1. S1

2. MCF7 M (high density) Day 3 Day 5 S2

3. AB S3

4. S4 NetworkspValueGenes from Active Data Chemotaxis7.991E-11IL-1 beta, CCR2, GRO-3, Lck, CCL13, Galpha(q)-specific peptide GPCRs, Galpha(i)-specific peptide GPCRs, SDF-1, IL- 16, CCL7, GRO-2, PD-ECGF (TdRPase), GCP2 Proteolysis_ECM remodeling1.820E-09MMP-13, MMP-14, TIMP3, MMP-1, TIMP4, MMP-15, MMP- 24, MMP-1, MMP-25, Stromelysin-1 Inflammation_Jak-STAT pathway 4.161E-09IL21R, CCR2, PDGF-R-beta, IL5RA, CCL13, PDGF receptor, IL- 2R gamma chain, IL-21 receptor, SDF-1, IL10RA, IGF-1, CCL14, IL-20 Proteolysis_Connective tissue degradation 4.951E-08MMP-13, MMP-14, TIMP3, MMP-19, TIMP4, MMP-15, MMP- 24, MMP-1, MMP-25, Stromelysin-1 Cell adhesion_leukocyte chemotaxis 9.863E-07CCR2, GRO-3, Lck, CCL13, Galpha(q)-specific peptide GPCRs, Galpha(i)-specific peptide GPCRs, SDF-1, CCL14, CCL7, GRO-2, GCP2 Immune response_Th17- derived cytokines 1.520E-06IL-1 beta, MMP-13, SDF-1, CCL7, RANKL(TNFSF11), GCP2, MMP-1, Stromelysin-1 Development_Blood vessel morphogenesis 2.810E-06IL-1beta, FGF8, Galpha(q)-specific peptide GPCRs, Galpha(i)- specific peptide GPCRs, MMP-19, SDF-1, ALK-2, VEGFR-2, TIE, PD-ECGF (TdRPase), VEGF-D Cell adhesion_Platelet- endothelium-leukocyte interactions 1.497E-05IL-1 beta, MMP-13, PDGF-R-beta, Endoglin, PDGF receptor, VEGFR-2, Thrombospondin 4, TGF-beta receptor type II, PDGF-R-alpha Apoptosis_Anti-Apoptosis mediated by external signals via PI3K/AKT 2.345E-05IL-1 beta, FGF8, PDGF-R-beta, PDGF receptor, GFRalpha1, IGF-1, VEGFR-2, NT-3, VEGF-D, PDGF-R-alpha

5. S5 DatasetNumber of patients Number in patient subset Comparison Scheutz et al14 DCIS vs IDC Ma et al (Ref 32) 6620Epithelium vs Stroma Boersma et al9583Epithelium vs Stroma

6. S6

7. S7 1750150012501000 0.0 0.2 0.4 0.6 0.8 1.0 1.2 30002950290028502800 0.0 0.2 0.4 0.6 0.8 1.0 350030002500200015001000 0.0 0.2 0.4 0.6 0.8 1.0 1.2 MCF-7 M (high) + E 2 MCF-7 M (high) + Veh MCF-7 M (low) + E 2 MCF-7 M (low) + Veh MCF-7 + Veh MCF-7 + E 2 Absorbance Wavenumber (cm -1 )

8. S8 1700150013001100 0.0 0.2 0.4 0.6 0.8 1.0 1.2 30002950290028502800 0.0 0.2 0.4 0.6 0.8 1.0 350030002500200015001000 0.0 0.2 0.4 0.6 0.8 1.0 1.2 MCF-7+ Veh MCF-7 + E 2 MCF-7+CM + Veh MCF-7+ CM E 2 Absorbance Wavenumber (cm -1 )

9. S9 MCF-7MCF-7 + HMF