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International Ophthalmology
Published in: International Ophthalmology 2/2020

01-02-2020 | Diabetic Retinopathy | Original Paper

Mining the proliferative diabetic retinopathy-associated genes and pathways by integrated bioinformatic analysis

Authors: Haiyan Sun, Yahui Cheng, Zhipeng Yan, Xiaokun Liu, Jun Zhang

Published in: International Ophthalmology | Issue 2/2020

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Abstract

Purpose

Diabetic retinopathy (DR) especially proliferative diabetic retinopathy (PDR) is a serious eye disease. We aimed to identify key pathway and hub genes associated with PDR by analyzing the expression of retinal fibrovascular tissue in PDR patients.

Methods

First raw data were downloaded from the Gene Expression Omnibus database. Median normalization was subsequently applied to preprocess. Differentially expressed genes (DEGs) analyzed with the Limma package. Weighted correlation network analysis (WGCNA) was utilized to build the co-expression network for all genes. Then, we compared the DEGs and modules filtered out by WGCNA. A protein–protein interaction network based on the STRING web site and the Cytoscape software was constructed by the overlapping DEGs. Next, the Gene Ontology term and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed. Finally, we used the Comparative Toxicogenomics Database to identify some important pathways and hub genes tightly related to PDR.

Results

Functional enrichment analysis showed that the pathway of cytokine–cytokine receptor interaction was significantly related to PDR eight hub genes which were associated with pathway including tumor necrosis factor (TNF), tumor necrosis factor receptor superfamily member 12A (TNFRSF12A), C-C chemokine 20 (CCL20), chemokine (C-X-C motif) ligand 2 (CXCL2), oncostatin M (OSM) interleukin 10 (IL10), interleukin 15 (IL 15), and interleukin 1B (IL1B).

Conclusions

We identified one pathway and eight hub genes, which were associated with PDR. The pathway provided references that will advance the understanding of mechanisms of PDR. Moreover, the hub genes may serve as therapeutic targets for precise diagnosis and treatment of PDR in the future.
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Metadata
Title
Mining the proliferative diabetic retinopathy-associated genes and pathways by integrated bioinformatic analysis
Authors
Haiyan Sun
Yahui Cheng
Zhipeng Yan
Xiaokun Liu
Jun Zhang
Publication date
01-02-2020
Publisher
Springer Netherlands
Published in
International Ophthalmology / Issue 2/2020
Print ISSN: 0165-5701
Electronic ISSN: 1573-2630
DOI
https://doi.org/10.1007/s10792-019-01158-w

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