Identifying diseases-related metabolites using random walk

BMC Bioinformatics

Liang Cheng¹  Jun Zhang²  Yang Hu³  Tianyi Zang³  Tianyi Zhao³  Ningyi Zhang³ 

[1] College of Bioinformatics Science and Technology, Harbin Medical University;Department of rehabilitation, Heilongjiang Province Land Reclamation Headquarters General Hospital;School of Life Science and Technology, Department of Computer Science and Technology, Harbin Institute of Technology;

关键词: Metabolites;    Similarity of diseases;    Similarity of metabolites;    Random walk;    InfDisSim;    MISIM;   

DOI  :  10.1186/s12859-018-2098-1

来源: DOAJ

【 摘 要 】

Abstract Background Metabolites disrupted by abnormal state of human body are deemed as the effect of diseases. In comparison with the cause of diseases like genes, these markers are easier to be captured for the prevention and diagnosis of metabolic diseases. Currently, a large number of metabolic markers of diseases need to be explored, which drive us to do this work. Methods The existing metabolite-disease associations were extracted from Human Metabolome Database (HMDB) using a text mining tool NCBO annotator as priori knowledge. Next we calculated the similarity of a pair-wise metabolites based on the similarity of disease sets of them. Then, all the similarities of metabolite pairs were utilized for constructing a weighted metabolite association network (WMAN). Subsequently, the network was utilized for predicting novel metabolic markers of diseases using random walk. Results Totally, 604 metabolites and 228 diseases were extracted from HMDB. From 604 metabolites, 453 metabolites are selected to construct the WMAN, where each metabolite is deemed as a node, and the similarity of two metabolites as the weight of the edge linking them. The performance of the network is validated using the leave one out method. As a result, the high area under the receiver operating characteristic curve (AUC) (0.7048) is achieved. The further case studies for identifying novel metabolites of diabetes mellitus were validated in the recent studies. Conclusion In this paper, we presented a novel method for prioritizing metabolite-disease pairs. The superior performance validates its reliability for exploring novel metabolic markers of diseases.

【 授权许可】

Unknown