Jung; Byungwook Lee
Bibliographic Citation
Nucleic Acids Research, vol. 46, pp. D52-D57
Publication Year
2018
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
ISSN
0305-1048
Publisher
Oxford Univ Press
DOI
http://dx.doi.org/10.1093/nar/gkx1017
Type
Article
Appears in Collections:
Korea Bioinformation Center > 1. Journal Articles
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