m7G-DPP: Identifying N7-methylguanosine sites based on dinucleotide physicochemical properties of RNA.

Abstract

N7-methylguanosine (m7G) modification is one of the most common post-transcriptional RNA modifications, which play vital role in the regulation of gene expression. Dysfunction of m7G may result to developmental defects and the appearance of some serious diseases. Thus, it is an urgent task to fast and accurate identifying m7G sites. In view of experimental approaches are costly and time-consuming, researchers focused their attention on computational models. Hence, in current study, we proposed a novel predictor called m7G-DPP to identify m7G sites. In the predictor, the RNA sequences were firstly encoded by physicochemical (PC) properties of dinucleotide. Then, sliding window approach was adopted to divide PC matrix into multiple matrixes, and Pearson s correlation coefficient (PCC), dynamic time warping (DTW), and distance correlation (DC) were employed to extract classification features at each window. Next, the least absolute shrinkage and selection operator (LASSO) algorithm was applied to select discriminative features. Finally, these selected features were fed into support vector machine to identify m7G sites. Experimental results showed that the proposed method is effective, which may play a complementary role in current m7G sites prediction studies. The MATLAB codes and dataset can be obtained from website at https://figshare.com/articles/online_resource/m7G-DPP/15000348.