Comprehensive Analysis of Cancer-related Genes: Challenging the Conventional Understanding of Oncogenes and Tumor Suppressor Genes

The exploration of oncogenes and their involvement in cancer development and progression is a cornerstone of oncology research. Numerous studies have aimed to identify genes potentially linked to cancer by comparing gene expression levels between cancerous and normal tissues. It is widely acknowledged that upregulated genes in cancer tissues often function as oncogenes, and their expression levels correlate with cancer progression, and a poorer prognosis, while downregulated genes exhibit the opposite correlation. However, contrary to common belief, our analysis using the TCGA databases reveals a significant association between higher expressions of many upregulated genes in cancer and a better prognosis, as well as lower disease progression. In contrast, our findings indicate a statistical association between downregulated genes in cancer and a poorer prognosis. This paper critically examines this discrepancy and addresses the key question: What is the underlying relationship between gene expression differences in cancer, their correlation with cancer progression, and patient survival? This exploration is crucial as the potential limitations of these commonly held assumptions can significantly impact cancer research methodology.