Identification of biological targets of therapeutic intervention for diabetic nephropathy with bioinformatics approach.

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.

Wu T ，Li Q ，Wu T ，Liu HY ... -  《-》

Revealing the underlying mechanism of diabetic nephropathy viewed by microarray analysis.

To explore the molecular mechanisms of diabetic nephropathy (DN) progression and provide the theoretical basis for treating DN, GSE1009 microarray data were downloaded from Gene Expression Omnibus database. Microarray data were obtained from glomeruli isolated from normal kidneys (n=3) and kidneys from patients with DN (n=3). We first screened the differentially expressed genes (DEGs) in kidneys by the Linear Models for Microarray Data package in R. Then the function of DEGs in DN was explored through Gene Ontology (GO) and KEGG pathway enrichment analyses. Critical DEGs for DN progression were investigated by constructing PPI network and mining significant modules. Afterwards, enriched protein domains of modules were analyzed by Interpro and DAVID. At last, the regulatory miRNAs for DEGs were calculated by WebGestalt, and DEGs-miRNAs network was visualized with Cytoscape. A total of 666 DEGs including 384 up- and 282 down-regulated genes were screened out. The up-regulated DEGs were significantly enriched in plasma membrane and signal transmission, and mainly participated in pathways of cytokine-cytokine receptor and neuroactive ligand-receptor interaction. The down-regulated DEGs significantly enriched in extracellular region and cytoskeletal protein binding, and mainly participated in ECM-receptor interaction and dilated cardiomyopathy. 2 PPI networks were constructed with confidence score>0.4. One significant module obtained from PPI network for up-regulated DEGs mainly enriched in protein domain of rhodopsin-like G protein-coupled receptors. The down-regulated DEGs were mainly regulated by 10 miRNAs clusters. Together, we constructed a comprehensive molecular network for DN progression and miR-1 and miR-25 might be theoretical targets for DN.

Qu W ，Han C ，Li M ，Zhang J ，Li L ... -  《-》

Investigation of mechanisms of mesenchymal stem cells for treatment of diabetic nephropathy via construction of a miRNA-TF-mRNA network.

Yang H ，Zhang X ，Xin G 《-》

Crucial genes associated with diabetic nephropathy explored by microarray analysis.

Wang Z ，Wang Z ，Zhou Z ，Ren Y ... -  《BMC Nephrology》

Gene expression profiling via bioinformatics analysis reveals biomarkers in laryngeal squamous cell carcinoma.

Guan GF ，Zheng Y ，Wen LJ ，Zhang DJ ，Yu DJ ，Lu YQ ，Zhao Y ，Zhang H ... -  《-》