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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

Taxonomic range

Eukaryota

Knowledge Domains

Subjects

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: Jul 04 2020 3:23 p.m.

This record is maintained by rdreos ORCID and pmeylan ORCID

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

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.yk1krv' by 'pmeylan' at 12:19, 22 Oct 2019 (approved):

	'description' has been modified:
		Before: 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.
		After: 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.

Edits to 'https://fairsharing.org/FAIRsharing.yk1krv' by 'pmeylan' at 10:27, 22 Oct 2019 (approved):

	'supportLinks' has been modified:
		Before:
			contact form|http://epd.vital-it.ch/webmail.php
			online documentation|http://epd.vital-it.ch/documents.php
		After:
			contact form|https://epd.epfl.ch/webmail.php
			online documentation|http://epd.epfl.ch/documents.php
		Added:
			contact form|https://epd.epfl.ch/webmail.php
			online documentation|http://epd.epfl.ch/documents.php
		Removed:
			contact form|http://epd.vital-it.ch/webmail.php
			online documentation|http://epd.vital-it.ch/documents.php

	'tools' has been modified:
		Before:
			Signal Search Analysis|2.0|http://ccg.vital-it.ch/ssa/
			ChIP-Seq|1.3|http://ccg.vital-it.ch/chipseq/
			Analyze||http://epd.vital-it.ch/EPDnew_study.php
			EPDnew selection tool||http://epd.vital-it.ch/EPDnew_select.php
			ExPASy Tools||http://www.expasy.org/genomics
		After:
			Signal Search Analysis|2.0|https://ccg.epfl.ch/ssa/
			ChIP-Seq|1.3|https://ccg.epfl.ch/chipseq/
			EPDnew analysis tool||https://epd.epfl.ch/EPDnew_study.php
			EPDnew selection tool||https://epd.epfl.ch/EPDnew_select.php
			ExPASy Tools||https://www.expasy.org/genomics
		Added:
			Signal Search Analysis|2.0|https://ccg.epfl.ch/ssa/
			ChIP-Seq|1.3|https://ccg.epfl.ch/chipseq/
			EPDnew analysis tool||https://epd.epfl.ch/EPDnew_study.php
			EPDnew selection tool||https://epd.epfl.ch/EPDnew_select.php
			ExPASy Tools||https://www.expasy.org/genomics
		Removed:
			Signal Search Analysis|2.0|http://ccg.vital-it.ch/ssa/
			ChIP-Seq|1.3|http://ccg.vital-it.ch/chipseq/
			Analyze||http://epd.vital-it.ch/EPDnew_study.php
			EPDnew selection tool||http://epd.vital-it.ch/EPDnew_select.php
			ExPASy Tools||http://www.expasy.org/genomics

	'dataProcesses' has been modified:
		Before:
			download
			ftp download
			advanced search
		After:
			download
			ftp download
		Added:
		Removed:
			advanced search

	'contactEmail' has been modified:
		Before: epd@isb-sib.ch
		After: ask-epd@googlegroups.com

	'contact' has been modified:
		Before: Ren? Dreos
		After: Philipp Bucher

	'miriam_id' has been modified:
		Before: MIR:00000408
		After: 

	'homepage' has been modified:
		Before: http://epd.vital-it.ch/
		After: https://epd.epfl.ch/

Edits to 'https://fairsharing.org/FAIRsharing.yk1krv' by 'The FAIRsharing Team' at 10:36, 08 Sep 2016 (approved):

	'contactORCID' has been modified:
		Before: 
		After: 0000-0002-0816-7775

Support

General

contact form	https://epd.epfl.ch/webmail.php
online documentation	http://epd.epfl.ch/documents.php

Additional Information

Contact

Philipp Bucher ORCID

Tools

Signal Search Analysis	https://ccg.epfl.ch/ssa/	2.0
ChIP-Seq	https://ccg.epfl.ch/chipseq/	1.3
EPDnew analysis tool	https://epd.epfl.ch/EPDnew_study.php
EPDnew selection tool	https://epd.epfl.ch/EPDnew_select.php
ExPASy Tools	https://www.expasy.org/genomics

Access / Retrieve Data

Conditions of Use

Data Access

download	https://epd.epfl.ch/EPD_download.php
ftp download	ftp://ccg.epfl.ch/epd/

Publications

The eukaryotic promoter database (EPD).

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