A two-step site and mRNA-level model for predicting microRNA targets

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.