m5U-GEPred: prediction of RNA 5-methyluridine sites based on sequence-derived and graph embedding features

5-Methyluridine (m⁵U) is one of the most common post-transcriptional RNA modifications, which is involved in a variety of important biological processes and disease development. The precise identification of the m⁵U sites allows for a better understanding of the biological processes of RNA and contributes to the discovery of new RNA functional and therapeutic targets. Here, we present m5U-GEPred, a prediction framework, to combine sequence characteristics and graph embedding-based information for m⁵U identification. The graph embedding approach was introduced to extract the global information of training data that complemented the local information represented by conventional sequence features, thereby enhancing the prediction performance of m⁵U identification. m5U-GEPred outperformed the state-of-the-art m⁵U predictors built on two independent species, with an average AUROC of 0.984 and 0.985 tested on human and yeast transcriptomes, respectively. To further validate the performance of our newly proposed framework, the experimentally validated m⁵U sites identified from Oxford Nanopore Technology (ONT) were collected as independent testing data, and in this project, m5U-GEPred achieved reasonable prediction performance with ACC of 91.84%. We hope that m5U-GEPred should make a useful computational alternative for m⁵U identification.