Abstract
One critical step in miRNA functional studies is to identify the gene targets that are directly regulated by miRNAs. In this chapter, we describe a computational algorithm and an online database, miRDB, for miRNA target prediction. In miRDB, flexible Web search interface has been developed for the retrieval of target prediction results generated by the newly developed computational algorithm. In addition, a wiki editing interface has been established to allow anyone with Internet access to make contributions on miRNA functional annotation. All data stored in miRDB are freely accessible at http://www.mirdb.org.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Lim LP, Lau NC, Garrett-Engele P, et al. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769–73.
Lewis BP, Burge CB, Bartel DP. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20.
Miranda KC, Huynh T, Tay Y, et al. (2006) A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 126:1203–17.
Rajewsky N. (2006) MicroRNA target predictions in animals. Nat Genet 38 Suppl:S8–13.
Sethupathy P, Corda B, Hatzigeorgiou AG. (2006) TarBase: a comprehensive database of experimentally supported animal microRNA targets. RNA 12:192–7.
Wang X, El Naqa IM. (2008) Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 24:325–32.
Wang X. (2008) miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 14:1012–7.
Linsley PS, Schelter J, Burchard J, et al. (2007) Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression. Mol Cell Biol 27:2240–52.
Hofacker IL. (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31:3429–31.
Gaidatzis D, van Nimwegen E, Hausser J, Zavolan M. (2007) Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics 8:69.
Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27:91–105.
Wang X, Wang X. (2006) Systematic identification of microRNA functions by combining target prediction and expression profiling. Nucleic Acids Res 34:1646–52.
Krek A, Grun D, Poy MN, et al. (2005) Combinatorial microRNA target predictions. Nat Genet 37:495–500.
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34:D140–4.
Mi H, Lazareva-Ulitsky B, Loo R, et al. (2005) The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res 33:D284–8.
Liang Y, Ridzon D, Wong L, Chen C. (2007) Characterization of microRNA expression profiles in normal human tissues. BMC Genomics 8:166.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Wang, X. (2010). Computational Prediction of MicroRNA Targets. In: Monticelli, S. (eds) MicroRNAs and the Immune System. Methods in Molecular Biology, vol 667. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-811-9_19
Download citation
DOI: https://doi.org/10.1007/978-1-60761-811-9_19
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-60761-810-2
Online ISBN: 978-1-60761-811-9
eBook Packages: Springer Protocols