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

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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.
Publisher
OXFORD UNIV PRESS
Issue Date
2018-01
Language
English
Article Type
Article
Citation

NUCLEIC ACIDS RESEARCH, v.46, no.D1, pp.D52 - D57

ISSN
0305-1048
DOI
10.1093/nar/gkx1017
URI
http://hdl.handle.net/10203/240142
Appears in Collection
BS-Journal Papers(저널논문)BiS-Journal Papers(저널논문)
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