P-TarPmiR

What is P-TarPmiR:

P-TarPmiR is a plant microRNA target prediction software.

Upon submitting a list of miRNAs and mRNAs P-TarPmiR will extract features from all possible miRNA and mRNA pairings. These features will be sent to a classifier trained on thousands of plant miRNA:mRNA interactions, resulting in a target prediction confidence for each pairing.

See Help page on how to use the software

Go to Analysis page to use the software

Abstract

microRNAs (miRNAs) are small non-coding ribonucleic acids that post-transcriptionally regulate gene expression through the targeting of messenger RNA (mRNAs). Most miRNA target predictors have focused on animal species and prediction performance drops substantially when applied to plant species. Several rule-based miRNA target predictors have been developed in plant species, but they often fail to discover new miRNA targets with non-canonical miRNA-mRNA binding. Here, the recently published TarDB database of plant miRNA-mRNA data is leveraged to retrain the TarPmiR miRNA target predictor for application on plant species. Rigorous experiment design across four plant test species demonstrates that animal-trained predictors fail to sustain performance on plant species, and that the use of plant-specific training data improves accuracy depending on the quantity of plant training data used. Surprisingly, our results indicate that the complete exclusion of animal training data leads to the most accurate plant-specific miRNA target predictor indicating that animal-based data may detract from miRNA target prediction in plants. Our final plant-specific miRNA prediction method, dubbed P-TarPmiR, is freely available for use at here. The final P-TarPmiR method is used to predict targets for all miRNA within the soybean genome. Those ranked predictions, together with GO term enrichment, are shared with the research community.