IR5hmcSC: Identifying RNA 5-hydroxymethylcytosine with multiple features based on stacking learning. (December 2021)

• Record Type: Journal Article
• Authors: Zhang, Shengli; Shi, Hongyan
• Is Part Of: Computational biology and chemistry. Volume 95(2021)
• Publication Date: 2021-12
• Subjects: RNA 5-hydroxymethylcytosine -- K-mer -- Pseudo structure status composition -- One-hot encoding -- Stacking; Chemistry -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; Biochemistry -- Data processing; Biology -- Data processing; Molecular biology -- Data processing; Periodicals; Electronic journals; 542.85
• DOI: 10.1016/j.compbiolchem.2021.107583
• Languages: English
• ISSNs: 1476-9271

Abstract

Abstract: RNA 5-hydroxymethylcytosine (5hmC) modification is the basis of the translation of genetic information and the biological evolution. The study of its distribution in transcriptome is fundamentally crucial to reveal the biological significance of 5hmC. Biochemical experiments can use a variety of sequencing-based technologies to achieve high-throughput identification of 5hmC; however, they are labor-intensive, time-consuming, as well as expensive. Therefore, it is urgent to develop more effective and feasible computational methods. In this paper, a novel and powerful model called iR5hmcSC is designed for identifying 5hmC. Firstly, we extract the different features by K-mer, Pseudo Structure Status Composition and One-Hot encoding. Subsequently, the combination of chi-square test and logistic regression is utilized as the feature selection method to select the optimal feature sets. And then stacking learning, an ensemble learning method including random forest (RF), extra trees (EX), AdaBoost (Ada), gradient boosting decision tree (GBDT), and support vector machine (SVM), is used to recognize 5hmC and non-5hmC. Finally, 10-fold cross-validation test is performed to evaluate the model. The accuracy reaches 85.27% and 79.92% on benchmark dataset and independent dataset, respectively. The result is better than the state-of-the-art methods, which indicates that our model is a feasible tool to identify 5hmC. The datasets and source code are freely available at https://github.com/HongyanShi026/iR5hmcSC . Graphical Abstract: ga1 Highlights: A new model named iR5hmcSC was proposed to predict RNA 5hmC sites. K-mer, Pseudo Structure Status Composition and One-Hot encoding are applied to extract features from the dataset. A new method combining chi-square test and logistic regression is used to reduce the dimensions of data. The stacking learning is adopted to classify the model.