title: Gene set enrichment analysis of pathways and transcription factors associated with diabetic retinopathy using a microarray dataset.
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.
authors.affiliation: Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui 230601, P.R. China.
authors.forename: Kan
authors.initials: K
authors.lastname: He
authors.affiliation: Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui 230601, P.R. China.
authors.forename: Wenwen
authors.initials: W
authors.lastname: Lv
authors.affiliation: Department of Ophthalmology, The Second Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui 230601, P.R. China.
authors.forename: Yuqing
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Ophthalmology, The Second Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China.
authors.forename: Liming
authors.initials: L
authors.lastname: Tao
authors.affiliation: Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui 230601, P.R. China.
authors.forename: Dahai
authors.initials: D
authors.lastname: Liu
mesh_terms: D030562:Databases, Protein; D003922:Diabetes Mellitus, Type 1 / Q000150:complications / Q000235:genetics / Q000473:pathology*; D003930:Diabetic Retinopathy / Q000378:metabolism / Q000473:pathology*; D066246:ErbB Receptors / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D047495:PPAR gamma / Q000235:genetics / Q000378:metabolism; D047492:Peroxisome Proliferator-Activated Receptors / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics; D051901:Smad4 Protein / Q000235:genetics / Q000378:metabolism; D058570:TOR Serine-Threonine Kinases / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D047495:PPAR gamma; D047492:Peroxisome Proliferator-Activated Receptors; C497796:SMAD4 protein, human; D051901:Smad4 Protein; D014157:Transcription Factors; C546842:MTOR protein, human; D066246:ErbB Receptors; D058570:TOR Serine-Threonine Kinases