Research Papers:

HGIMDA: Heterogeneous graph inference for miRNA-disease association prediction

Xing Chen _, Chenggang Clarence Yan, Xu Zhang, Zhu-Hong You, Yu-An Huang and Gui-Ying Yan

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Oncotarget. 2016; 7:65257-65269. https://doi.org/10.18632/oncotarget.11251

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Xing Chen1,*, Chenggang Clarence Yan2,*, Xu Zhang3, Zhu-Hong You4, Yu-An Huang5, Gui-Ying Yan6

1School of Information and Electrical Engineering, China University of Mining and Technology, Xuzhou, China

2Institute of Information and Control, Hangzhou Dianzi University, Hangzhou, China

3School of Mechanical, Electrical & Information Engineering, Shandong University, Weihai, China

4School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China

5Department of Computing, Hong Kong Polytechnic University, Hong Kong, China

6Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China

*The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Correspondence to:

Xing Chen, email: [email protected]

Gui-Ying Yan, email: [email protected]

Keywords: microRNA, disease, microRNA-disease association, heterogeneous network, similarity

Received: May 12, 2016     Accepted: July 28, 2016     Published: August 12, 2016


Recently, microRNAs (miRNAs) have drawn more and more attentions because accumulating experimental studies have indicated miRNA could play critical roles in multiple biological processes as well as the development and progression of human complex diseases. Using the huge number of known heterogeneous biological datasets to predict potential associations between miRNAs and diseases is an important topic in the field of biology, medicine, and bioinformatics. In this study, considering the limitations in the previous computational methods, we developed the computational model of Heterogeneous Graph Inference for MiRNA-Disease Association prediction (HGIMDA) to uncover potential miRNA-disease associations by integrating miRNA functional similarity, disease semantic similarity, Gaussian interaction profile kernel similarity, and experimentally verified miRNA-disease associations into a heterogeneous graph. HGIMDA obtained AUCs of 0.8781 and 0.8077 based on global and local leave-one-out cross validation, respectively. Furthermore, HGIMDA was applied to three important human cancers for performance evaluation. As a result, 90% (Colon Neoplasms), 88% (Esophageal Neoplasms) and 88% (Kidney Neoplasms) of top 50 predicted miRNAs are confirmed by recent experiment reports. Furthermore, HGIMDA could be effectively applied to new diseases and new miRNAs without any known associations, which overcome the important limitations of many previous computational models.

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