Screening potential biomarkers for colorectal cancer based on weighted gene co-expression network analysis
Objective:Screening potential biomarkers for colorectal cancer(CRC)by weighted gene co-expression network analysis.Methods:The limma and sva programs were used to screen the differential expression genes(DEGs)in the CRC group and normal control group.The gene expression data sets GSE44076 and GSE21815 were obtained from the GEO database.Through the use of the WGCNA,the most stable gene clusters were identified.Genes that were differentially co-expressed were obtained by intersecting the module's genes with DEGs.Genes showing varied co-expression were analyzed for enrichment using the Metascape web tool.The protein-protein interaction network(PPI)was constructed using the string database,and Cytoscape software was employed to calculate the degree value,which was then used to identify the top 10 highly connected genes as important genes.Key genes were subjected to survival analysis and differential expression in the GEPIA database.Key gene diagnostic value was assessed using ROC curves.Clinical colorectal cancer tissues and adjacent tissues were analyzed for key gene expression levels using RT-qPCR.Results:The combined datasets of GSE44076 and GSE21815 yielded 925 differentially expressed genes,110 major module genes were derived using WGCNA,and 86 differently co-expressed genes were screened at the junction of the two.Post-enrichment analysis indicated that differentially expressed genes were mainly concentrated in chromatin,nuclear matrix,mitotic cell cycle,cytoplasmic division,DNA metabolism and regulation of chromosome structure,and DNA replication.KEGG pathway enrichment analysis screened a total of 10 key genes,including BUB1,CDK1,TOP2A,NUF2,CEP55,MAD2L1,TPX2,AURKA,UBE2C,and KIF4A.The results of GEPIA database analysis showed that key genes were highly expressed in colorectal cancer,and BUB1,MAD2L1 and AURKA were correlated with the prognosis of colorectal cancer.CDK1 and MAD2L1 were correlated with clinical stage,and the ROC curve showed that CDK1 and MAD2L1 had good diagnostic efficacy.RT-qPCR results showed that MAD2L1,CDK1,BUB1 and AURKA were significantly upregulated in colorectal cancer tissues.Conclusion:The important genes MAD2L1,CDK1,BUB1,and AURKA are implicated in the development of colorectal cancer and may serve as biomarkers for the disease.
Differentially expressed geneWeighted gene coexpression networkColorectal cancer
万方数据
维普
