The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools
By René Dreos, Giovanna Ambrosini, Rouaïda Cavin Périer, Philipp Bucher. Nucleic Acids Res., 2014
324 citations recorded by the source corpus.
We present an update of EPDNew (http://epd.vital-it.ch), a recently introduced new part of the Eukaryotic Promoter Database (EPD) which has been described in more detail in a previous NAR Database Issue. EPD is an old database of experimentally characterized eukaryotic POL II promoters, which are conceptually defined as transcription initiation sites or regions. EPDnew is a collection of automatically compiled, organism-specific promoter lists complementing the old corpus of manually compiled promoter entries of EPD. This new part is exclusively derived from next generation sequencing data from high-throughput promoter mapping experiments. We report on the recent growth of EPDnew, its extension to additional model organisms and its improved integration with other bioinformatics resources developed by our group, in particular the Signal Search Analysis and ChIP-Seq web servers.
Subfields: Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/d064795c991bbd990f1b82a36a1248ee9d4eece4
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In Genetics
- Maria Anisimova
- David Haussler
- Manuel Gil
- Gaston H. Gonnet
- Laurent Excoffier
- Samuel Neuenschwander
- C. von Mering
- Stefan Zoller
In Molecular Biology
- Torsten Schwede
- Lorenza Bordoli
- Gabriel Studer
- Antoine Daina
- Adrian M. Altenhoff
- J. Haas
- Konstantin Arnold
- Vincent Zoete
Citations in the corpus
- GeneHancer: genome-wide integration of enhancers and target genes in GeneCards (2017, methodology): “In view of the enhancer–promoter interrelations, we have directly assessed the overlap between our candidate enhancers and promoters from an independent source, the Eukaryotic Promoter Database (EPD) (60), as well as from Ensembl.”
- The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases (2015, background): “ch) is an annotated database of eukaryotic POL II promoters for which the transcription start site has been experimentally defined (42).”
- The UCSC Genome Browser database: 2021 update (2020, methodology): “The transcription start sites from the Eukaryotic Promoter Database (28,29) were incorporated into the Promoters from EPDnew track (Expression Group) for human (hg38 and hg19) and mouse (mm10) assemblies.”