Key gene screening for colorectal cancer expression and prognosis based on bioinformatics analysis
Objective To identify differentially expressed genes(DEGs)in colorectal cancer and explore key pathways and genes in colorectal cancer due to the relatively high incidence of colorectal cancer.Methods The gene expression profiles GSE211496,GSE6988 and GSE29900 data sets from the gene expres-sion comprehensive data set were selected,and the GEO2R analysis tool was used to analyze and download the relevant data.The online database miRDB and TargetScan were used to predict the target genes of the differ-ential miRNAs in the GSE29900 data set.Then,the DEGs intersection of the three databases was taken by Wayne diagram,and the DAVID database tool was used for Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis.Then Protein-Protein Interactions(PPI)protein interaction tool was used for network construction and visualization by Cytoscape software.Hub gene expres-sion was verified by The Cancer Genome Atlas(TCGA)database.Receiver operating characteristic(ROC)curve analysis was performed on Hub genes consistent with TCGA database expression using pROC package.Finally,Kaplan-Meier plotter online tool detection was used to analyze the prognosis of colorectal cancer pa-tients.Results A total of 2 570 DEGs(p.adj＜0.01 and | log2FC| ≥ 1)in GSE211496 dataset,406 DEGs(p.adj＜0.01 and|log2 FC |≥ 1)in GSE6988 dataset and 99 differentially expressed miRNAs(p.adj＜0.01 and |log2 FC | ≥1)in GSE29900 dataset were screened out,and 14 938 target genes of differentially expressed miR-NAs were predicted.A total of 30 target genes were obtained by overlapping the target genes with DEGs.The results of KEGG pathway showed that the target genes were mainly enriched in vascular smooth muscle con-traction and mineral absorption pathways.The top 10 Hub genes were screened from the PPI network by con-nectivity.The TCGA database of Hub genes verified that MYL9,ACTG2,AGT and PDGFRA were consistent with the expression of GSE211496 data set.Analysis of the four Hub genes for the diagnosis of colorectal cancer showed that gene AGT(AUC=0.901,95％CI 0.868-0.933)was positively correlated with the pre-diction of colorectal cancer,while gene MYL9(AUC=0.820,95％CI 0.757-0.884),gene ACTG2(AUC=0.855,95％CI 0.802-0.908)and gene PDGFRA(AUC=0.815,95％CI 0.772-0.858)were negatively corre-lated with the prediction of colorectal cancer.Gene MYL9,ACTG2 and PDGFRA had certain accuracy in the diagnosis of colorectal cancer,and gene AGT had high accuracy in the diagnosis of colorectal cancer.Kaplan-Meier survival analysis showed that low expression of PDGFRA,ACTG2 and MYL9 indicated better progno-sis,and the differences were statistically significant(P＜0.05).Conclusion In this study,four genes were screened and identified as hub genes in colorectal cancer by bioinformatics analysis.These genes include PDG-FRA,ACTG2,MYL9 and AGT,which will provide some new directions for colorectal cancer research.
万方数据
维普
