General Information
| Description | A comprehensive database of chromatin interactions |
| Homepage | http://4dgenome.int-med.uiowa.edu |
Publications
4DGenome: a comprehensive database of chromatin interactions
Motivation
: The 3D structure of the genome plays a critical role in regulating gene expression. Recent progress in mapping technologies for chromatin interactions has led to a rapid increase in this kind of interaction data. This trend will continue as research in this burgeoning field intensifies.
Results:
We describe the 4DGenome database that stores chromatin interaction data compiled through comprehensive literature curation. The database currently covers both low- and high-throughput assays, including 3C, 4C-Seq, 5C, Hi-C, ChIA-PET and Capture-C. To complement the set of interactions detected by experimental assays, we also include interactions predicted by a recently developed computational method with demonstrated high accuracy. The database currently contains ∼8 million records, covering 102 cell/tissue types in five organisms. Records in the database are described using a standardized file format, facilitating data exchange. The vast major of the interactions were assigned a confidence score. Using the web interface, users can query and download database records via a number of annotation dimensions. Query results can be visualized along with other genomics datasets via links to the UCSC genome browser. We anticipate that 4DGenome will be a valuable resource for investigating the spatial structure-and-function relationship of genomes.
Availability and Implementation:
4Dgenome is freely accessible at http://4dgenome.int-med.uiowa.edu. The database and web interface are implemented in MySQL, Apache and JavaScript with all major browsers supported.
Contact:
kai-tan@uiowa.edu
Supplementary Information:
Supplementary Materials are available at Bioinformatics online.
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