Bioinformatics analysis to identify the differentially expressed genes of glaucoma

Yan,Xiang; Yuan,Fei; Chen,Xiuping; Dong,Chunqiong

doi:10.3892/mmr.2015.4030

Bioinformatics analysis to identify the differentially expressed genes of glaucoma

Authors:
- Xiang Yan
- Fei Yuan
- Xiuping Chen
- Chunqiong Dong
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Affiliations: Department of Ophthalmology, Pudong District Gongli Hospital, Shanghai 200135, P.R. China, Department of Ophthalmology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
Published online on: July 2, 2015 https://doi.org/10.3892/mmr.2015.4030
Pages: 4829-4836
Copyright: © Yan et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

The aim of the present study was to screen the differentially expressed genes (DEGs) associated with glaucoma and investigate the changing patterns of the expression of these genes. The GSE2378 gene microarray data of glaucoma was downloaded from the Gene Expression Omnibus database, which included seven normal samples and eight glaucoma astrocyte samples. Taking into account the corresponding associations between the probe ID and gene symbols, the DEGs were identified prior to and subsequent to the summation of probe level values using the Limma package in R language, followed by Gene Ontology (GO) and pathway enrichment analyses. Interaction networks of the DEGs were constructed using the Biomolecular Interaction Network Database, and cluster analysis of the genes in the networks was performed using ClusterONE. Subsequent to the summation of probe value, a total of 223 genes were identified as DEGs between the normal and glaucoma samples, including 74 downregulated and 149 upregulated genes. In addition, the DEGs were found to be associated with several functions, including response to wounding, extracellular region part and calcium ion binding. The most significantly enriched pathways were complement and coagulation cascades, arrhythmogenic right ventricular cardiomyopathy and extracellular matrix (ECM)‑receptor interaction. Furthermore, interaction networks were constructed of the DEGs prior to and subsequent to the summation of probe values, and HNF4A and CEBPD were identified as hub genes. Additionally, 37 and 31 GO terms were identified to be enriched in the two DEGs of the networks prior to and subsequent to summation, respectively. The results indicated the identified genes associated with ECM as important, and the CEBPD gene was considered to be a critical gene in glaucoma. The findings of the present study offer a potential reference value in further investigations of glaucoma at the gene level.

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