Gene set enrichment analysis of pathways and transcription factors associated with diabetic retinopathy using a microarray dataset

He,Kan; Lv,Wenwen; Zhang,Qing; Wang,Yuqing; Tao,Liming; Liu,Dahai

doi:10.3892/ijmm.2015.2220

Gene set enrichment analysis of pathways and transcription factors associated with diabetic retinopathy using a microarray dataset

Authors:
- Kan He
- Wenwen Lv
- Qing Zhang
- Yuqing Wang
- Liming Tao
- Dahai Liu
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Affiliations: Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui 230601, P.R. China, Department of Ophthalmology, The Second Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
Published online on: May 22, 2015 https://doi.org/10.3892/ijmm.2015.2220
Pages: 103-112
Copyright: © He et al. This is an open access article distributed under the terms of Creative Commons Attribution License [CC BY_NC 3.0].

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Abstract

Diabetic retinopathy (DR) is a serious microvascular complication of diabetes, which causes visual disability and blindness. Several studies have used gene expression profiling of DR to identify the key genes involved in this process; however, few studies have focused on the associated pathways and transcription factors (TFs), or on the co-expression patterns at the multiple pathways level. In this study, we employed a microarray dataset from the public database library of the Gene Expression Omnibus (GEO) associated with DR and applied gene set enrichment analysis (GSEA) to this dataset and performed candidate TF selection. As a result, 10 upregulated pathways, including the type I diabetes mellitus and peroxisome proliferator-activated receptor (PPAR) signaling pathways, as well as 59 downregulated pathways, including the ErbB signaling pathway and the mammalian target of rapamycin (mTOR) signaling pathway, were identified as DR‑related pathways. The majority of these pathways have been previously identified, but some were novel. Finally, co-expression networks of related pathways were constructed using the significant core genes and TFs, such as PPARγ and SMAD4. The results of our study may enhance our understanding of the molecular mechanisms associated DR at the genome-wide level.

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