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BMC Genomics. 2015 Dec 15;16:1060. doi: 10.1186/s12864-015-2282-x.

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

Author information

1
Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan. sato@bioreg.kyushu-u.ac.jp.
2
AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, 812-8582, Japan. sato@bioreg.kyushu-u.ac.jp.
3
Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan. mikita@bioreg.kyushu-u.ac.jp.
4
AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, 812-8582, Japan. mikita@bioreg.kyushu-u.ac.jp.

Abstract

BACKGROUND:

Hi-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.

RESULTS:

We 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.

CONCLUSION:

ChromContact 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/ .

PMID:
26666652
PMCID:
PMC4678698
DOI:
10.1186/s12864-015-2282-x
[Indexed for MEDLINE]
Free PMC Article

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