Eukaryotic Promoter Database

EPD (Eukaryotic Promoter Database) is a biological database

and web resource of eukaryotic RNA polymerase II promoters
EPD
with experimentally defined transcription start sites.[1] Originally, Content
EPD was a manually curated resource relying on transcript Description Database of
mapping experiments (mostly primer extension and nuclease
experimentally
protection assays) targeted at individual genes and published in
defined
academic journals. More recently, automatically generated
eukaryotic RNA
promoter collections derived from electronically distributed high-
Polymerase II
throughput data produced with the CAGE or TSS-Seq [2][3]
protocols were added as part of a special subsection named promoters
EPDnew.[4] The EPD web server offers additional services, Organisms Eukaryotes
including an entry viewer which enables users to explore the Contact
genomic context of a promoter in a UCSC Genome Browser
window, and direct links for uploading EPD-derived promoter Research center Swiss Institute of
subsets to associated web-based promoter analysis tools of the Bioinformatics
Signal Search Analysis (SSA) (http://ccg.vital-it.ch/ssa/)[5] and Primary citation PMID 23193273
ChIP-Seq (http://ccg.vital-it.ch/chipseq/) servers. EPD also (https://pubmed.
features a collection of position weight matrices (PWMs) for ncbi.nlm.nih.gov/
common promoter sequence motifs. 23193273)
Release date 1986
History and Impact
Access

EPD was created in 1986 as an electronic version of a eukaryotic Website epd.epfl.ch (http
promoter compilation published in an article[6] and has been s://epd.epfl.ch/)
regularly updated since then. The database was initially distributed Download URL http://ccg.epfl.ch/
on magnetic tapes as part of the EMBL data library[7] and later via (http://ccg.epfl.c
the Internet. The collaboration between EPD and the EMBL h/)
library was cited as a pioneering example of remote nucleotide
sequence annotation by domain experts.[8] EPD has played an Miscellaneous
instrumental role in the development and evaluation of promoter License Free without
prediction algorithms[9] as it is broadly considered the most registration
accurate promoter resource.[10] As of November 2014, it has been Curation policy Yes – manual
cited about 2500 times in scientific literature.[11] EPD has also and automatic
received ample coverage by textbooks in bioinformatics (e.g. [12])
and systems biology (e.g. [13]).

