title: 3CDB: a manually curated database of chromosome conformation capture data.
abstract: 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;http://3cdb.big.ac.cn). 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:http://3cdb.big.ac.cn.
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Xiaoxiao
authors.initials: X
authors.lastname: Yun
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Lili
authors.initials: L
authors.lastname: Xia
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Bixia
authors.initials: B
authors.lastname: Tang
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Feifei
authors.initials: F
authors.lastname: Li
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China zhangzhihua@big.ac.cn.
authors.forename: Zhihua
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D000818:Animals; D002843:Chromatin / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D002875:Chromosomes / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D066289:Data Curation; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D023281:Genomics; D006801:Humans; D051379:Mice
chemical_list: D002843:Chromatin