Improving miRNA target prediction with gene expression profiles

TargetExpress is a tool to improve microRNA target predictions by adding gene expression information from particular cell types. Although our method is applicable to any species for which miRNA target predictions and gene expression data are available, the web interface currently supports human and mouse.

Our method works by combining popular predictors (currently TargetScan, microT-CDS, and MIRZA) with experimental expression profiles, using machine learning techniques. The result is a set of target predictions for any miRNA, but re-ranked to take into consideration the expression level of each target.

TargetExpress not only performs better than either TargetScan, microT-CDS, and MIRZA, but the targets that are predicted as functional tend to have annotations that are more coherent with the known biological function of the miRNA.


How to cite

If you use TargetExpress, please cite the following publication:

Improving microRNA target prediction with gene expression profiles. Ovando-Vázquez C, Lepe-Soltero D and Abreu-Goodger C. BMC Genomics. 2016; 17:364. doi: 10.1186/s12864-016-2695-1.


For suggestions or requests, send us an email to targetexpress at ceiabreulab dot org.