DeepLGP: a novel deep learning method for prioritizing lncRNA target genes

Motivation: Although long non-coding RNAs (lncRNAs) have limited capacity for encoding proteins, they have been verified as biomarkers in the occurrence and development of complex diseases. Recent wet-lab experiments have shown that lncRNAs function by regulating the expression of protein-coding genes (PCGs), which could also be the mechanism responsible for causing diseases. Currently, lncRNA-related biological data are increasing rapidly. Whereas, no computational methods have been designed for predicting the novel target genes of lncRNA. Results: In this study, we present a graph convolutional network (GCN) based method, named DeepLGP, for prioritizing target PCGs of lncRNA. First, gene and lncRNA features were selected, these included their location in the genome, expression in 13 tissues and miRNA-mediated lncRNA-gene pairs. Next, GCN was applied to convolve a gene interaction network for encoding the features of genes and lncRNAs. Then, these features were used by the convolutional neural network for prioritizing target genes of lncRNAs. In 10-cross validations on two independent datasets, DeepLGP obtained high area under curves (0.90-0.98) and area under precision-recall curves (0.91-0.98). We found that IncRNA pairs with high similarity had more overlapped target genes. Further experiments showed that genes targeted by the same lncRNA sets had a strong likelihood of causing the same diseases, which could help in identifying disease-causing PCGs.