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iPseU-Layer: Identifying RNA Pseudouridine Sites Using Layered Ensemble Model

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Abstract

Pseudouridine represents one of the most prevalent post-transcriptional RNA modifications. The identification of pseudouridine sites is an essential step toward understanding RNA functions, RNA structure stabilization, translation process, and RNA stability; however, high-throughput experimental techniques remain expensive and time-consuming in lab explorations and biochemical processes. Thus, how to develop an efficient pseudouridine site identification method based on machine learning is very important both in academic research and drug development. Motived by this, we present an effective layered ensemble model designated as iPseU-Layer for identification of RNA pseudouridine sites. The proposed iPseU-Layer approach is essentially based on three different machine learning layers including: feature selection layer, feature extraction and fusion layer, and prediction layer. The feature selection layer reduces the dimensionality, which can be regarded as a data pre-processing stage. The feature extraction and fusion layer utilizes an ensemble method which is implemented through various machine learning algorithms to generate some outputs. The prediction layer applies classic random forest to identify the final results. Furthermore, we systematically conduct the validation experiments using cross-validation tests and independent test with the current state-of-the-art models. The proposed iPseU-Layer provides a promising predictive performance in terms of sensitivity, specificity, accuracy and Matthews correlation coefficient. Collectively, these findings indicate that the framework of iPseU-Layer is a feasible and effective strategy for the prediction of RNA pseudouridine sites.

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Acknowledgements

This work was supported by the Research Foundation for Advanced Talents (Nos. 2019BS007, 31401204) of Henan University of Technology and the National Natural Science Foundation of China under Grants (Nos. 61673082, 61773352).

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Authors and Affiliations

  1. Key Laboratory of Grain Information Processing and Control, Ministry of Education, Henan University of Technology, Zhengzhou, 450001, People’s Republic of China

    Yashuang Mu

  2. College of Information Science and Engineering, Henan University of Technology, Zhengzhou, 450001, People’s Republic of China

    Yashuang Mu

  3. School of Science, Dalian Maritime University, Dalian, 116026, People’s Republic of China

    Ruijun Zhang & Lidong Wang

  4. School of Control Science and Engineering, Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, 116024, People’s Republic of China

    Xiaodong Liu

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  1. Yashuang Mu
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Mu, Y., Zhang, R., Wang, L. et al. iPseU-Layer: Identifying RNA Pseudouridine Sites Using Layered Ensemble Model. Interdiscip Sci Comput Life Sci 12, 193–203 (2020). https://doi.org/10.1007/s12539-020-00362-y

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