Database Commons

a catalog of biological databases

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

Database Profile

General information

Full name: Chromosome Conformation Capture Database
Description: a database of 3C determined functional chromatin interactions
Year founded: 2016
Last update: 2016-01-18
Real time : Checking...
Country/Region: China

Contact information

University/Institution: Beijing Institute of Genomics, Chinese Academy of Sciences
Address: NO.1 Beichen West Road, Chaoyang District
City: Beijing
Province/State: Beijing
Country/Region: China
Contact name (PI/Team): Zhihua Zhang
Contact email (PI/Helpdesk):


3CDB: a manually curated database of chromosome conformation capture data. [PMID: 27081154]
Yun X, Xia L, Tang B, Zhang H, Li F, Zhang Z.

Chromosome conformation capture (3C) is a biochemical technology to analyse contact frequencies between selected genomic sites in a cell population. Its recent genomic variants, e.g. Hi-C/ chromatin interaction analysis by paired-end tag (ChIA-PET), have enabled the study of nuclear organization at an unprecedented level. However, due to the inherent low resolution and ultrahigh cost of Hi-C/ChIA-PET, 3C is still the gold standard for determining interactions between given regulatory DNA elements, such as enhancers and promoters. Therefore, we developed a database of 3C determined functional chromatin interactions (3CDB; To construct 3CDB, we searched PubMed and Google Scholar with carefully designed keyword combinations and retrieved more than 5000 articles from which we manually extracted 3319 interactions in 17 species. Moreover, we proposed a systematic evaluation scheme for data reliability and classified the interactions into four categories. Contact frequencies are not directly comparable as a result of various modified 3C protocols employed among laboratories. Our evaluation scheme provides a plausible solution to this long-standing problem in the field. A user-friendly web interface was designed to assist quick searches in 3CDB. We believe that 3CDB will provide fundamental information for experimental design and phylogenetic analysis, as well as bridge the gap between molecular and systems biologists who must now contend with noisy high-throughput data.Database URL: © The Author(s) 2016. Published by Oxford University Press.

Database (Oxford). 2016:2016() | 4 Citations (from Europe PMC, 2022-05-14)


All databases:
4162/5177 (19.625%)
Genotype phenotype and variation:
591/752 (21.543%)
662/829 (20.265%)
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Record metadata

Created on: 2017-03-27
Curated by:
Dong Zou [2021-11-17]
Dong Zou [2018-03-08]
Lina Ma [2017-06-02]
Shixiang Sun [2017-03-27]