DENdb: database of integrated human enhancers

Database : the Journal of Biological Databases and Curation
Haitham AshoorVladimir B Bajic

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/.

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Citations

Nov 13, 2015·Expert Review of Gastroenterology & Hepatology·M A Blum MurphyJaffer A Ajani
Jan 10, 2019·Database : the Journal of Biological Databases and Curation·Zena CaiYousong Peng
Jun 13, 2017·Database : the Journal of Biological Databases and Curation·Simon FishilevichDana Cohen
Apr 4, 2017·Nature Genetics·Colby ChiangIra M Hall
Oct 28, 2017·Nucleic Acids Research·Zhen WangZhengdong D Zhang
May 8, 2018·Nature Medicine·Jose V Sanchez-MutJohannes Gräff
Sep 25, 2018·Nucleic Acids Research·Jing WangYu Shyr
Jan 13, 2019·International Journal of Molecular Sciences·Marta KubiakMarzena Anna Lewandowska
Dec 5, 2015·Briefings in Bioinformatics·Dimitrios KleftogiannisVladimir B Bajic
Jun 13, 2018·Briefings in Bioinformatics·Elena RojanoJames R Perkins
Jun 6, 2018·Nature Methods·Xian AdiconisJoshua Z Levin
Jan 29, 2019·Database : the Journal of Biological Databases and Curation·Ran KangZhiyun Guo
Oct 13, 2020·Nucleic Acids Research·Wanwen ZengRui Jiang
Oct 9, 2020·Disease Markers·Xiaona ZhangJunsong Han
Nov 14, 2020·Database : the Journal of Biological Databases and Curation·Davide DalfovoAlessandro Romanel
Jun 24, 2021·NAR Genomics and Bioinformatics·Pengyu Ni, Zhengchang Su

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Datasets Mentioned

BETA
GM12878

Methods Mentioned

BETA
ChIP-seq

Software Mentioned

PEDB
CSI
ENCODE Epigenome Roadmap
VISTA enhancer browser
HOCOMOCO
Atlas
UCSC genome browser
kmer
PReMod
DEEP

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