title: A guide through present computational approaches for the identification of mammalian microRNA targets.
abstract: Computational microRNA (miRNA) target prediction is a field in flux. Here we present a guide through five widely used mammalian target prediction programs. We include an analysis of the performance of these individual programs and of various combinations of these programs. For this analysis we compiled several benchmark data sets of experimentally supported miRNA-target gene interactions. Based on the results, we provide a discussion on the status of target prediction and also suggest a stepwise approach toward predicting and selecting miRNA targets for experimental testing.
authors.affiliation: Center for Bioinformatics, University of Pennsylvania, Philadelphia Pennsylvania 19104, USA.
authors.forename: Praveen
authors.initials: P
authors.lastname: Sethupathy
authors.forename: Molly
authors.initials: M
authors.lastname: Megraw
authors.forename: Artemis G
authors.initials: AG
authors.lastname: Hatzigeorgiou
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D020121:5' Untranslated Regions / Q000235:genetics; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D018390:Gene Targeting / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D011237:Predictive Value of Tests; D012333:RNA, Messenger / Q000235:genetics; D012680:Sensitivity and Specificity; D012984:Software
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D035683:MicroRNAs; D012333:RNA, Messenger