Supplementary Materials from High Intratumoral Stromal Content Defines Reactive Breast Cancer as a Low-risk Breast Cancer Subtype

<p>Statistical methods for RPPA; Supplemental references; Supplemental Figure S1: RPPA heatmap of TCGA cohort; Supplemental Figure S2: Diagram of RPPA proteins differentially expressed in Cluster II; Supplemental Figure S3: Expression of caveolin-1 by IHC in IDC; Supplemental Figure S4: Expression of E-cadherin by IHC in IDC; Supplemental Figure S5: Expression of RBM15 by IHC in IDC; Supplemental Figure S6: Association of RPPA subtypes with mRNA of selected genes; Supplemental Figure S7: Heatmap of RPPA protein expression of ER-pos breast cancer cell lines (IDC and ILC) and normal breast tissue; Supplemental Figure S8: Waterfall plots of RPPA proteins marked cancer or stroma derived in Reactive breast cancer (Cluster II); Supplemental Figure S9: Percent stroma as determined by compartment areas and cell counts; Supplemental Figure S10: Subtyping of MDACC ER-positive/HER2-negative breast cancers by RPPA; Supplemental Figure S11: Imaging summary for cell density and α-SMA scoring of TCGA cases; Supplemental Figure S12: Expression of α-SMA by IHC in ILC; Supplemental Figure S13: Expression of α-SMA by IHC of IDC; Supplemental Figure S14: Tumor purity, stromal scoring, EMT scoring, and immune scoring of RPPA subtypes; Supplemental Figure S15: Components of Nottingham grade for IDC; Supplemental Figure S16: RPPA heatmap of cases with matched normal tissues; Supplemental Table S1: The coefficient estimates of the final model using the core TCGA samples; Supplemental Table S2: The sensitivity, specificity and false discovery rate (FDR) from the test data sets using the final models from Table S1</p>