DENdb: database of integrated human enhancers

Database (Oxford). 2015 Sep 5;2015:bav085. doi: 10.1093/database/bav085. Print 2015.

Abstract

Enhancers are cis-acting DNA regulatory regions that play a key role in distal control of transcriptional activities. Identification of enhancers, coupled with a comprehensive functional analysis of their properties, could improve our understanding of complex gene transcription mechanisms and gene regulation processes in general. We developed DENdb, a centralized on-line repository of predicted enhancers derived from multiple human cell-lines. DENdb integrates enhancers predicted by five different methods generating an enriched catalogue of putative enhancers for each of the analysed cell-lines. DENdb provides information about the overlap of enhancers with DNase I hypersensitive regions, ChIP-seq regions of a number of transcription factors and transcription factor binding motifs, means to explore enhancer interactions with DNA using several chromatin interaction assays and enhancer neighbouring genes. DENdb is designed as a relational database that facilitates fast and efficient searching, browsing and visualization of information. Database URL: http://www.cbrc.kaust.edu.sa/dendb/.

Publication types

  • Dataset
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Nucleic Acid*
  • Humans
  • Nucleotide Motifs*
  • Response Elements*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism

Substances

  • Transcription Factors