A Deep Learning Method for MiRNA/IsomiR Target Detection

• Published in: bioRxiv
• Main Authors: Talukder, Amlan, Zhang, Wencai, Li, Xiaoman, Hu, Haiyan
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 05.04.2022
• Subjects: Deep learning; Isoforms; MicroRNAs; miRNA; mRNA; Seeds
• DOI: 10.1101/2022.04.04.487002

Motivation: Accurate identification of microRNA (miRNA) targets at base-pair resolution has been an open problem for over a decade. The recent discovery of miRNA isoforms (isomiRs) adds more complexity to this problem. Despite the existence of many methods, none considers isomiRs, and their performance is still suboptimal. We hypothesize that by taking the isomiR-mRNA interaction into account and applying a deep learning model to study miRNA-mRNA interaction features, we may improve the accuracy of miRNA target predictions. Results: We developed a deep learning tool called DMISO to capture the intricate features of miRNA/isomiR-mRNA interactions. Based on 10-fold cross-validation, DMISO showed high precision (95%) and recall (90%). Evaluated on three independent datasets, DMISO had superior performance to five tools, including three popular conventional tools and two recently developed deep learning-based tools. By applying two popular feature interpretation strategies, we demonstrated the importance of the miRNA regions other than their seeds and the potential contribution of the RNA-binding motifs within miRNAs/isomiRs and mRNAs to the miRNA/isomiR-mRNA interactions. Availability: The source code and tool are available at http://hulab.ucf.edu/research/projects/DMISO. Competing Interest Statement The authors have declared no competing interest.