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FCMDAP: using miRNA family and cluster information to improve the prediction accuracy of disease related miRNAs

Authors
  • Li, Xiaoying1
  • Lin, Yaping1
  • Gu, Changlong1
  • Yang, Jialiang2
  • 1 Hunan University, College of Computer Science and Electronic Engineering, Changsha, Hunan, 410082, China , Changsha (China)
  • 2 Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, 10029, USA , New York (United States)
Type
Published Article
Journal
BMC Systems Biology
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Apr 05, 2019
Volume
13
Issue
Suppl 2
Identifiers
DOI: 10.1186/s12918-019-0696-9
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundBiological experiments have confirmed the association between miRNAs and various diseases. However, such experiments are costly and time consuming. Computational methods help select potential disease-related miRNAs to improve the efficiency of biological experiments.MethodsIn this work, we develop a novel method using multiple types of data to calculate miRNA and disease similarity based on mutual information, and add miRNA family and cluster information to predict human disease-related miRNAs (FCMDAP). This method not only depends on known miRNA-diseases associations but also accurately measures miRNA and disease similarity and resolves the problem of overestimation. FCMDAP uses the k most similar neighbor recommendation algorithm to predict the association score between miRNA and disease. Information about miRNA cluster is also used to improve prediction accuracy.ResultFCMDAP achieves an average AUC of 0.9165 based on leave-one-out cross validation. Results confirm the 100, 98 and 96% of the top 50 predicted miRNAs reported in case studies on colorectal, lung, and pancreatic neoplasms. FCMDAP also exhibits satisfactory performance in predicting diseases without any related miRNAs and miRNAs without any related diseases.ConclusionsIn this study, we present a computational method FCMDAP to improve the prediction accuracy of disease related miRNAs. FCMDAP could be an effective tool for further biological experiments.

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