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Exp Clin Endocrinol Diabetes 2014; 122(10): 587-591
DOI: 10.1055/s-0034-1382033
Article
© J. A. Barth Verlag in Georg Thieme Verlag KG Stuttgart · New York

Identification of Biological Targets of Therapeutic Intervention for Diabetic Nephropathy with Bioinformatics Approach

T. Wu
1   Department of Nephrology, The Second Hospital of Shandong University, Jinan, Shandong Province, China
,
Q Li
2   Institute of Biomedical Engineering, School of Medicine, Shandong University, Jinan, Shandong Province, China
,
T. Wu
3   Qilu University of Technology, Jinan, Shandong, China
,
H. Y. Liu
1   Department of Nephrology, The Second Hospital of Shandong University, Jinan, Shandong Province, China
› Author Affiliations
Further Information

Publication History

received 08 January 2014
first decision 31 March 2014

accepted 28 May 2014

Publication Date:
08 July 2014 (online)

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Abstract

We aimed to discover the potential microRNA (miRNA) targets for diabetic nephropathy (DN) treatment. The microarray data of GSE1009 was downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between DN patients and normal individuals were analyzed using limma package. The significant miRNAs targeting DEGs were collected based on Web-based Gene Set Enrichment Analysis Toolkit (WebGestalt) system. Then we predicted the protein-protein interaction (PPI) pairs regulated by significant miRNAs and constructed the PPI pairs-miRNA network using Cytoscape software. Besides, the significant function modules were explored using Molecular Complex Detection (MCODE) and Biological Networks Gene Ontology (BiNGO) plugin. Total 752 DEGs were obtained, including 318 down-regulated ones and 434 up-regulated ones. There were 10 significant miRNAs, among which miRNA-25 was the most significant. The PPI pairs-miRNA network was established with 103 PPI pairs and 10 miRNAs. Three function modules were obtained, including module A involved with miRNA-29, module B with miRNA-106 and module C with miRNA-124A and miRNA-21B. MiRNA-25, 29, 124 and 21 play key roles in DN progression and these miRNAs may be potential targets for DN treatment.

Key words

diabetic nephropathy - microarray data - differential expression genes - protein pairs - microRNAs
 

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