Figure 3. Compartment-specific gene expression markers of BTNBC.

(A) comparison of ESTIMATE stromal score between PDX, TCGA, CCLE and clinical stroma samples. (B) fold changes achieved by MMP12 between BTNBC and ER+ luminal-B samples across all platforms (*p < 0.01). (C) derivation of tumor specific BTNBC markers exclusive to cell line and PDX datasets. (D) emergence of tumor specific markers in low stroma TCGA samples (*p < 0.05). (E) overlap of stromal [10], EMT [20], CSC [21] and reactive stroma [22] signatures with BTNBC markers derived from human PDX and TCGA samples. (F) comparison of log₁₀ p-values achieved across sample types by overlap with each of the four signatures (*p < 0.05). CSC: cancer stem cell, EMT: epithelial-mesenchymal transition, MMP12: Matrix Metalloproteinase 12.