mirDIP : microRNA Data Integration Portal

References :

DIANA-microT (ver. 3.0)
  • Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA et al: Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics 2009, 10:295.
  • Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K et al: DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res 2009, 37(Web Server issue):W273-276.
microRNA.org (Sept. 2010)
  • Betel D, Koppal A, Agius P, Sander C, Leslie C. (2010) Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biology 11, R90
  • Betel, D., Wilson, M., Gabow, A., Marks, D.S. and Sander, C. (2008). The microRNA.org resource: targets and expression. Nucleic Acids Res 36, D149-53.
  • John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C. and Marks, D.S. (2004). Human MicroRNA targets. PLoS Biol 2, e363.
microCosm (ver. 5 )
  • Enright, A.J., John, B., Gaul, U., Tuschl, T., Sander, C. and Marks, D.S. (2003). MicroRNA targets in Drosophila. Genome Biol 5, R1.
  • Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A. and Enright, A.J. (2006). miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34, D140-4.
  • Griffiths-Jones, S., Saini, H.K., van Dongen, S. and Enright, A.J. (2008). miRBase: tools for microRNA genomics. Nucleic Acids Res 36, D154-8.
picTar (Mar. 2007)
  • Chen, K. and Rajewsky, N. (2006). Natural selection on human microRNA binding sites inferred from SNP data. Nat Genet 38, 1452-6.
  • Grun, D., Wang, Y.L., Langenberger, D., Gunsalus, K.C. and Rajewsky, N. (2005). microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 1, e13.
  • Krek, A. et al. (2005). Combinatorial microRNA target predictions. Nat Genet 37, 495-500.
  • Lall, S. et al. (2006). A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol 16, 460-71.
PITA (ver. 6 Aug. 2008)
  • Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U. and Segal, E. (2007). The role of site accessibility in microRNA target recognition. Nat Genet 39, 1278-84.
RNA22 (May. 2011)
  • Miranda, K.C., Huynh, T., Tay, Y., Ang, Y.S., Tam, W.L., Thomson, A.M., Lim, B. and Rigoutsos, I. (2006). A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126, 1203-17.
TargetScan (Release 6.2 June. 2012)
  • Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP. (2011). Weak Seed-Pairing Stability and High Target-Site Abundance Decrease the Proficiency of lsy-6 and Other miRNAs. Nat Struct Mol Biol. 18:1139-46.
  • Friedman, R.C., Farh, K.K., Burge, C.B. and Bartel, D.P. (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19, 92-105.
  • Grimson, A., Farh, K.K., Johnston, W.K., Garrett-Engele, P., Lim, L.P. and Bartel, D.P. (2007). MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27, 91-105.
  • Lewis, B.P., Burge, C.B. and Bartel, D.P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20.
mirDB (2008)
  • Wang X, El Naqa I. (2008) Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 24:325-332. Wang X. (2008). miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 14:1012-1017
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Shirdel EA, Xie W, Mak TW, Jurisica I, 2011 NAViGaTing the Micronome . Using Multiple MicroRNA Prediction Databases to Identify Signalling Pathway-Associated MicroRNAs. PLoS ONE 6(2): e17429. doi:10.1371/journal.pone.0017429