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PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction
You, ZH (You, Zhu-Hong); Huang, ZA (Huang, Zhi-An); Zhu, ZX (Zhu, Zexuan); Yan, GY (Yan, Gui-Ying); Li, ZW (Li, Zheng-Wei); Wen, ZK (Wen, Zhenkun); Chen, X (Chen, Xing)
2017
Source PublicationPLOS COMPUTATIONAL BIOLOGY
ISSN1553-734X
Volume13Issue:3Pages:1-22
Abstract

In the recent few years, an increasing number of studies have shown that microRNAs (miRNAs) play critical roles in many fundamental and important biological processes. As one of pathogenetic factors, the molecular mechanisms underlying human complex diseases still have not been completely understood from the perspective of miRNA. Predicting potential miRNA-disease associations makes important contributions to understanding the pathogenesis of diseases, developing new drugs, and formulating individualized diagnosis and treatment for diverse human complex diseases. Instead of only depending on expensive and time-consuming biological experiments, computational prediction models are effective by predicting potential miRNA-disease associations, prioritizing candidate miRNAs for the investigated diseases, and selecting those miRNAs with higher association probabilities for further experimental validation. In this study, Path-Based MiRNA-Disease Association (PBMDA) prediction model was proposed by integrating known human miRNA-disease associations, miRNA functional similarity, disease semantic similarity, and Gaussian interaction profile kernel similarity for miRNAs and diseases. This model constructed a heterogeneous graph consisting of three interlinked sub-graphs and further adopted depth-first search algorithm to infer potential miRNA-disease associations. As a result, PBMDA achieved reliable performance in the frameworks of both local and global LOOCV (AUCs of 0.8341 and 0.9169, respectively) and 5-fold cross validation (average AUC of 0.9172). In the cases studies of three important human diseases, 88% (Esophageal Neoplasms), 88% (Kidney Neoplasms) and 90% (Colon Neoplasms) of top-50 predicted miRNAs have been manually confirmed by previous experimental reports from literatures. Through the comparison performance between PBMDA and other previous models in case studies, the reliable performance also demonstrates that PBMDA could serve as a powerful computational tool to accelerate the identification of disease-miRNA associations.

DOI10.1371/journal.pcbi.1005455
WOS IDWOS:000398031900018
Citation statistics
Document Type期刊论文
Identifierhttp://ir.xjipc.cas.cn/handle/365002/4787
Collection多语种信息技术研究室
Affiliation1.Chinese Acad Sci, Xinjiang Tech Inst Phys & Chem, Urumqi, Peoples R China
2.Shenzhen Univ, Coll Comp Sci & Software Engn, Shenzhen, Peoples R China
3.Chinese Acad Sci, Acad Math & Syst Sci, Beijing, Peoples R China
4.China Univ Min & Technol, Sch Comp Sci & Technol, Xuzhou, Peoples R China
5.China Univ Min & Technol, Sch Informat & Control Engn, Xuzhou, Peoples R China
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GB/T 7714
You, ZH ,Huang, ZA ,Zhu, ZX ,et al. PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction[J]. PLOS COMPUTATIONAL BIOLOGY,2017,13(3):1-22.
APA You, ZH .,Huang, ZA .,Zhu, ZX .,Yan, GY .,Li, ZW .,...&Chen, X .(2017).PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction.PLOS COMPUTATIONAL BIOLOGY,13(3),1-22.
MLA You, ZH ,et al."PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction".PLOS COMPUTATIONAL BIOLOGY 13.3(2017):1-22.
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