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Using Network Distance Analysis to Predict lncRNA–miRNA Interactions

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Interdisciplinary Sciences: Computational Life Sciences Aims and scope Submit manuscript

Abstract

LncRNA–miRNA interactions contribute to the regulation of therapeutic targets and diagnostic biomarkers in multifarious human diseases. However, it remains difficult to experimentally identify lncRNA–miRNA associations at large scale, and computational prediction methods are limited. In this study, we developed a network distance analysis model for lncRNA–miRNA association prediction (NDALMA). Similarity networks for lncRNAs and miRNAs were calculated and integrated with Gaussian interaction profile (GIP) kernel similarity. Then, network distance analysis was applied to the integrated similarity networks, and final scores were obtained after confidence calculation and score conversion. Our model obtained satisfactory results in fivefold cross validation, achieving an AUC of 0.8810 and an AUPR of 0.8315. Moreover, NDALMA showed superior prediction performance over several other network algorithms, and we tested the suitability and flexibility of the model by comparing different types of similarity. In addition, case studies of the relationships between lncRNAs and miRNAs were conducted, which verified the reliability of our method in predicting lncRNA–miRNA associations. The datasets and source code used in this study are available at https://github.com/Liu-Lab-Lnu/NDALMA.

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Funding

This work was supported by the National Natural Science Foundation of China (No: 82003655), Key R&D Program of Liaoning Province (No: 2019JH2/10300041), Scientific Research Project from Department of Education of Liaoning Province (No: LQN201906), and Shenyang Science and Technology Plan Project (No: 17-65-7-00 and 20-203-6-00).

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Authors and Affiliations

  1. School of Life Science, Liaoning University, Shenyang, 110036, China

    Li Zhang & Huawei Feng

  2. Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Shenyang, Liaoning University, Shenyang, 110036, China

    Li Zhang & Hongsheng Liu

  3. Technology Innovation Center for Computer Simulating and Information Processing of Bio-Macromolecules of Shenyang, Shenyang, 110036, China

    Li Zhang & Hongsheng Liu

  4. School of Information, Liaoning University, Shenyang, 110036, China

    Pengyu Yang

  5. School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China

    Qi Zhao

  6. School of Pharmacy, Liaoning University, Shenyang, 110036, China

    Hongsheng Liu

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  1. Li Zhang
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  3. Huawei Feng
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  4. Qi Zhao
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Correspondence to Qi Zhao or Hongsheng Liu.

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Zhang, L., Yang, P., Feng, H. et al. Using Network Distance Analysis to Predict lncRNA–miRNA Interactions. Interdiscip Sci Comput Life Sci 13, 535–545 (2021). https://doi.org/10.1007/s12539-021-00458-z

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  • DOI: https://doi.org/10.1007/s12539-021-00458-z

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