The eukaryotic promoter database (EPD) - PubMed (original) (raw)
The eukaryotic promoter database (EPD)
R C Périer et al. Nucleic Acids Res. 2000.
Abstract
The Eukaryotic Promoter Database (EPD) 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 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 bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. WWW-based interfaces have been developed 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 http://www.epd.isb-sib.ch
Similar articles
- The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data.
Praz V, Périer R, Bonnard C, Bucher P. Praz V, et al. Nucleic Acids Res. 2002 Jan 1;30(1):322-4. doi: 10.1093/nar/30.1.322. Nucleic Acids Res. 2002. PMID: 11752326 Free PMC article. - The Eukaryotic Promoter Database (EPD): recent developments.
Périer RC, Junier T, Bonnard C, Bucher P. Périer RC, et al. Nucleic Acids Res. 1999 Jan 1;27(1):307-9. doi: 10.1093/nar/27.1.307. Nucleic Acids Res. 1999. PMID: 9847211 Free PMC article. - The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.
Schmid CD, Praz V, Delorenzi M, Périer R, Bucher P. Schmid CD, et al. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D82-5. doi: 10.1093/nar/gkh122. Nucleic Acids Res. 2004. PMID: 14681364 Free PMC article. - [Description of eukaryotic promoters in the EPD database].
Bucher P. Bucher P. Mol Biol (Mosk). 1997 Jul-Aug;31(4):616-25. Mol Biol (Mosk). 1997. PMID: 9340489 Review. Russian. No abstract available. - SPEM: a parser for EMBL style flat file database entries.
Pocock MR, Hubbard T, Birney E. Pocock MR, et al. Bioinformatics. 1998;14(9):823-4. doi: 10.1093/bioinformatics/14.9.823. Bioinformatics. 1998. PMID: 9918956 Review.
Cited by
- lncRNAfunc: a knowledgebase of lncRNA function in human cancer.
Yang M, Lu H, Liu J, Wu S, Kim P, Zhou X. Yang M, et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D1295-D1306. doi: 10.1093/nar/gkab1035. Nucleic Acids Res. 2022. PMID: 34791419 Free PMC article. - Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters.
Gagniuc P, Ionescu-Tirgoviste C. Gagniuc P, et al. BMC Genomics. 2012 Sep 28;13:512. doi: 10.1186/1471-2164-13-512. BMC Genomics. 2012. PMID: 23020586 Free PMC article. - NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence.
Down TA, Hubbard TJ. Down TA, et al. Nucleic Acids Res. 2005 Mar 10;33(5):1445-53. doi: 10.1093/nar/gki282. Print 2005. Nucleic Acids Res. 2005. PMID: 15760844 Free PMC article. - Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes.
Reddy TE, Shakhnovich BE, Roberts DS, Russek SJ, DeLisi C. Reddy TE, et al. Nucleic Acids Res. 2007;35(3):e20. doi: 10.1093/nar/gkl1062. Epub 2007 Jan 3. Nucleic Acids Res. 2007. PMID: 17204484 Free PMC article. - Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites.
Suzuki Y, Taira H, Tsunoda T, Mizushima-Sugano J, Sese J, Hata H, Ota T, Isogai T, Tanaka T, Morishita S, Okubo K, Sakaki Y, Nakamura Y, Suyama A, Sugano S. Suzuki Y, et al. EMBO Rep. 2001 May;2(5):388-93. doi: 10.1093/embo-reports/kve085. EMBO Rep. 2001. PMID: 11375929 Free PMC article.
References
- Ghosh D. (1999) Nucleic Acids Res., 27, 315–317. Updated article in this issue: Nucleic Acids Res. (2000), 28, 308–310. - PubMed
- Kolchanov N.A., Ananko,E.A., Podkolodnaya,O.A., Ignatieva,E.V., Stepanenko,I.L., Kel-Margoulis,O.V., Kel,A.E., Merkulova,T.I., Goryachkovskaya,T.N., Busygina,T.V., Kolpakov,F.A., Podkolodny,N.L., Naumochkin,A.N. and Romashchenko,A.G. (1999) Nucleic Acids Res., 27, 303–306. Updated article in this issue: Nucleic Acids Res. (2000), 28, 298–301. - PubMed
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources