Fig. 6

Protein abundance profiles separate breast tumors into two groups with greatly different patient survival. a Consensus matrix plot of NMF clustering for 59 breast tumors based on protein abundance levels in these tumors. Two groups of tumors emerged. Group 1 represents tumors enriched for the basal-like subtype (P < 0.01, Fisher’s exact test) while group 2 represents tumors enriched for the luminal A subtype (P = 0.03). Myc signaling was the strongest classifier for these two tumor groups (P < 1 × 10⁻⁸, Fisher’s exact test); most tumors in group 1 contained a Myc activation signature. For analysis, protein counts were normalized and log transformed, and consensus matrices were computed at K = 2–7. NMF class assignment for K = 2 was the most robust. The consensus index for each pair of samples is represented by a color gradient from white (0%) to red (100%) in the consensus matrix. b Enrichment pattern for transcription factor binding sites in genes that encode differently expressed proteins between tumor groups 1 and 2. Group 1—upregulated proteins are commonly encoded by genes with a predicted Myc binding motif, highlighted in red bars. Different bars represent different Myc binding motifs. GSEA enrichment score is captured by the blue dots. c Kaplan-Meier survival analysis comparing tumors in group 1 with tumors in group 2. Survival of patients in group 1 was significantly shorter than the survival of patients in group 2 (log-rank test, P = 0.027; HR = 2.65, 95% CI 1.08–6.51, using Cox regression)