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. 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

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Free PMC article

ChromContact: A Web Tool for Analyzing Spatial Contact of Chromosomes From Hi-C Data

Tetsuya Sato et al. BMC Genomics. .
Free PMC article

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/ .

Figures

Fig. 1
Fig. 1
An example of a known long-range enhancer–promoter interaction in the human MYC locus. A 2-Mb genomic interval around the human MYC locus (genome assembly hg19) is shown in the UCSC Genome Browser. There are three tracks (from the top): (i) contact profile at 10-kb resolution obtained from Hi-C data; (ii) profile for H3K4me1; and (iii) profile for DNase I hypersensitivity sites, for each of the six cell types (GM12878, K562, IMR90, HUVEC, HMEC, and NHEK). Different colors are used for each of the six cell types. The anchor, which contains the transcription start site of MYC, is indicated by dark-colored highlights in the contact profiles. The colorectal cancer associated SNP, rs6983267, and gene annotations are shown at the bottom. The position of the SNP and the corresponding peaks in the profiles are indicated by a rounded rectangle
Fig. 2
Fig. 2
Two examples of long-range enhancer–promoter interactions in ZEB2 and PAX6 loci. Only the cell type with the most significant interaction is shown in each example. For each example, there are four tracks (from the top): (i) contact profile at 10-kb resolution obtained from Hi-C data; (ii) profile for H3K4me1; and (iii) profile for DNase I hypersensitivity sites; and (iv) gene annotations. The anchors, which contain the transcription start sites of the respective genes, are indicated by dark-colored highlights in the contact profiles. The positions of the enhancers are indicated by rounded rectangles. a A 800-kb genomic interval around the human ZEB2 locus (genome assembly hg19). b A 800-kb genomic interval around the human PAX6 locus (genome assembly hg19)

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