miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts

摘要

Author summary microRNAs are small RNA molecules that regulate biological processes by binding to the 3'UTR of a gene and their dysregulation is associated with several diseases. Computationally predicting these targets remains a challenge as they only partially match their target and so there can be hundreds of targets for a single microRNA. Current tools assume that most of the knowledge defining a microRNA-gene interaction can be captured by analysing the binding produced in the seed region ( the first 8nt in the miRNA). However, recent studies show that the whole microRNA can be important and form non-canonical targets. Here, we use a target prediction methodology that relies on deep neural networks to automatically learn the relevant features describing microRNA-gene interactions for predicting microRNA targets. This means we make no assumptions about what is important, leaving the task to the deep neural network. A key part of the work is obtaining a suitable dataset. Thus, we collected and curated more than 150,000 experimentally verified microRNA targets and used them to train the network. Using this approach, we are able to gain a better understanding of non-canonical targets and to improve the accuracy of state-of-the-art prediction tools.