title: 4DGenome: a comprehensive database of chromatin interactions.
abstract: BACKGROUND
  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.
authors: Department of Internal Medicine and.
authors: Li
authors: L
authors: Teng
authors: Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52242, USA.
authors: Bing
authors: B
authors: He
authors: Department of Internal Medicine and.
authors: Jiahui
authors: J
authors: Wang
authors: Department of Internal Medicine and.
authors: Kai
authors: K
authors: Tan
mesh_terms: D002843:Chromatin / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D005786:Gene Expression Regulation; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans
chemical_list: D002843:Chromatin