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2023-11-17EPDnew FTP repository archived in zenodo:   [showhide]

Snapshot of the EPDnew FTP directory of November 2023. The acronym EPDnew refers to the newer versions of the Eukaryotic Promoter Database published in the format introduced in 2013. The directory contains all database versions for 15 model organisms released since then.

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 collection of databases of experimentally validated promoters for selected model organisms. Evidence comes from TSS-mapping from high-throughput expreriments such as CAGE and Oligocapping. The resulting databases are the following:
  • Animals:
    • Homo sapiens: 29598 promoters,
    • Macaca mulatta: 9575 promoters,
    • Mus musculus: 25111 promoters,
    • Rattus norvegicus: 12601 promoters,
    • Gallus gallus: 6127 promoters,
    • Canis familiaris: 7545 promoters,
    • Drosophila melanogaster: 16972 promoters,
    • Apis mellifera: 6493 promoters,
    • Danio rerio: 10728 promoters,
    • Caenorhabditis elegans: 7120 promoters;
  • Plants:
    • Arabidopsis thaliana: 22703 promoters;
    • Zea mays: 17081 promoters;
  • Fungi:
    • Saccharomyces cerevisiae: 5117 promoters,
    • Schizosaccharomyces pombe: 4802 promoters;
  • Invertebrates:
    • Plasmodium falciparum: 5597 promoters.
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.
Latest research from us that uses EPD:

Computational identification and experimental characterization of preferred downstream positions in human core promoters. Dreos R, Sloutskin A, Malachi N, Ideses D, Bucher P, Juven-Gershon T. PLoS Comput Biol. 2021 Aug 12;17(8):e1009256. doi: 10.1371/journal.pcbi.1009256; PMID: 34383743

Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters. Dreos, R., Ambrosini, G., Bucher, P. PLOS Comp Biol (2016) doi: 10.1371/journal.pcbi.1005144; PMID: 27716823

Please cite us using the following references:

EPDnew database description:
EPD in 2020: enhanced data visualization and extension to ncRNA promoters. Meylan P, Dreos R, Ambrosini G, Groux R, Bucher P. Nucleic Acids Res. 2020 Jan 8;48(D1):D65-D69. doi: 10.1093/nar/gkz1014; PMID: 31680159.

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; PMID: 25378343

Last update October 2019