3CDB: a manually curated database of chromosome conformation capture data
3CDB: a manually curated database of chromosome conformation capture data
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3CDB：手动管理的染色体构象捕获数据数据库
DOI：
10.1093/database/baw044
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发表时间：
2016-04-14
影响因子：
5.8
通讯作者：
Zhang, Zhihua
中科院分区：
文献类型：
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作者：
Yun, Xiaoxiao;Xia, Lili;Zhang, Zhihua
染色体构象捕获 (3C) 是一种生化技术，用于分析细胞群中选定基因组位点之间的接触频率。它最近的基因组变异，例如通过双端标签 (ChIA-PET) 进行 Hi-C/染色质相互作用分析，使核组织的研究达到了前所未有的水平。然而，由于 Hi-C/ChIA-PET 固有的低分辨率和超高成本，3C 仍然是确定给定调控 DNA 元件（例如增强子和启动子）之间相互作用的黄金标准。因此，我们开发了一个3C确定的功能性染色质相互作用数据库（3CDB；http://3cdb.big.ac.cn）。为了构建 3CDB，我们通过精心设计的关键词组合搜索了 PubMed 和 Google Scholar，检索了 5000 多篇文章，从中手动提取了 17 个物种的 3319 个相互作用。此外，我们提出了数据可靠性的系统评估方案，并将相互作用分为四类。由于实验室间采用了各种修改后的 3C 协议，接触频率无法直接比较。我们的评估方案为该领域这个长期存在的问题提供了一个可行的解决方案。用户友好的网络界面旨在帮助 3CDB 中的快速搜索。我们相信 3CDB 将为实验设计和系统发育分析提供基础信息，并弥合分子生物学家和系统生物学家之间的差距，他们现在必须应对嘈杂的高通量数据。
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.