Dataset Information

EPMDA: an expression-profile based computational model for microRNA-disease association prediction.

ABSTRACT: MicroRNA has become a new star molecule for understanding multiple biological processes and the mechanism of various complex human diseases. Even though a number of computational models have been proposed for predicting the association between microRNAs and various human diseases, most of them are mainly based on microRNA functional similarity and heterogeneous biological networks which suffer from inevitable computational error and bias. In this work, considering the limitation of information resource used by existing methods, we proposed EPMDA model which is the first computational method using the expression profiles of microRNAs to predict the most potential microRNAs associated with various diseases. Based on the dataset constructed from HMDD v2.0 database, EPMDA obtained AUCs of 0.8945 and 0.8917 based on the leave-one-out and 5-fold cross validation, respectively. Furthermore, EPMDA was applied to two important human diseases. As a result, 80% and 88% microRNAs in the top-25 lists of Colon Neoplasms and Kidney Neoplasms were confirmed by other databases. The performance comparison of EPMDA with existing prediction models and classical algorithms also demonstrated the reliable prediction ability of EPMDA. It is anticipated that EPMDA can be used as an effective computational tool for future biomedical researches.

SUBMITTER: Huang YA

PROVIDER: S-EPMC5675613 | biostudies-other | 2017 Oct

REPOSITORIES: biostudies-other

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EPMDA: an expression-profile based computational model for microRNA-disease association prediction.

Huang Yu-An YA You Zhu-Hong ZH Li Li-Ping LP Huang Zhi-An ZA Xiang Lu-Xuan LX Li Xiao-Fang XF Lv Lin-Tao LT

Oncotarget 20170628 50

MicroRNA has become a new star molecule for understanding multiple biological processes and the mechanism of various complex human diseases. Even though a number of computational models have been proposed for predicting the association between microRNAs and various human diseases, most of them are mainly based on microRNA functional similarity and heterogeneous biological networks which suffer from inevitable computational error and bias. In this work, considering the limitation of information r ...[more]

PMID: 29152061

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Project description: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.

Dataset Information

EPMDA: an expression-profile based computational model for microRNA-disease association prediction.

Publications

EPMDA: an expression-profile based computational model for microRNA-disease association prediction.

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