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DeepKPred: Prediction and Functional Analysis of Lysine 2-Hydroxyisobutyrylation Sites Based on Deep Learning

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Abstract

Protein 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, plays a role in various cellular processes. To gain a comprehensive understanding of its regulatory mechanisms, it is crucial to identify the sites of 2-hydroxyisobutyrylation. Therefore, we developed a novel ensemble method, DeepKPred, for predicting species-specific 2-hydroxyisobutyrylation sites. We employed one-hot and AAindex encoding schemes to construct features from protein sequences and integrated two densely convolutional neural networks and two long short-term memory networks to build the model. In the 5-fold cross-validation dataset, DeepKPred achieved AUC values of 0.859, 0.804, 0.821, and 0.819 for Human, Candida albicans, Rice, Wheat, and Physcomitrella patens. Additionally, function analysis further indicated that different organisms tend to engage in distinct biological processes and pathways. Detailed analysis can help us learn more about the mechanism of 2-hydroxyisobutyrylation and provide insights for associated experimental verification.

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Funding

This work is supported by grants from the Natural Science Foundation of China (12071024) and the statistics and materials interdisciplinary Project No.00003957.

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Authors and Affiliations

  1. Department of Statistics, University of Science and Technology Beijing, Beijing, 100083, China

    Shiqi Fan & Yan Xu

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  1. Shiqi Fan
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  2. Yan Xu
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Contributions

YX conceived and designed the experiments. SF performed the experiments and wrote the paper. YX. revised the manuscript. All the authors read and agreed on the final manuscript.

Corresponding author

Correspondence to Yan Xu.

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The authors declare no competing financial interests.

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I hereby declare that this manuscript is the result of our (Shiqi Fan and Yan Xu) independent creation under the reviewers’ comments. Except for the quoted contents, this manuscript does not contain any research achievements that have been published or written by other individuals or groups. I am the corresponding author of this manuscript. The legal responsibility of the statement shall be borne by me.

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Fan, S., Xu, Y. DeepKPred: Prediction and Functional Analysis of Lysine 2-Hydroxyisobutyrylation Sites Based on Deep Learning. Ann. Data. Sci. 11, 693–707 (2024). https://doi.org/10.1007/s40745-023-00504-1

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  • DOI: https://doi.org/10.1007/s40745-023-00504-1

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