13-07-2015 -- Release of EPD version 124

This resource allows the access to several databases of experimentally validated promoters: EPD and EPDnew databases. They differ by the validation technique used and the coverage. EPD is a collection of eukaryotic promoters derived from published articles. Instead, the EPDnew databases (HT-EPD) are the result of merging EPD promoters whith in-house analysis of promoter-specific high-throughput data for selected organisms only. This process gives EPDnew high precision and high coverage.

EPDnew is a new collection of experimentally validated promoters in human, mouse, D. melanogaster and zebrafish genomes. Evidence comes from TSS-mapping from high-throughput expreriments such as CAGE and Oligocapping. ChIP-seq experiments on H2AZ, H3K4me3, Pol-II and DNA methylation are also taken into account during the analysis. The resulting database contains 23360 promoters for the human (H. sapiens) collection, 21239 promoters for the mouse (M. musculus) collection, 15073 promoters for the D. melanogaster collection, 10728 promoters for the zebrafish (D. rerio) collection, 7120 promoters for the worm (C. elegans) collection and 10229 promoters for the A. thaliana collection.
The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. This database contains 4806 promoters from several species.

Please cite us using the following references:

Promoters analysis tools:
The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools. Dreos, R., Ambrosini, G., Périer, R., Bucher, P. Nucleic Acids Res. (2014) doi: 10.1093/nar/gku1111; PUBMED  25378343

EPDnew methods description:
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. Dreos, R., Ambrosini, G., Périer, R., Bucher, P. Nucleic Acids Res. (2013) 41(Database issue):D157-64; PUBMED  23193273

Last update Aug. 2015