Using Network Distance Analysis to Predict lncRNA–miRNA Interactions
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,...
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Published in | Interdisciplinary sciences : computational life sciences Vol. 13; no. 3; pp. 535 - 545 |
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Main Authors | , , , , |
Format | Journal Article |
Language | English |
Published |
Singapore
Springer Singapore
01.09.2021
Springer Nature B.V |
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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
.
Graphic Abstract |
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AbstractList | 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.Graphic 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 .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 . 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 . Graphic Abstract |
Author | Zhao, Qi Feng, Huawei Yang, Pengyu Zhang, Li Liu, Hongsheng |
Author_xml | – sequence: 1 givenname: Li surname: Zhang fullname: Zhang, Li organization: School of Life Science, Liaoning University, Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Shenyang, Liaoning University, Technology Innovation Center for Computer Simulating and Information Processing of Bio-Macromolecules of Shenyang – sequence: 2 givenname: Pengyu surname: Yang fullname: Yang, Pengyu organization: School of Information, Liaoning University – sequence: 3 givenname: Huawei surname: Feng fullname: Feng, Huawei organization: School of Life Science, Liaoning University – sequence: 4 givenname: Qi orcidid: 0000-0001-9713-1864 surname: Zhao fullname: Zhao, Qi email: zhaoqi@lnu.edu.cn organization: School of Computer Science and Software Engineering, University of Science and Technology Liaoning – sequence: 5 givenname: Hongsheng surname: Liu fullname: Liu, Hongsheng email: liuhongsheng@lnu.edu.cn organization: Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Shenyang, Liaoning University, Technology Innovation Center for Computer Simulating and Information Processing of Bio-Macromolecules of Shenyang, School of Pharmacy, Liaoning University |
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Snippet | LncRNA–miRNA interactions contribute to the regulation of therapeutic targets and diagnostic biomarkers in multifarious human diseases. However, it remains... LncRNA-miRNA interactions contribute to the regulation of therapeutic targets and diagnostic biomarkers in multifarious human diseases. However, it remains... |
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SubjectTerms | Algorithms Biomarkers Biomedical and Life Sciences Case studies Computational Biology/Bioinformatics Computational Science and Engineering Computer Appl. in Life Sciences Computer applications Health Sciences Life Sciences Mathematical and Computational Physics Medicine miRNA Original Research Article Predictions Similarity Source code Statistics for Life Sciences Theoretical Theoretical and Computational Chemistry Therapeutic targets |
Title | Using Network Distance Analysis to Predict lncRNA–miRNA Interactions |
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