ChromContact
ChromContact analyzes spatial chromosome contacts from Hi-C data to compute locus-specific contact profiles that support interpretation of three-dimensional chromosomal architecture.
Key Features:
- Hi-C data analysis: Processes Hi-C datasets to analyze spatial chromosome contacts.
- Locus-specific contact profiling: Calculates detailed contact profiles for specified genomic loci.
- UCSC Genome Browser integration: Generates links to the UCSC Genome Browser to visualize Hi-C interactions alongside genomic annotations.
Scientific Applications:
- Investigating long-range promoter-enhancer interactions: Identifies spatial contacts linking promoters and distal enhancers using Hi-C contact profiles.
- Functional interpretation of GWAS markers and ChIP-seq peaks: Maps GWAS markers and ChIP-seq peaks to spatial contacts to infer potential regulatory targets distant from annotated genes.
Methodology:
Computes locus-specific contact profiles from Hi-C data and generates UCSC Genome Browser links for integration with genomic annotations.
Topics
Details
- License:
- GPL-3.0
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Programming Languages:
- PHP, Perl
- Added:
- 5/7/2018
- Last Updated:
- 12/10/2018
Operations
Publications
Sato T, Suyama M. ChromContact: A web tool for analyzing spatial contact of chromosomes from Hi-C data. BMC Genomics. 2015;16(1). doi:10.1186/s12864-015-2282-x. PMID:26666652. PMCID:PMC4678698.
PMID: 26666652
PMCID: PMC4678698
Funding: - Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan: 21510215, 22132005, 26550089