Bladder cancer RNA-Seq data analysis highlighted significant insights into the molecular mechanisms and biological processes underlying tumorigenesis. Utilizing R packages such as edgeR, limma, and DESeq2, we preprocessed and normalized the data to identify differentially expressed genes (DEGs). Unsupervised learning methods, including PCA, facilitated the classification of these DEGs, revealing critical pathways associated with DNA replication, DNA repair, and cell cycle control. Gene ontology enrichment analysis further delineated the affected biological processes, cellular components, and molecular functions. Notably, our findings identified potential biomarkers, particularly the genes PER2 and CRY2, which are integral to the circadian rhythm pathway. Additionally, we observed that protein complexes CLOCK/BMAL1, CLOCK/BMAL2, and BMAL1/NPAS2 regulate the expression of several clock genes via E-boxes. The study also constructed a differential gene network in bladder cancer, providing insights into the regulatory functions of key genes involved in tumor progression. These findings not only enhance our understanding of bladder cancer biology but also pave the way for potential therapeutic targets and biomarkers.
