MicroRNA and microRNA target database

MicroRNA and microRNA target database

This microRNA database and microRNA targets database is a compilation of databases and web portals and servers used for microRNAs and their targets. MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (ncRNAs) that regulate gene expression by targeting messenger RNAs[1].

Contents

microRNA target gene databases

Name Description type Link References
targetScan targetScan is Search for predicted microRNA targets in animals database,webserver website [2]
StarBase starBase is a database for exploring microRNA-target interaction maps from Argonaute (Ago) CLIP-Seq (HITS-CLIP) and degradome sequencing (Degradome-Seq, PARE) data. database website [3]
TarBase A comprehensive database of experimentally supported animal microRNA targets database website [4]
Diana-microT DIANA-microT 3.0 is an algorithm based on several parameters calculated individually for each microRNA and it combines conserved and non-conserved microRNA recognition elements into a final prediction score. webserver webserver [5]
miRecords an integrated resource for microRNA-target interactions. database website [6]
PicTar PicTar is Combinatorial microRNA target predictions. database,webserver,predictions website [7]
PITA PITA, incorporates the role of target-site accessibility, as determined by base-pairing interactions within the mRNA, in microRNA target recognition. webserver,predictions predictions [8]
RepTar A database of inverse miRNA target predictions, based on the RepTar algorithm that is independent of evolutionary conservation considerations and is not limited to seed pairing sites. database website [9]
RNA22 First finds putative microRNA binding sites in the sequence of interest, then identifies the targeted microRNA. webserver,predictions webserver [10]
.

microRNA database

Name Description type Link References
miRBase miRBase database is a searchable database of published miRNA sequences and annotation. database website [11]
deepBase deepBase is a database for annotating and discovering small and long ncRNAs (microRNAs, siRNAs, piRNAs...) from high-throughput deep sequencing data. database website [12]
microRNA.org microRNA.org is a ddatabase for Experimentally observed microRNA expression patterns and predicted microRNA targets & target downregulation scores. database website [13]
miRGen 2.0 miRGen 2.0: a database of microRNA genomic information and regulation database website [14]
miRNAMap miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes database website [15]
PMRD PMRD: plant microRNA database database website [16]
.

References

  1. ^ Bartel, D. P. (2009). "MicroRNAs: target recognition and regulatory functions". Cell 136 (2): 215–233. doi:10.1016/j.cell.2009.01.002. PMID 19167326.  edit
  2. ^ Lewis BP, Burge CB, Bartel DP. (2005). "Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.". Cell 120 (1): 15–20. doi:10.1016/j.cell.2004.12.035. PMID 15652477. 
  3. ^ Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. (2011). "starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data.". Nucl. Acids Res. 39 (Database issue): 1–8. doi:10.1093/nar/gkq1056. PMC 3013664. PMID 21037263. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3013664. 
  4. ^ Sethupathy P, Corda B, Hatzigeorgiou AG. (2006). "TarBase: A comprehensive database of experimentally supported animal microRNA targets.". RNA. 12 (2): 192–197. doi:10.1261/rna.2239606. PMID 16373484. 
  5. ^ Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG (2009). "Accurate microRNA target prediction correlates with protein repression levels.". BMC Bioinformatics 10: 295. doi:10.1186/1471-2105-10-295. PMC 2752464. PMID 19765283. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2752464. 
  6. ^ Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. (2009). "miRecords: an integrated resource for microRNA-target interactions.". Nucl. Acids Res. 37 (Database issue): D105-110. doi:10.1093/nar/gkn851. PMID 18996891. 
  7. ^ Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N (2005). "Combinatorial microRNA target predictions.". Nat Genet 37 (5): 495–500. doi:10.1038/ng1536. PMID 15806104. 
  8. ^ Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E (2007). "The role of site accessibility in microRNA target recognition.". Nat Genet 39 (10): 1278–84. doi:10.1038/ng2135. PMID 17893677. 
  9. ^ Elefant, Naama; Berger Amnon, Shein Harel, Hofree Matan, Margalit Hanah, Altuvia Yael (Jan 2011). "RepTar: a database of predicted cellular targets of host and viral miRNAs" (in eng). Nucleic Acids Res. (England) 39 (Database issue): D188-94. doi:10.1093/nar/gkq1233. PMC 3013742. PMID 21149264. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3013742. 
  10. ^ Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I (2006). "A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes.". Cell 126 (6): 1203–17. doi:10.1016/j.cell.2006.07.031. PMID 16990141. 
  11. ^ Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. (2008). "miRBase: tools for microRNA genomics.". Nucl. Acids Res. 36: D154-D158. doi:10.1093/nar/gkm952. PMC 2238936. PMID 17991681. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2238936. 
  12. ^ Yang JH, Shao P, Zhou H, Chen YQ, Qu LH. (2010). "deepBase: a database for deeply annotating and mining deep sequencing data.". Nucl. Acids Res. 38 (Database issue): D123-130. doi:10.1093/nar/gkp943. PMC 2808990. PMID 19966272. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2808990. 
  13. ^ Betel D, Wilson M, Gabow A, Marks DS, Sander C. (2007). "The microRNA.org resource: targets and expression.". Nucl. Acids Res. 36 (Database issue): D149-153. doi:10.1093/nar/gkm995. PMC 2238905. PMID 18158296. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2238905. 
  14. ^ Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T, Hatzigeorgiou AG. (2010). "miRGen 2.0: a database of microRNA genomic information and regulation.". Nucl. Acids Res. 38 (Database issue): D137-41. doi:10.1093/nar/gkp888. PMC 2808909. PMID 19850714. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2808909. 
  15. ^ Hsu PW, Huang HD, Hsu SD, Lin LZ, Tsou AP, Tseng CP, Stadler PF, Washietl S, Hofacker IL. (2006). "miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.". Nucl. Acids Res. 34 (Database issue): D135-139. doi:10.1093/nar/gkj135. PMC 1347497. PMID 16381831. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1347497. 
  16. ^ Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z. (2010). "PMRD: plant microRNA database.". Nucl. Acids Res. 38 (Database issue): D806-813. doi:10.1093/nar/gkp818. PMC 2808885. PMID 19808935. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2808885. 

Further reading

External links


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