ChromContact: A web tool for analyzing spatial contact of chromosomes from Hi-C data

BMC Genomics

Software

Tetsuya Sato¹  Mikita Suyama¹ 

[1] Medical Institute of Bioregulation, Kyushu University, 812-8582, Fukuoka, Japan;AMED-CREST, Japan Agency for Medical Research and Development, 812-8582, Fukuoka, Japan;

关键词: Hi-C;    Long-range interaction;    Enhancer;   

DOI  :  10.1186/s12864-015-2282-x

 received in 2015-08-31, accepted in 2015-12-08,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundHi-C analysis has revealed the three-dimensional architecture of chromosomes in the nucleus. Although Hi-C data contains valuable information on long-range interactions of chromosomes, the data is not yet widely utilized by molecular biologists because of the quantity of data.ResultsWe developed a web tool, ChromContact, to utilize the information obtained by Hi-C. The web tool is designed to be simple and easy to use. By specifying a locus of interest, ChromContact calculates contact profiles and generates links to the UCSC Genome Browser, enabling users to visually examine the contact information with various annotations.ConclusionChromContact provides wide-range of molecular biologists with a user-friendly means to access high-resolution Hi-C data. One of the possible applications of ChromContact is investigating novel long-range promoter-enhancer interactions. This facilitates the functional interpretation of statistically significant markers identified by GWAS or ChIP-seq peaks that are located far from any annotated genes. ChromContact is freely accessible at http://bioinfo.sls.kyushu-u.ac.jp/chromcontact/.

【 授权许可】

CC BY   
© Sato and Suyama. 2015