4DGenome: a comprehensive database of chromatin interactions

Bioinformatics. 2015 Aug 1;31(15):2560-4. doi: 10.1093/bioinformatics/btv158. Epub 2015 Mar 18.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Chromatin / genetics*
  • Chromatin / metabolism*
  • Computational Biology / methods*
  • Databases, Factual*
  • Gene Expression Regulation
  • Genome, Human*
  • Genomics / methods*
  • Humans


  • Chromatin