databases > DOI:10.25504/FAIRsharing.yk1krv

ready Eukaryotic Promoter Database

Abbreviation:EPD

General Information
The Eukaryotic Promoter Database (EPD) provides accurate transcription start site (TSS) information for promoters of 15 model organisms, from human to yeast to the malaria parasite Plasmodium falciparum. While the original database was a manually curated database based on published experiments, new promoter collections are now produced entirely automatically (under the name “EPDnew”) based on high-throughput transcript mapping data and high-quality gene annotation resources. Corresponding functional genomics data can be viewed in a genome browser, queried or analyzed via web interfaces, or exported in standard formats like FASTA or BED for subsequent analysis with other tools; of note, EPD is tightly integrated with two tool suites developed by our group: ChIP-Seq (https://ccg.epfl.ch/chipseq) and Signal Search Analysis (https://ccg.epfl.ch/ssa), for analysis of chromatin context and sequence motif respectively. EPD provides promoter viewers, designed with the aim of integrating and displaying information from different sources about, for instance, histone marks, transcription factor-binding sites or SNPs with known phenotypes. These viewers rely upon the UCSC genome browser as a visualization platform, which enables users to view data tracks from EPD jointly with tracks from UCSC or public track hubs.

Homepage https://epd.epfl.ch/

Countries that developed this resource Switzerland

Created in 1988

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How to cite this record FAIRsharing.org: EPD; Eukaryotic Promoter Database; DOI: https://doi.org/10.25504/FAIRsharing.yk1krv; Last edited: Oct. 22, 2019, 12:43 p.m.; Last accessed: Oct 21 2020 5:06 p.m.


This record is maintained by rdreos  ORCID  and pmeylan  ORCID

Record updated: Oct. 22, 2019, 12:19 p.m. by pmeylan.

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Publications

The eukaryotic promoter database (EPD).

Périer RC, Praz V, Junier T, Bonnard C, Bucher P.
Nucleic Acid Res. 2000

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The Eukaryotic Promoter Database (EPD): recent developments.

Périer RC, Junier T, Bonnard C, Bucher P.
Nucleic Acid Res. 1999

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The Eukaryotic Promoter Database EPD.

Cavin Périer R, Junier T, Bucher P.
Nucleic Acid Res. 1998

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Compilation and analysis of eukaryotic POL II promoter sequences

Bucher,P. and Trifonov,E.N.
Nucleic Acids Res. 1986

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The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools.

Dreos, R., Ambrosini, G., Périer, R., Bucher, P.
Nucleic Acid Res. 2015

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EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era.

Dreos R, Ambrosini G, Cavin Périer R, Bucher P.
Nucleic Acid Res. 2013

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EPD in its twentieth year: towards complete promoter coverage of selected model organisms.

Schmid CD, Perier R, Praz V, Bucher P.
Nucleic Acid Res. 2006

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The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.

Schmid CD, Praz V, Delorenzi M, Périer R, Bucher P.
Nucleic Acid Res. 2004

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The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data.

Praz V, Périer R, Bonnard C, Bucher P.
Nucleic Acid Res. 2002

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Grant Number(s)

  • 31-063933 (Swiss National Sciences Foundation (SNCF))

  • 31-54782.98 (Swiss National Sciences Foundation (SNCF))

  • 31003A_125193 (Swiss National Sciences Foundation (SNCF))

  • 3100A0-104248 (Swiss National Sciences Foundation (SNCF))

  • 95.0236-1 (Swiss Federal Office for Education and Science, Neuchtel, Switzerland)