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| 2024-03-18 | Join IBIS! New TF binding specificity challenge open for registrationhttps://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:
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This resource allows the access to several databases of experimentallyvalidated promoters: EPD and EPDnew databases. They differ by thevalidation technique used and the coverage. EPD is a collection ofeukaryotic promoters derived from published articles. Instead, theEPDnew databases (HT-EPD) are the result of merging EPD promoterswith in-house analysis of promoter-specific high-throughput data forselected organisms only. This process gives EPDnewhighprecision 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:
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| 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 contains4806 promoters from several species. | ||
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