Eukaryotic Promoter Database Explained

EPD
Description:Database of experimentally defined eukaryotic RNA Polymerase II promoters
Organism:Eukaryotes
Center:Swiss Institute of Bioinformatics
Pmid:23193273
Released:1986
Url:epd.expasy.org
License:Free without registration
Curation:Yes – manual and automatic

EPD (Eukaryotic Promoter Database) is a biological database and web resource of eukaryotic RNA polymerase II promoters with experimentally defined transcription start sites.[1] Originally, EPD was a manually curated resource relying on transcript mapping experiments (mostly primer extension and nuclease protection assays) targeted at individual genes and published in academic journals. More recently, automatically generated promoter collections derived from electronically distributed high-throughput data produced with the CAGE or TSS-Seq [2] [3] protocols were added as part of a special subsection named EPDnew.[4] The EPD web server offers additional services, including an entry viewer which enables users to explore the genomic context of a promoter in a UCSC Genome Browser window, and direct links for uploading EPD-derived promoter subsets to associated web-based promoter analysis tools of the Signal Search Analysis (SSA)[5] and ChIP-Seq servers. EPD also features a collection of position weight matrices (PWMs) for common promoter sequence motifs.

History and Impact

EPD was created in 1986 as an electronic version of a eukaryotic promoter compilation published in an article[6] and has been regularly updated since then. The database was initially distributed on magnetic tapes as part of the EMBL data library[7] and later via the Internet. The collaboration between EPD and the EMBL library was cited as a pioneering example of remote nucleotide sequence annotation by domain experts.[8] EPD has played an instrumental role in the development and evaluation of promoter prediction algorithms[9] as it is broadly considered the most accurate promoter resource.[10] As of November 2014, it has been cited about 2500 times in scientific literature.[11] EPD has also received ample coverage by textbooks in bioinformatics (e.g. [12]) and systems biology (e.g. [13]).

External links

Notes and References

  1. Cavin Périer. R. Junier. T. Bucher. P. The Eukaryotic Promoter Database EPD.. Nucleic Acids Research. 1 January 1998. 26. 1. 353–7. 9399872. 10.1093/nar/26.1.353. 147208.
  2. Tsuchihara. K. Suzuki. Y. Wakaguri. H. Irie. T. Tanimoto. K. Hashimoto. S. Matsushima. K. Mizushima-Sugano. J. Yamashita. R. Nakai. K. Bentley. D. Esumi. H. Sugano. S. Massive transcriptional start site analysis of human genes in hypoxia cells.. Nucleic Acids Research. April 2009. 37. 7. 2249–63. 19237398. 10.1093/nar/gkp066. 2673422.
  3. Yamashita. R. Sugano. S. Suzuki. Y. Nakai. K. DBTSS: DataBase of Transcriptional Start Sites progress report in 2012.. Nucleic Acids Research. January 2012. 40. Database issue. D150-4. 22086958. 10.1093/nar/gkr1005. 3245115.
  4. Dreos. R. Ambrosini. G. Cavin Périer. R. Bucher. P. EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era.. Nucleic Acids Research. January 2013. 41. Database issue. D157-64. 23193273. 10.1093/nar/gks1233. 3531148.
  5. Ambrosini. G. Praz. V. Jagannathan. V. Bucher. P. Signal search analysis server.. Nucleic Acids Research. 1 July 2003. 31. 13. 3618–20. 12824379. 10.1093/nar/gkg611. 169017.
  6. Bucher. P. Trifonov. EN. Compilation and analysis of eukaryotic POL II promoter sequences.. Nucleic Acids Research. 22 December 1986. 14. 24. 10009–26. 3808945. 10.1093/nar/14.24.10009. 341352.
  7. Cameron. GN. The EMBL data library.. Nucleic Acids Research. 11 March 1988. 16. 5. 1865–7. 3353226. 10.1093/nar/16.5.1865. 338182.
  8. Fuchs. R. Cameron. GN. Molecular biological databases: the challenge of the genome era.. Progress in Biophysics and Molecular Biology. 1991. 56. 3. 215–45. 1771233. 10.1016/0079-6107(91)90014-j. free.
  9. Fickett. JW. Hatzigeorgiou. AG. Eukaryotic promoter recognition.. Genome Research. September 1997. 7. 9. 861–78. 9314492. 10.1101/gr.7.9.861 . free.
  10. Book: Barnes M.R.. Bioinformatics for Geneticists: A Bioinformatics Primer for the Analysis of Genetic Data.. 10.1086/590603. 2007. John Wiley & Sons. Chichester. 978-0470059173. 285. 2nd.
  11. Number of results returned from a search in Google Scholar. (Google Scholar)
  12. Book: Ye. Shui Qing. Bioinformatics a practical approach. 2008. Chapman & Hall/CRC. Boca Raton. 978-1584888116.
  13. Book: Klipp. E.. Systems biology in practice concepts, implementation and application. 2005. Wiley-VCH. Weinheim. 352760488X.

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