| Content | |
|---|---|
| Description | Database of experimentally defined eukaryotic RNA Polymerase II promoters |
| Organisms | Eukaryotes |
| Contact | |
| Research center | Swiss Institute of Bioinformatics |
| Primary citation | PMID 23193273 |
| Release date | 1986 |
| Access | |
| Website | epd.expasy.org |
| Miscellaneous | |
| License | Free without registration |
| Curation policy | 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]).
References
- ^ Cavin Périer, R; Junier, T; Bucher, P (1 January 1998). "The Eukaryotic Promoter Database EPD". Nucleic Acids Research. 26 (1): 353–7. doi: 10.1093/nar/26.1.353. PMC 147208. PMID 9399872.
- ^ 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". Nucleic Acids Research. 37 (7): 2249–63. doi: 10.1093/nar/gkp066. PMC 2673422. PMID 19237398.
- ^ Yamashita, R; Sugano, S; Suzuki, Y; Nakai, K (January 2012). "DBTSS: DataBase of Transcriptional Start Sites progress report in 2012". Nucleic Acids Research. 40 (Database issue): D150-4. doi: 10.1093/nar/gkr1005. PMC 3245115. PMID 22086958.
- ^ Dreos, R; Ambrosini, G; Cavin Périer, R; Bucher, P (January 2013). "EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era". Nucleic Acids Research. 41 (Database issue): D157-64. doi: 10.1093/nar/gks1233. PMC 3531148. PMID 23193273.
- ^ Ambrosini, G; Praz, V; Jagannathan, V; Bucher, P (1 July 2003). "Signal search analysis server". Nucleic Acids Research. 31 (13): 3618–20. doi: 10.1093/nar/gkg611. PMC 169017. PMID 12824379.
- ^ Bucher, P; Trifonov, EN (22 December 1986). "Compilation and analysis of eukaryotic POL II promoter sequences". Nucleic Acids Research. 14 (24): 10009–26. doi: 10.1093/nar/14.24.10009. PMC 341352. PMID 3808945.
- ^ Cameron, GN (11 March 1988). "The EMBL data library". Nucleic Acids Research. 16 (5): 1865–7. doi: 10.1093/nar/16.5.1865. PMC 338182. PMID 3353226.
- ^ Fuchs, R; Cameron, GN (1991). "Molecular biological databases: the challenge of the genome era". Progress in Biophysics and Molecular Biology. 56 (3): 215–45. doi: 10.1016/0079-6107(91)90014-j. PMID 1771233.
- ^ Fickett, JW; Hatzigeorgiou, AG (September 1997). "Eukaryotic promoter recognition". Genome Research. 7 (9): 861–78. doi: 10.1101/gr.7.9.861. PMID 9314492.
- ^ Barnes M.R. (2007). Bioinformatics for Geneticists: A Bioinformatics Primer for the Analysis of Genetic Data (2nd ed.). Chichester: John Wiley & Sons. p. 285. doi: 10.1086/590603. ISBN 978-0470059173.
- ^ Number of results returned from a search in Google Scholar. (Google Scholar)
- ^ Ye, Shui Qing (2008). Bioinformatics a practical approach. Boca Raton: Chapman & Hall/CRC. ISBN 978-1584888116.
- ^ Klipp, E. (2005). Systems biology in practice concepts, implementation and application. Weinheim: Wiley-VCH. ISBN 352760488X.
External links
- SIB - Swiss Institute of Bioinformatics
- SSA Signal Search Analysis server
- ChIP-Seq ChIP-seq On-line Analysis Tools
- PWMTools Position Weight Matrix model generation and evaluation tools
| Content | |
|---|---|
| Description | Database of experimentally defined eukaryotic RNA Polymerase II promoters |
| Organisms | Eukaryotes |
| Contact | |
| Research center | Swiss Institute of Bioinformatics |
| Primary citation | PMID 23193273 |
| Release date | 1986 |
| Access | |
| Website | epd.expasy.org |
| Miscellaneous | |
| License | Free without registration |
| Curation policy | 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]).
References
- ^ Cavin Périer, R; Junier, T; Bucher, P (1 January 1998). "The Eukaryotic Promoter Database EPD". Nucleic Acids Research. 26 (1): 353–7. doi: 10.1093/nar/26.1.353. PMC 147208. PMID 9399872.
- ^ 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". Nucleic Acids Research. 37 (7): 2249–63. doi: 10.1093/nar/gkp066. PMC 2673422. PMID 19237398.
- ^ Yamashita, R; Sugano, S; Suzuki, Y; Nakai, K (January 2012). "DBTSS: DataBase of Transcriptional Start Sites progress report in 2012". Nucleic Acids Research. 40 (Database issue): D150-4. doi: 10.1093/nar/gkr1005. PMC 3245115. PMID 22086958.
- ^ Dreos, R; Ambrosini, G; Cavin Périer, R; Bucher, P (January 2013). "EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era". Nucleic Acids Research. 41 (Database issue): D157-64. doi: 10.1093/nar/gks1233. PMC 3531148. PMID 23193273.
- ^ Ambrosini, G; Praz, V; Jagannathan, V; Bucher, P (1 July 2003). "Signal search analysis server". Nucleic Acids Research. 31 (13): 3618–20. doi: 10.1093/nar/gkg611. PMC 169017. PMID 12824379.
- ^ Bucher, P; Trifonov, EN (22 December 1986). "Compilation and analysis of eukaryotic POL II promoter sequences". Nucleic Acids Research. 14 (24): 10009–26. doi: 10.1093/nar/14.24.10009. PMC 341352. PMID 3808945.
- ^ Cameron, GN (11 March 1988). "The EMBL data library". Nucleic Acids Research. 16 (5): 1865–7. doi: 10.1093/nar/16.5.1865. PMC 338182. PMID 3353226.
- ^ Fuchs, R; Cameron, GN (1991). "Molecular biological databases: the challenge of the genome era". Progress in Biophysics and Molecular Biology. 56 (3): 215–45. doi: 10.1016/0079-6107(91)90014-j. PMID 1771233.
- ^ Fickett, JW; Hatzigeorgiou, AG (September 1997). "Eukaryotic promoter recognition". Genome Research. 7 (9): 861–78. doi: 10.1101/gr.7.9.861. PMID 9314492.
- ^ Barnes M.R. (2007). Bioinformatics for Geneticists: A Bioinformatics Primer for the Analysis of Genetic Data (2nd ed.). Chichester: John Wiley & Sons. p. 285. doi: 10.1086/590603. ISBN 978-0470059173.
- ^ Number of results returned from a search in Google Scholar. (Google Scholar)
- ^ Ye, Shui Qing (2008). Bioinformatics a practical approach. Boca Raton: Chapman & Hall/CRC. ISBN 978-1584888116.
- ^ Klipp, E. (2005). Systems biology in practice concepts, implementation and application. Weinheim: Wiley-VCH. ISBN 352760488X.
External links
- SIB - Swiss Institute of Bioinformatics
- SSA Signal Search Analysis server
- ChIP-Seq ChIP-seq On-line Analysis Tools
- PWMTools Position Weight Matrix model generation and evaluation tools