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2024-03-18Join IBIS! New TF binding specificity challenge open for registration https://ibis.autosome.org   [showhide]

IBIS is an open challenge in Inferring Binding Specificities of human transcription factors from multiple experiment types with bioinformatics & machine learning. Have a look at our website, participate in our discussion forums, or contact us by email:

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 with 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 experiments such as CAGE and Oligocapping. The resulting databases are the following:
  • Animals:
    • Homo sapiens (hg38): 29598 promoters MOUNTED
    • Macaca mulatta (rheMac8): 9575 promoters MOUNTED
    • Mus musculus (mm10): 25111 promoters MOUNTED
    • Rattus norvegicus (rn6): 12601 promoters MOUNTED
    • Gallus gallus (galGal5): 6127 promoters MOUNTED
    • Canis familiaris (canFam3): 7545 promoters MOUNTED
    • Drosophila melanogaster (dm6): 16972 promoters MOUNTED
    • Apis mellifera (amel5): 6493 promoters MOUNTED
    • Danio rerio (danRer7): 10728 promoters MOUNTED
    • Caenorhabditis elegans (ce6): 7120 promoters MOUNTED
  • Plants:
    • Arabidopsis thaliana (araTha1): 22703 promoters MOUNTED
    • Zea mays (zm3): 17081 promoters MOUNTED
    • Hordeum vulgare (MorexV3): 21193 promoters MOUNTED
  • Fungi:
    • Saccharomyces cerevisiae (sacCer3): 5117 promoters MOUNTED
    • Schizosaccharomyces pombe (spo2): 4802 promoters MOUNTED
  • Invertebrates:
    • Plasmodium falciparum (pfa2): 5597 promoters MOUNTED
EPD
  • Animals:
    • Homo sapiens (hg18): MOUNTED
    • Pan troglodytes (panTro2): MOUNTED
    • Mus musculus (mm9): MOUNTED
    • Rattus norvegicus (rn4): MOUNTED
    • Gallus gallus (galGal3): MOUNTED
    • Bos taurus (bosTau3): MOUNTED
    • Drosophila melanogaster (dm3): MOUNTED
    • Caenorhabditis elegans (ce6): MOUNTED
  • Plants:
    • Arabidopsis thaliana (araTha1): MOUNTED
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 November 2024