Fig. 2

Proteomic and network analysis of TNAC tumor progression. (a) Heatmap showing variations in protein expression across normal, DCIS, and invasive TNAC tissues. Each cell represents the standardized score of protein abundance in an individual sample, with colors indicating relative expression levels. (b) Venn diagram showing the number and percentage of significantly altered proteins unique to or shared among normal, DCIS, and invasive groups. (c) Co-expression network of protein modules identified by WGCNA. A total of 3277 proteins were grouped into five modules (ME0–ME4), each represented by a distinct color. ME0 contains unclustered proteins and serves only as a reference, while ME1–ME4 correspond to functional modules enriched for distinct biological processes. (d) Correlation heatmap of module eigengenes (ME1–ME4) with clinical groups (normal, DCIS, invasive TNAC). ME0 represents unclustered proteins and is shown only as a reference. Positive correlations are shown in red, negative correlations in blue, with color intensity proportional to the correlation coefficient. (e) Module–trait relationships for pre- versus post-chemotherapy samples, highlighting treatment-associated shifts in module expression. (f) Signaling pathways illustrating the upregulation of proteins involved in PI3K/AKT, androgen receptor (AR) signaling in invasive TNAC. The figure highlights the increased expression of key regulators, including PI3K, AKT, mTOR, AR, and RAC.