microRNA target prediction

in different gene regions

You can search miRNA-gene target predictions by miRNA name and/or gene name.

TargetS: human miRNA-gene target predictions

Currently available microRNA (miRNA) target prediction algorithms require the presence of a conserved seed match to the 5 end of the miRNA and limits the target sites to the 3' untranslated regions of mRNAs. However, it has been noted that these requirements may be too stringent, leading to a substantial number of missing targets. We have developed TargetS, a novel computational approach for predicting miRNA targets with the target sites located along entire gene sequences, which permits finding additional targets that are not located in the 3 un-translated regions. Our model is based on both canonical seed matching and non-canonical seed pairing, which discovers targets that allow one bit GU wobble. It does not rely on evolutionary conservation, so it allows the detection of species-specific miRNA-mRNA interactions and makes it suitable for analyzing un-conserved genomic sequences. To test the performance of our approach, we have imported the widely used benchmark dataset revealing fold-changes in protein production corresponding to each of the five selected microRNAs. Compared to well-known miRNA target prediction tools, including TargetScanS, PicTar and MicroT_CDS, our method yields the highest sensitivity, while achieving a comparable level of accuracy.

The software used to generate the miRNA predictions is available for download.

The University of Texas Medical School
Yin Liu Lab (