DENdb: database of integrated human enhancers

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/

[1]  Melissa J. Landrum,et al.  RefSeq: an update on mammalian reference sequences , 2013, Nucleic Acids Res..

[2]  Morteza Mohammad Noori,et al.  Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features , 2014, PLoS Comput. Biol..

[3]  David A. Orlando,et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.

[4]  T. Mikkelsen,et al.  The NIH Roadmap Epigenomics Mapping Consortium , 2010, Nature Biotechnology.

[5]  Michael R. Green,et al.  Transcriptional regulatory elements in the human genome. , 2006, Annual review of genomics and human genetics.

[6]  Inna Dubchak,et al.  VISTA Enhancer Browser—a database of tissue-specific human enhancers , 2006, Nucleic Acids Res..

[7]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[8]  C. Kai,et al.  CAGE: cap analysis of gene expression , 2006, Nature Methods.

[9]  A. Dean,et al.  Enhancer function: mechanistic and genome-wide insights come together. , 2014, Molecular cell.

[10]  J. Lieb,et al.  What are super-enhancers? , 2014, Nature Genetics.

[11]  Katherine S. Pollard,et al.  Integrating Diverse Datasets Improves Developmental Enhancer Prediction , 2013, PLoS Comput. Biol..

[12]  Cesare Furlanello,et al.  A promoter-level mammalian expression atlas , 2015 .

[13]  Kai Tan,et al.  Discover regulatory DNA elements using chromatin signatures and artificial neural network , 2010, Bioinform..

[14]  Dongwon Lee,et al.  kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets , 2013, Nucleic Acids Res..

[15]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[16]  T. Mikkelsen,et al.  Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. , 2013, Genome research.

[17]  Timothy J. Durham,et al.  Systematic analysis of chromatin state dynamics in nine human cell types , 2011, Nature.

[18]  Li Teng,et al.  4DGenome: a comprehensive database of chromatin interactions , 2015, Bioinform..

[19]  Nathan C. Sheffield,et al.  The accessible chromatin landscape of the human genome , 2012, Nature.

[20]  Hiroki R Ueda,et al.  Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock , 2008, Proceedings of the National Academy of Sciences.

[21]  Li Teng,et al.  4DGenome: a comprehensive database of chromatin interactions , 2015, Bioinform..

[22]  B. L,et al.  The accessible chromatin landscape of the human genome , 2016 .

[23]  Boris Lenhard,et al.  Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. , 2009, Developmental biology.

[24]  A. Stark,et al.  Transcriptional enhancers: from properties to genome-wide predictions , 2014, Nature Reviews Genetics.

[25]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[26]  V. Bajic,et al.  DEEP: a general computational framework for predicting enhancers , 2014, Nucleic acids research.

[27]  Vladimir B. Bajic,et al.  HOCOMOCO: a comprehensive collection of human transcription factor binding sites models , 2012, Nucleic Acids Res..

[28]  H. Chandler.  Database , 1985 .

[29]  Timothy J. Durham,et al.  "Systematic" , 1966, Comput. J..

[30]  William Stafford Noble,et al.  Unsupervised pattern discovery in human chromatin structure through genomic segmentation , 2012, Nature Methods.

[31]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[32]  Wei Wang,et al.  Comparative annotation of functional regions in the human genome using epigenomic data , 2013, Nucleic acids research.

[33]  Dustin E. Schones,et al.  Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes , 2009, Cell.

[34]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[35]  Tao Liu,et al.  CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human , 2012, Bioinform..

[36]  Nathaniel D Heintzman,et al.  Finding distal regulatory elements in the human genome. , 2009, Current opinion in genetics & development.

[37]  Wei Xie,et al.  RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State , 2013, PLoS Comput. Biol..

[38]  Michael Q. Zhang,et al.  Combinatorial patterns of histone acetylations and methylations in the human genome , 2008, Nature Genetics.

[39]  Manolis Kellis,et al.  ChromHMM: automating chromatin-state discovery and characterization , 2012, Nature Methods.

[40]  R. Young,et al.  Transcription of eukaryotic protein-coding genes. , 2000, Annual review of genetics.

[41]  Mathieu Blanchette,et al.  PReMod: a database of genome-wide mammalian cis-regulatory module predictions , 2006, Nucleic Acids Res..

[42]  William Stafford Noble,et al.  FIMO: scanning for occurrences of a given motif , 2011, Bioinform..

[43]  William Stafford Noble,et al.  Integrative annotation of chromatin elements from ENCODE data , 2012, Nucleic acids research.