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

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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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Authors and Affiliations

  1. Department of Ophthalmology, The Third Hospital of Hebei Medical University, No. 139 Ziqiang Road, Qiaoxi District, Shijiazhuang, 050051, Hebei Province, China

    Haiyan Sun, Zhipeng Yan, Xiaokun Liu & Jun Zhang

  2. Department of Ophthalmology, The First Central Hospital of Baoding City, Baoding No. 1 Central Hospital, Baoding, 071000, Hebei Province, China

    Yahui Cheng

Authors
  1. Haiyan Sun
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  2. Yahui Cheng
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  3. Zhipeng Yan
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  4. Xiaokun Liu
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  5. Jun Zhang
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Contributions

HS carried out the conception and design of the research, YC participated in the acquisition of data. ZY carried out the analysis and interpretation of data. XL and JZ conceived the study, participated in its design and coordination, and helped to draft the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Jun Zhang.

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The authors declare that they have no conflict of interests.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Informed consent was obtained from all individual participants included in the study.

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Sun, H., Cheng, Y., Yan, Z. et al. Mining the proliferative diabetic retinopathy-associated genes and pathways by integrated bioinformatic analysis. Int Ophthalmol 40, 269–279 (2020). https://doi.org/10.1007/s10792-019-01158-w

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  • DOI: https://doi.org/10.1007/s10792-019-01158-w

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