Journal
BMC BIOINFORMATICS
Volume 21, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s12859-020-3515-9
Keywords
miRNA-disease association; Similarity measurement; Performance evaluation
Categories
Funding
- National Natural Science Foundation of China [61862026]
- Natural Science Foundation of Jiangxi, China [20181BAB202008]
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Background As regulators of gene expression, microRNAs (miRNAs) are increasingly recognized as critical biomarkers of human diseases. Till now, a series of computational methods have been proposed to predict new miRNA-disease associations based on similarity measurements. Different categories of features in miRNAs are applied in these methods for miRNA-miRNA similarity calculation. Benchmarking tests on these miRNA similarity measures are warranted to assess their effectiveness and robustness. Results In this study, 5 categories of features, i.e. miRNA sequences, miRNA expression profiles in cell-lines, miRNA expression profiles in tissues, gene ontology (GO) annotations of miRNA target genes and Medical Subject Heading (MeSH) terms of miRNA-associated diseases, are collected and similarity values between miRNAs are quantified based on these feature spaces, respectively. We systematically compare the 5 similarities from multi-statistical views. Furthermore, we adopt a rule-based inference method to test their performance on miRNA-disease association predictions with the similarity measurements. Comprehensive comparison is made based on leave-one-out cross-validations and a case study. Experimental results demonstrate that the similarity measurement using MeSH terms performs best among the 5 measurements. It should be noted that the other 4 measurements can also achieve reliable prediction performance. The best-performed similarity measurement is used for new miRNA-disease association predictions and the inferred results are released for further biomedical screening. Conclusions Our study suggests that all the 5 features, even though some are restricted by data availability, are useful information for inferring novel miRNA-disease associations. However, biased prediction results might be produced in GO- and MeSH-based similarity measurements due to incomplete feature spaces. Similarity fusion may help produce more reliable prediction results. We expect that future studies will provide more detailed information into the 5 feature spaces and widen our understanding about disease pathogenesis.
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