(精选)MicroRNA Analysis教学课件.pptVIP

Other properties of microRNA targets MicroRNA targets are conserved across species. (Stark et al. 2003) Tend to appear in clusters. For lins, comparison is between C. elegans and C. briggsae. For hid, comparison is between D. melanogaster and D. pseudoobscura. Another property of microRNA targets Sequence conservations of target sites Better complementary to the 5’ ends of the miRNAs. Interesting properties of microRNA targets Clusters of microRNA targets Extensive co-occurrence of the sites for different microRNAs in target 3’ UTRs. MicroRNA Targets Prediction Databases Scientific Use Case Scenarios What are the target genes of a given miRNA? What are the miRNAs targeting a given gene and what are their binding sites? What is the tissue expression profile of a given miRNA (or set of miRNAs)? What is the miRNA expression profile in a given tissue (or set of tissues)? * miRNA Tools Nat Methods. 2006 Nov;3(11):881-6 miRNA Tools FEBS Journal 276 (2009) 2150–2156 Target prediction tools covered in today’s workshop Targetscan miRBase Argonaute TargetScan (Lewis et al., Cell 2003) TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. As an option, nonconserved sites are also predicted. Also identified are sites with mismatches in the seed region that are compensated by conserved 3 pairing. In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using the context scores of the sites. TargetScanHuman considers matches to annotated human UTRs and their orthologs, as defined by UCSC whole-genome alignments. / Targetscan (Lewis et al. Cell 2003) Given a microRNA that is conserved in multiple species and a set of orthologous 3’ UTR sequences: Use 7 nt segment of the miRNA as the ‘microRNA seed’ to find the perfect complementary motifs in the UTR regions. Extend each seeds to find the best energy Assign a Z score. Give a ra