ABSTRACT In this study, we identified gene modules and representative candidate biomarkers linked to clinical progression in patients with UBC. Weighted gene co‐expression network analysis (WGCNA) was used to identify gene modules associated with TNM staging in UBC patients. Enrichment analysis was conducted on differentially expressed genes (DEGs). Hub genes were identified using Cytoscape software. The expression levels of hub genes were analyzed through DEG analysis. Finally, methylation profiles of the identified hub genes were examined using the OncoDB database. Three gene modules were found related to TNM staging. Enrichment analysis of DEGs revealed biological functions related to cytoskeleton development, muscle tissue function, cytoskeleton organization, and signaling pathways. A total of 10 hub genes were identified, showing downregulation in tumor tissues compared with normal tissues, including ACTG2, CNN1, ACTA2, TPM1, CALD1, TAGLN, MYH11, MYLK, MYL9, and LMOD1. Methylation profiling indicated hypermethylation of promoter regions in MYH11, ACTG2, and ACTA2 in tumor tissues relative to normal tissues. In conclusion, we identified two statistically significant gene modules and seven candidate biomarkers associated with TNM stages in UBC patients. These findings enhance understanding of tumor progression in UBC and may serve as potential prognostic markers.
Arshia Azmoudeh (Mon,) studied this question.