# Common Molecular Mechanisms and Biomarkers in Breast, Colon and Ovarian Cancer
## 3 Results
### Validation  
The PPI analysis revealed the involvement of core proteins in multiple KEGG and REACTOME pathways associated with breast, colon, and ovarian cancer. These results suggest the potential for identifying these proteins as common markers across these types of cancer. However, to clarify this possibility and identify common biomarkers, a preliminary validation using cancer patient samples was performed using the GEPIA2 database. The expression levels (RNA-seq) of 16 proteins from the MCODE1, MCODE2, and MCODE3 clusters in patients with breast cancer, colon cancer, rectum cancer, and ovarian cancer, compared to normal tissue expression levels, were analyzed (Figures 9 and S2). Some of the proteins studied showed a statistically significant increase in expression in specific cancer types (\(p\)-value cutoff: 0.01), such as CASP3, CTNNB1, BRCA2, and CHEK2 in colon and rectum cancer; MSH6 in breast cancer; PARP1 in breast and ovarian cancer; TP53 in colon, rectum, and ovarian cancer; and ERBB2 in breast and rectal cancer (Supplementary Figure S2). However, it is crucial to highlight that the protein MSH2 exhibited a statistically significant increase in expression (\(p\)-value cutoff: 0.01) in samples from patients with all four cancer types (breast, colon, rectal, and ovarian). Additionally, the protein KIT showed a significant alteration in expression levels across all four cancer  
Figure 8: Protein–protein interaction network of MCODE clusters—analysis of REACTOME pathways. (**a**) REACTOME pathways related to DNA repair. FDR values ranged from 0.0037 to 1.20 \(\times\) 10\({}^{-6}\). (**b**) REACTOME pathways related to apoptosis and pyprotosis. FDR values ranged from 0.00093 to 0.009.  
types, but with a decrease in expression compared to normal tissue (\(p\)-value cutoff: 0.01) (Figure 9). The analysis revealed that MSH2 and KIT exhibited statistically significant differential expression across breast, colon, and ovarian cancer. In contrast, other identified proteins displayed variable expression patterns, with some showing differential expression in certain cancers but not in others. The consistent regulation of MSH2 and KIT suggests their potential role as transversal biomarkers. The study of overall survival in patients with breast, colon, rectum, and ovarian cancer was conducted by considering all of them together. Survival was evaluated based on the gene expression levels (RNA-seq) of the MSH2 and KIT genes, which are potential common biomarkers (Figure 10). The sample of patients (\(n=929\)) with high MSH2 gene expression showed better survival compared to those with low gene expression (\(n=929\)), whose prognosis was poorer (\(p=1.7\times 10^{-5}\)) (Figure 10a). Patients (\(n=924\)) with high KIT gene expression also exhibited a better prognosis compared to those with low expression of the gene (\(n=929\)) (\(p=0\)) (Figure 10b). The survival analyses in this study were conducted using the GEPIA2 platform, which employs the Log-rank test (Mantel-Cox test) for hypothesis testing, and automatically calculates hazard ratios (HR) along with 95% confidence intervals (CI). The cutoff for high and low gene expression levels was set at 50%. The survival curves generated by GEPIA2 include dotted lines representing the 95% CI, ensuring the robustness of the statistical evaluation. Given that GEPIA automatically performs these calculations based  
Figure 9: Expression levels (RNA-seq) of MSH2 and KIT proteins in tumor patient samples with breast invasive carcinoma (BRCA), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), and ovarian serous cystadenocarcinoma (OV). Num (T): Number of tumor patients (in red). Num (N): Number of normal patients (in grey). * \(p\)-value cutoff: 0.01.  
on curated datasets, we directly report the HR and CI values provided by the platform without additional model adjustments, as shown in Figure 10.  
Survival analysis revealed a potential link between MSH2 and KIT expression levels and patient outcomes.