Screening Of Key Genes And Pathways Involved In IgA Nephropathy Based On GEO Database

Objective:IgA nephropathy(IgAN)is the most common primary glomerulonephritis in the world.And its pathogenesis is not completely clear.In this study,we analyze the bioinformatics data of IgA nephropathy gene chip in GEO(Gene Expressed Omnibus)database,to explore the molecular mechanism of IgA nephropathy.Methods:1.Download the gene chip data GSE115857,GSE93798 and GSE37463 from NCBI’s GEO database.Differentially expressed genes(DEGs)were read,pre-processed and screened by using affy and limma packages of R language.Differences in gene expressed were expressed by fold change(FC).The screening criteria were P<0.05 and |logFC|>1.2.Use clusterProfiler package of R software to perform Gene Ontology(GO)analysis and Kyto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis on DEGs.3.Protein-protein interaction(PPI)on obtained DEGs was analyzed by STRING online database,and visualized by Cytoscape software.12 algorithms in plug-in CytoHubba were used to rank genes,and select the top 10 genes of each algorithm.Using UpSetR package of R software to visualize the genes,and screen the hub genes.The Pearson correlation analysis was used to explore the correlation of hub genes.4.Receiver operating characteristic(ROC)analysis was used to test the validity of the hub genes.5.The expression level of hub genes mRNA was verified by Nephroseq database.Results:1.Select the data from the GPL14663 platform in the GSE37463 dataset,and screen out 164 DEGs,including 118 up-regulated genes and 46 down-regulated genes;321 DEGs were screened in the GSE93798 dataset,including 97 up-regulated genes and 224 down-regulated genes.296 DEGs were screened in the GSE115857 dataset,including 131 up-regulated genes and 165 down-regulated genes;21 DEGs were finally integrated by RRA algorithm,including 6 up-regulated genes and 15 down-regulated genes.2.Results of GO enrichment analysis:Cellular Component(CC):DEGs are mainly enriched in transcriptional regulatory complex.Biological Process(BP):DEGs were mainly enriched in signal transduction and cell differentiation,including cellular response to extracellular stimulus,DNA-templated transcription initiation,intracellular receptor signaling pathway,skeletal muscle cell differentiation,and positive regulation of pri-miRNA transcription by RNA polymeraseⅡ.Molecular function(MF):DEGs are mainly enriched in the items of transcriptional activator’s activity and binding response,including DNA-binding transcription activator activity,RNA polymerase Ⅱ specificity,nuclear receptor activity,ligand-activated transcription factor activity,and glucocorticoid receptor binding.3.Results of KEGG pathway enrichment analysis:DEGs are mainly enriched in colorectal cancer pathway,Leishmania infection pathway,B cell receptor signaling pathway,MAPK signaling pathway,Toll-like receptor signaling pathway,T cell receptor signaling pathway,and cancer pathway,pantothenate and coenzyme A biosynthesis pathway.4.The protein-protein interaction network was constructed by STRING online database,12 algorithms in plug-in CytoHubba of Cytoscape software were used to select genes.Finally,using UpSetR package of R software to screen out 5 hub genes:FOS,JUN,NR4A2,NR4A3,EGR3.The Pearson correlation analysis of the hub genes showed that there was a positive correlation between the five genes.The five genes were analyzed by ROC curve has good diagnostic efficacy.5.The correlation between the expression of hub genes and IgAN was verified by the Nephroseq database.The results of the Nephroseq database showed that compared with normal kidney donors,the expression of FOS,JUN,NR4A2,NR4A3,and EGR3 genes in IgAN patients was down-regulated.The expression level are consistent with our hub genes.Conclusion:1.A total of 21 differentially expressed genes were screened from 3 microarray datasets of IgA nephropathy,including 6 up-regulated genes and 15 down-regulated genes.2.FOS,JUN,NR4A2,NR4A3 and EGR3 may play an important role in the development of IgAN.