CCSI: a database providing chromatin-chromatin spatial interaction information.
CCSI: a database providing chromatin-chromatin spatial interaction information.
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CCSI：提供染色质-染色质空间相互作用信息的数据库。
DOI：
10.1093/database/bav124
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发表时间：
2016
期刊：
影响因子：
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通讯作者：
Xiong Yuanyan
中科院分区：
文献类型：
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作者：
Xie Xiaowei;Ma Wenbin;Songyang Zhou;Luo Zhenhua;Huang Junfeng;Dai Zhiming;Xiong Yuanyan
远端调控元件通过空间相互作用调节基因转录，单核苷酸多态(SNPs)与远端基因表达通过空间邻近联系在一起，这有助于解释疾病相关非编码区SNPs的因果作用。因此，对染色质空间相互作用的研究为阐明疾病发病机制中的转录调控机制开辟了新的途径。最近，通过3C、4C、5C、CHIA-PET和Hi-C技术揭示了越来越多的染色质相互作用。为了解释和利用这些相互作用，我们通过整合和注释来自已发表文献、UCSC数据库和NCBI GEO数据库的91组染色质相互作用数据，构建了染色质-染色质空间相互作用数据库，总共产生了3017962个成对相互作用(错误发现率 <； 0.05)，涵盖了人、小鼠和酵母。已经设计了一个网络界面来提供对染色质相互作用的访问。CCSI的主要特征是(I)在搜索页面中显示染色质相互作用和相应的基因、增强子和SNP；(Ii)在下载页面中提供完整的相互作用数据集、增强子和SNP信息；以及(Iii)为相互作用数据的注释提供分析管道。总之，CCSI将有助于探索与基因、调节区和SNP之间的空间相互作用相关的疾病发病机制中的转录调控机制。数据库网址：http://120.79.23.67/ccsi/search.php
Distal regulatory elements have been shown to regulate gene transcription through spatial interactions, and single nucleotide polymorphisms (SNPs) are linked with distal gene expression by spatial proximity, which helps to explain the causal role of disease-associated SNPs in non-coding region. Therefore, studies on spatial interactions between chromatin have created a new avenue for elucidating the mechanism of transcriptional regulation in disease pathogenesis. Recently, a growing number of chromatin interactions have been revealed by means of 3C, 4C, 5C, ChIA-PET and Hi-C technologies. To interpret and utilize these interactions, we constructed chromatin–chromatin spatial interaction (CCSI) database by integrating and annotating 91 sets of chromatin interaction data derived from published literature, UCSC database and NCBI GEO database, resulting in a total of 3 017 962 pairwise interactions (false discovery rate < 0.05), covering human, mouse and yeast. A web interface has been designed to provide access to the chromatin interactions. The main features of CCSI are (i) showing chromatin interactions and corresponding genes, enhancers and SNPs within the regions in the search page; (ii) offering complete interaction datasets, enhancer and SNP information in the download page; and (iii) providing analysis pipeline for the annotation of interaction data. In conclusion, CCSI will facilitate exploring transcriptional regulatory mechanism in disease pathogenesis associated with spatial interactions among genes, regulatory regions and SNPs.Database URL: http://120.79.23.67/ccsi/search.php