SCCPMD: Probability matrix decomposition method subject to corrected similarity constraints for inferring long non-coding RNA–disease associations

Accumulating evidence has demonstrated various associations of long non-coding RNAs (lncRNAs) with human diseases, such as abnormal expression due to microbial influences that cause disease. Gaining a deeper understanding of lncRNA–disease associations is essential for disease diagnosis, treatment,...

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Veröffentlicht in:Frontiers in microbiology Jg. 13; S. 1093615
Hauptverfasser: Lin, Lieqing, Chen, Ruibin, Zhu, Yinting, Xie, Weijie, Jing, Huaiguo, Chen, Langcheng, Zou, Minqing
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Switzerland Frontiers Media S.A 11.01.2023
Schlagworte:
associations prediction
constraint probability matrix decomposition
disease
lncRNA-long noncoding RNA
Microbiology
similarity correction
similarity correction
associations prediction
disease
lncRNA-long noncoding RNA
constraint probability matrix decomposition
ISSN:1664-302X, 1664-302X
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Zusammenfassung:Accumulating evidence has demonstrated various associations of long non-coding RNAs (lncRNAs) with human diseases, such as abnormal expression due to microbial influences that cause disease. Gaining a deeper understanding of lncRNA–disease associations is essential for disease diagnosis, treatment, and prevention. In recent years, many matrix decomposition methods have also been used to predict potential lncRNA-disease associations. However, these methods do not consider the use of microbe-disease association information to enrich disease similarity, and also do not make more use of similarity information in the decomposition process. To address these issues, we here propose a correction-based similarity-constrained probability matrix decomposition method (SCCPMD) to predict lncRNA–disease associations. The microbe-disease associations are first used to enrich the disease semantic similarity matrix, and then the logistic function is used to correct the lncRNA and disease similarity matrix, and then these two corrected similarity matrices are added to the probability matrix decomposition as constraints to finally predict the potential lncRNA–disease associations. The experimental results show that SCCPMD outperforms the five advanced comparison algorithms. In addition, SCCPMD demonstrated excellent prediction performance in a case study for breast cancer, lung cancer, and renal cell carcinoma, with prediction accuracy reaching 80, 100, and 100%, respectively. Therefore, SCCPMD shows excellent predictive performance in identifying unknown lncRNA–disease associations.
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Edited by: Qi Zhao, University of Science and Technology Liaoning, China
This article was submitted to Systems Microbiology, a section of the journal Frontiers in Microbiology
Reviewed by: Chun-Chun Wang, China University of Mining and Technology, China; Li Zhang, Liaoning University, China
ISSN:1664-302X
1664-302X
DOI:10.3389/fmicb.2022.1093615