Our fine-tuned models developed from the breast cancer cohort can predict the point mutation of TP53 (AUC 0.705) and Notch2 (AUC 0.656), the copy number alteration of FGFR1 (AUC 0.676), the p53 pathway activity (AUC 0.602) from mRNA expression data, and the activities of Myc pathway (AUC 0.658) and PI3K pathway (AUC 0.601) from CNA data. The gene discussed is PIK3CA; the disease is breast carcinoma.