AUTHOR=Liu Yinbo , Shen Yingying , Wang Hong , Zhang Yong , Zhu Xiaolei 

TITLE=m5Cpred-XS: A New Method for Predicting RNA m5C Sites Based on XGBoost and SHAP

JOURNAL=Frontiers in Genetics

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.853258

DOI=10.3389/fgene.2022.853258

ISSN=1664-8021

ABSTRACT=<p>As one of the most important post-transcriptional modifications of RNA, 5-cytosine-methylation (m5C) is reported to closely relate to many chemical reactions and biological functions in cells. Recently, several computational methods have been proposed for identifying m5C sites. However, the accuracy and efficiency are still not satisfactory. In this study, we proposed a new method, m5Cpred-XS, for predicting m5C sites of <italic>H. sapiens</italic>, <italic>M. musculus</italic>, and <italic>A. thaliana</italic>. First, the powerful SHAP method was used to select the optimal feature subset from seven different kinds of sequence-based features. Second, different machine learning algorithms were used to train the models. The results of five-fold cross-validation indicate that the model based on XGBoost achieved the highest prediction accuracy. Finally, our model was compared with other state-of-the-art models, which indicates that m5Cpred-XS is superior to other methods. Moreover, we deployed the model on a web server that can be accessed through <ext-link ext-link-type="uri" xlink:href="http://m5cpred-xs.zhulab.org.cn/" xmlns:xlink="http://www.w3.org/1999/xlink">http://m5cpred-xs.zhulab.org.cn/</ext-link>, and m5Cpred-XS is expected to be a useful tool for studying m5C sites.</p>