Fig. 3

Differential expression and functional enrichment analysis of TNAC normal, DCIS, and invasive tissues. (Left) Volcano plots illustrating differentially expressed proteins across three comparisons: invasive vs. normal, DCIS vs. normal, and invasive vs. DCIS. The x-axis represents log₂ fold change, while the y-axis represents –log₁₀ p-value. Significantly altered proteins (p < 0.05, |log₂ fold change| > 1) are highlighted in black. (Middle) Top enriched Gene Ontology (GO) terms for upregulated proteins in each comparison, categorized by molecular functions and biological processes (p < 0.05, log₂ fold change > 1). The numbers beside the dots represent fold enrichment. The dot size represents the number of proteins involved, while the color gradient indicates the adjusted p-value. (Right) Top enriched GO terms for downregulated proteins in each comparison (p < 0.05, log₂₂fold change < − 1). The numbers beside the dots represent fold enrichment. The dot size corresponds to the number of proteins in each category, and the color represents statistical significance (adjusted p-values). The results highlight distinct molecular features of TNAC progression, including cadherin and GTPase binding in invasive tumors and extracellular matrix remodeling in DCIS.