miGAP: miRNA–Gene Association Prediction Method Based on Deep Learning Model

Abstract

MicroRNAs (miRNAs) are small RNA molecules consisting of approximately 22 nucleotides; they regulate gene expression and are employed in the development of therapeutics for intractable diseases. Predicting the association between miRNAs and genes is crucial for understanding their roles in molecular processes. miRNA–gene associations have been studied using deep learning methods, but these methods present various constraints. Through addressing the limitations of previous methods, this study aimed to achieve better performance than the state-of-the-art (SOTA) methods for studying miRNA–gene associations. We constructed the most extensive embedded dataset to date, comprising 717,728 miRNA–gene pairs, specifically designed for our deep learning model. Further, we applied an embedding method used for protein embedding for transforming our gene sequence data. Moreover, we constructed a sophisticated negative dataset based on three distance criteria, unlike most studies that randomly designate negative data. Leveraging the data and insights from these approaches, we built a deep learning model with the best performance among SOTA miRNA–gene studies (area under the receiver operating characteristic curve = 0.9834). In addition, we conducted a case study using the learned model to predict potential positive data. We also aimed to identify miRNAs closely associated with a gene linked to various cancers.