302–303Nucleic Acids Research,2000,Vol.28,No.1©2000Oxford University Press
The Eukaryotic Promoter Database(EPD)
Rouaïda Cavin Périer,Viviane Praz,Thomas Junier,Claude Bonnard and Philipp Bucher* Swiss Institute of Bioinformatics and Swiss Institute for Experimental Cancer Research,Ch.des Boveresses155, 1066-Epalinges s/Lausanne,Switzerland
Received October6,1999;Accepted October8,1999
ABSTRACT
四川移动网上营业厅充值The Eukaryotic Promoter Database(EPD)is an anno-tated 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 a description of the initiation site mapping data,exhaustive cross-references to the EMBL nucleotide sequence database,SWISS-PROT, TRANSFAC and other databases,as well as biblio-graphic references.EPD is structured in a way that facilitates dynamic extraction of biologically mean-ingful promoter subsets for comparative sequence analysis.WWW-based interfaces have been d evel-oped that enable the user to view EPD entries in different formats,to select and extract promoter sequences according to a variety of criteria,and to navigate to related databases exploiting different cross-references.The EPD web site also features yearly updated base frequency matrices for major eukaryotic promoter elements.EPD can be accessed at www.epd.isb-sib.ch
DATABASE DESCRIPTION
The term promoter has two different meanings in biology:(i)a gene region immediately upstream of a transcription initiation site,and(ii)a cis-acting genetic element controlling the rate of transcription initiation of a gene.The Eukaryotic Promoter Database(EPD)is a database of promoters in the former sense. Information about promoters in the latter sense can be found in other databases such as TRANSFAC(1),ooTFD(2),TRRD (3),PlantCARE(4)and PLACE(5).
EPD was originally designed as a resource for comparative sequence analysis and,as such,has played an instrumental role in the characterization of eukaryotic transcription control elements(6,7),as well as in the development of eukaryotic promoter prediction algorithms(8).The main purpose of the database is to keep track of experimental data that define transcription initiation sites of eukaryotic genes.This type of functional information is linked to promoter sequences via mac
hine-readable pointers to positions within sequences of the EMBL nucleotide sequence database(9).
EPD is a rigorously selected,curated and quality-controlled database.In order to be included,a promoter must fulfill a number of conditions laid down in the user manual.Most importantly,the transcription start site must be mapped experimentally with an estimated precision of 5bp or higher. All information in EPD originates from a critical examination and independent interpretation of the experimental data presented in the cited research publications.Published conclusions and feature table annotations in EMBL entries are never blindly relied upon.At present,EPD is confined to promoters recognized by the RNA POL II system of higher eukaryotes(multicellular plants and animals).Note that this restriction does not a priori exclude viral promoters.
EPD is also a strictly non-redundant database.The general rule is that one entry corresponds to one transcription initiation site in a genome.Organisms are distinguished at the taxonomic level of the species.According to this policy,data from different literature sources pertaining to the same transcription initiation sites are represented by the same entry.Likewise, promoters belonging to different alleles of the same gene,or to the same gene in different subspecies,are covered by the same entry regardless of whether they differ in sequence.The user manual provides more details about how certain non-trivial cases such as promoters of tandemly repeated genes or retro-transpos
able elements,are handled.
A comprehensive description of the contents and format of EPD has been published earlier(10).User interfaces and software support for local installations have been previously described(11).
RECENT DEVELOPMENTS
Database
The objective of exhaustive cross-referencing between EPD promoters and EMBL sequences is being given high priority at the moment,especially with regard to genomes that are complete(Caenorhabditis elegans)or at an advanced stage of sequencing(Arabidopsis,Drosophila,human).As a consequence, the number of EMBL cross-references has increased by>1000 since last year(Table1).Moreover,the internal EPD cross-references have been revised.Until now,such links were only used to connect alternative promoters of the same gene.In future releases,promoters of different genes occurring at a short distance from each other(<1000bp),will also be cross-referenced.Such pairs of promoters usually promote transcription in opposite directions and often share upstream regulatory elements.As a new format feature,a keyword(KW)line type
斜发沸石
*To whom correspondence should be addressed.Tel:+41216925892;Fax:+41216925945;Email:philipp.bucher@isrec.unil.ch
Nucleic Acids Research,2000,Vol.28,No.1303
has been introduced and so far been populated with keywords imported from SWISS-PROT(12).This feature is intended to enhance the query capabilities of various access tools.Additional keywords relating to properties of the promoter rather than to properties of the corresponding gene product will be added in the near future.
Documentation
The user manual has been extensively revised.Bibliographic references have been added to the section explaining the representation of transcript mapping data.Some of them are accompanied by direct hyperlinks to figures in online journals exemplifying a particular technique.Several additional documents have recently been made available over the web.One contains a list of all‘homology groups’defined in EPD.Such groups consist of homologous promoters exhibiting significant sequence similarity in the–79to+20region among themselves. Another document presents the hierarchical promoter classifi-cation system of EPD.
Promoter element descriptions
Weight matrix descriptions of four major eukaryotic promoter elements(TATA-box,initiator,GC-box and CCAAT-box) have previously been derived from EPD release17(7).We have now decided to make updated versions of such matrices available on a yearly basis from the EPD web pages.The latest versions were produced from EPD release60using a Baum–Welch hidden Markov model training algorithm(program buildmodel of SAM release1.3.3,Hughey&Krogh1998,www. cse.ucsc.edu/research/compbio/sam.html).
ACCESS
FTP
The following files are available from ftp.epd.isb-sib.ch/pub/ databases/epd
•Flat-files containing the EPD database in the new and in the old format.
•EPD user manual.
•Sequence libraries in EMBL and FASTA format containing promoter sequences from–499to+100relative to the tran-scription start site.
•A slightly reduced version of EPD in ASN.1format designed for import into the GenBank–Entrez data environment(13), including a formal data description in ASN1.•Icarus scripts for indexing EPD by SRS(14).
WWW
The following services are offered at www.epd.isb-sib.ch •Access to EPD entries by ID or accession number.The following formats are available:text only,HTML and HTML combined with a graphic representation of sequence objects by a Java applet(15).
•A page for downloading promoter sequence subsets defined in EPD.
•Access to EPD entries and corresponding promoter sequences via a query form.
北一辉Access to EPD via SRS is provided by the Swiss EMBNet node at /
SUPPLEMENTARY MATERIAL
Relevant URL links are available at NAR Online.
ACKNOWLEDGEMENT
EPD is funded in part by grant31-54782.98from the Swiss National Science Foundation.
REFERENCES
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Table1.Database cross-references in EPD release60
Database Number of links EPD internal188
EMBL(9)2978 TRANSFAC(1)1700
东北农业大学学报
SWISS-PROT(12)1058
FlyBase(16)116
MIM(17)234
MGD(18)126 MEDLINE2393
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