Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://3dgd.biosino.org
Full name: 3D Genome Database
Description: 3DGD (3D Genome Database), is a database that currently collected Hi-C data on four species, for easy accessing and visualization of chromatin 3D structure data.
Year founded: 2013
Last update: 2013-11-17
Version: v1.1
Accessibility:
Manual:
Unaccessible
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Country/Region: China
Data type:
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Address: 320 Yue Yang Road, Shanghai 200031, P. R. China
City: Shanghai
Province/State:
Country/Region: China
Contact name (PI/Team): Yixue Li
Contact email (PI/Helpdesk): yxli@sibs.ac.cn

Publications

24526713
The 3DGD: a database of genome 3D structure. [PMID: 24526713]
Li C, Dong X, Fan H, Wang C, Ding G, Li Y.

The studies of chromatin 3D structure help us to understand its formation and function. Techniques combining chromosome conformation capture and next generation sequencing can capture chromatin structure information and has been applied to several different species and cell lines. We built 3DGD (3D Genome Database), a database that currently collected Hi-C data on four species, for easy accessing and visualization of chromatin 3D structure data. With the integration of other omics data such as genome-wide protein-DNA-binding data, this data source would be useful for researchers interested in chromatin structure and its biological functions. The 3DGD v1.1, data browser, downloadable files and documentation are available at: http://3dgd.biosino.org/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Bioinformatics. 2014:30(11) | 9 Citations (from Europe PMC, 2021-06-19)

Ranking

All databases:
3313/5061 (34.558%)
Interaction:
535/771 (30.739%)
Structure:
438/700 (37.571%)
Gene genome and annotation:
953/1350 (29.481%)
3313
Total Rank
9
Citations
1.286
z-index

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Record metadata

Created on: 2015-06-28
Curated by:
Dong Zou [2018-03-08]
Mengwei Li [2016-04-11]
Mengwei Li [2016-03-31]
Mengwei Li [2016-03-24]
lin liu [2016-01-13]
Mengwei Li [2015-11-21]
Lina Ma [2015-06-30]
Zhang Zhang [2015-06-29]
Lina Ma [2015-06-29]
Zhang Zhang [2015-06-28]