References
1. Cavin Périer, R; Junier, T; Bucher, P (1 January 1998). "The Eukaryotic Promoter Database
EPD" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC147208). Nucleic Acids Research. 26
(1): 353–7. doi:10.1093/nar/26.1.353 (https://doi.org/10.1093%2Fnar%2F26.1.353).
PMC 147208 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC147208). PMID 9399872 (http
s://pubmed.ncbi.nlm.nih.gov/9399872).
 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 (April
2009). "Massive transcriptional start site analysis of human genes in hypoxia cells" (https://w
ww.ncbi.nlm.nih.gov/pmc/articles/PMC2673422). Nucleic Acids Research. 37 (7): 2249–63.
doi:10.1093/nar/gkp066 (https://doi.org/10.1093%2Fnar%2Fgkp066). PMC 2673422 (https://
www.ncbi.nlm.nih.gov/pmc/articles/PMC2673422). PMID 19237398 (https://pubmed.ncbi.nl
m.nih.gov/19237398).
3. Yamashita, R; Sugano, S; Suzuki, Y; Nakai, K (January 2012). "DBTSS: DataBase of
Transcriptional Start Sites progress report in 2012" (https://www.ncbi.nlm.nih.gov/pmc/article
s/PMC3245115). Nucleic Acids Research. 40 (Database issue): D150-4.
doi:10.1093/nar/gkr1005 (https://doi.org/10.1093%2Fnar%2Fgkr1005). PMC 3245115 (http
s://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245115). PMID 22086958 (https://pubmed.ncbi.
nlm.nih.gov/22086958).
4. Dreos, R; Ambrosini, G; Cavin Périer, R; Bucher, P (January 2013). "EPD and EPDnew,
high-quality promoter resources in the next-generation sequencing era" (https://www.ncbi.nl
m.nih.gov/pmc/articles/PMC3531148). Nucleic Acids Research. 41 (Database issue): D157-
64. doi:10.1093/nar/gks1233 (https://doi.org/10.1093%2Fnar%2Fgks1233). PMC 3531148
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531148). PMID 23193273 (https://pubmed.
ncbi.nlm.nih.gov/23193273).
5. Ambrosini, G; Praz, V; Jagannathan, V; Bucher, P (1 July 2003). "Signal search analysis
server" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169017). Nucleic Acids Research.
31 (13): 3618–20. doi:10.1093/nar/gkg611 (https://doi.org/10.1093%2Fnar%2Fgkg611).
PMC 169017 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169017). PMID 12824379 (http
s://pubmed.ncbi.nlm.nih.gov/12824379).
6. Bucher, P; Trifonov, EN (22 December 1986). "Compilation and analysis of eukaryotic POL II
promoter sequences" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC341352). Nucleic
Acids Research. 14 (24): 10009–26. doi:10.1093/nar/14.24.10009 (https://doi.org/10.1093%
2Fnar%2F14.24.10009). PMC 341352 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413
52). PMID 3808945 (https://pubmed.ncbi.nlm.nih.gov/3808945).
7. Cameron, GN (11 March 1988). "The EMBL data library" (https://www.ncbi.nlm.nih.gov/pmc/
articles/PMC338182). Nucleic Acids Research. 16 (5): 1865–7. doi:10.1093/nar/16.5.1865 (h
ttps://doi.org/10.1093%2Fnar%2F16.5.1865). PMC 338182 (https://www.ncbi.nlm.nih.gov/pm
c/articles/PMC338182). PMID 3353226 (https://pubmed.ncbi.nlm.nih.gov/3353226).
8. Fuchs, R; Cameron, GN (1991). "Molecular biological databases: the challenge of the
genome era" (https://doi.org/10.1016%2F0079-6107%2891%2990014-j). Progress in
Biophysics and Molecular Biology. 56 (3): 215–45. doi:10.1016/0079-6107(91)90014-j (http
s://doi.org/10.1016%2F0079-6107%2891%2990014-j). PMID 1771233 (https://pubmed.ncbi.
nlm.nih.gov/1771233).
9. Fickett, JW; Hatzigeorgiou, AG (September 1997). "Eukaryotic promoter recognition" (https://
doi.org/10.1101%2Fgr.7.9.861). Genome Research. 7 (9): 861–78. doi:10.1101/gr.7.9.861 (ht
tps://doi.org/10.1101%2Fgr.7.9.861). PMID 9314492 (https://pubmed.ncbi.nlm.nih.gov/93144
92).
10. Barnes, [edited by] Michael (2007). Bioinformatics for Geneticists a Bioinformatics Primer for
the Analysis of Genetic Data (https://archive.org/details/bioinformaticsfo00barn_899)
(2nd ed.). Chichester: John Wiley & Sons. p. 285 (https://archive.org/details/bioinformaticsfo
00barn_899/page/n308). ISBN 978-0470059173. {{cite book}}: |first1= has
generic name (help)
11. Number of results returned from a search in Google Scholar. (Google Scholar) (https://schola
r.google.com/scholar?hl=en&q=%22EPD%22+%2Bpromoter&btnG=&as_sdt=1%2C5&as_s
dtp=)
12. Ye, Shui Qing (2008). Bioinformatics a practical approach. Boca Raton: Chapman &
Hall/CRC. ISBN 978-1584888116.
13. Klipp, E. (2005). Systems biology in practice concepts, implementation and application.
Weinheim: Wiley-VCH. ISBN 352760488X.

External links
SIB (https://www.sib.swiss/) - Swiss Institute of Bioinformatics
SSA (https://ccg.epfl.ch/ssa/) Signal Search Analysis server
ChIP-Seq (https://ccg.epfl.ch/chipseq/) ChIP-seq On-line Analysis Tools
PWMTools (https://ccg.epfl.ch/pwmtools/) Position Weight Matrix model generation and
evaluation tools

Retrieved from "https://en.wikipedia.org/w/index.php?title=Eukaryotic_Promoter_Database&oldid=1162791149"