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Database Commons - CCSI

CCSI

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Short name CCSI
Full name Chromatin–Chromatin Spatial Interaction
Description CCSI integrats 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.
URL http://songyanglab.sysu.edu.cn/ccsi
Year founded 2016
Last update & version 2016-02-11    
Availability Not Available
University/Institution hosted Sun Yat-Sen University
Address Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences
City Guangzhou
Province/State Guangdong
Country/Region China
Contact name Yuanyan Xiong
Contact email xyyan@mail.sysu.edu.cn
Data type(s)
Major organism(s)
Keyword(s)
  • 3C
  • 4C
  • 5C
  • ChIA-PET
  • Hi-c
Publication(s)
  • CCSI: a database providing chromatin-chromatin spatial interaction information. [PMID: 26868054]

    Xiaowei Xie, Wenbin Ma, Zhou Songyang, Zhenhua Luo, Junfeng Huang, Zhiming Dai, Yuanyan Xiong
    Database : the journal of biological databases and curation 2016:2016
    0 Citations (Google Scholar as of 2017-03-07)

    Abstract: 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://songyanglab.sysu.edu.cn/ccsi. © The Author(s) 2016. Published by Oxford University Press.

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Tags

Interaction and Network
Homo sapiens Mus musculus Saccharomyces cerevisiae
3C 4C 5C ChIA-PET Hi-c

Record metadata

  • Created on: 2017-03-07
  • Curated by:
    • Shixiang Sun [2017-03-07]
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