Evaluating Dataset-Specific Variability and Reproducibility of CDH1 (E-cadherin) Expression in Breast Cancer Using GEO2R

Breast cancer is a major global health burden, with alterations in gene expression contributing to tumor progression. The CDH1 gene, encoding E-cadherin, plays a critical role in maintaining epithelial integrity, and its loss has been associated with increased invasiveness and metastasis in breast cancer. This study aimed to evaluate the differential expression of CDH1 using the GSE15852 dataset. Gene expression data were obtained from the Gene Expression Omnibus (GEO) and analyzed using the GEO2R platform, comparing tumor and normal samples. Differential expression was assessed based on log fold change (logFC) and statistical significance. The analysis revealed that CDH1 is significantly downregulated in breast cancer, with a logFC of −2.386, a p-value of 2.72 × 10⁻¹¹, and an adjusted p-value of 3.68 × 10⁻¹⁴. These findings indicate a substantial and statistically significant reduction in CDH1 expression in tumor tissues. In conclusion, CDH1 is markedly downregulated in breast cancer, supporting its role as a tumor suppressor. GEO2R provides a reliable approach for preliminary gene expression analysis; however, further validation is required to confirm these findings.