A two-step site and mRNA-level model for predicting microRNA targets
Journal article, Peer reviewed
Permanent lenke
http://hdl.handle.net/11250/2384314Utgivelsesdato
2010Metadata
Vis full innførselSamlinger
Sammendrag
Background: Despite experiments showing that the number of microRNA (miRNA) target sites is critical for miRNA
targeting, most existing methods focus on identifying individual miRNA target sites and do not model
contributions of multiple target sites to miRNA regulation. To address this possible fault, we developed a miRNA
target prediction model that recognizes the individual characteristics of functional binding sites and the global
characteristics of miRNA-targeted mRNAs.
Results: Benchmark experiments showed that this two-step model generally had a higher overall performance
than other established miRNA target prediction algorithms and that the model was especially suited to identify
true miRNA targets among genes that all contain conserved target sites.
Conclusions: This improved performance could partly be explained by the model not relying on conservation
when predicting targets. The critical factors for the model’s performance, however, were mRNA-level features that
characterized the number and strength of individual target sites within the mRNA. The model is available for
online predictions or as pre-computed predictions on the human genome http://tare.medisin.ntnu.no/mirna_target.