Supplementary Figure S1-S9 from Comprehensive Genomic Analysis Identifies Novel Subtypes and Targets of Triple-Negative Breast Cancer

Figure S1. Full clustering metrics in support of a 4 cluster model in the discovery set with membership as defined by TNBCType. Figure S2. Full clustering metrics in support of a 4 cluster model in the validation set with membership as defined by the TNBCType tool Figure S3. Allred scores for clinical IHC of ER, PR, and Her2 protein expression for samples in the discovery and validation sets. Figure S4. Gene expression for discovery and validation sets by NMF Figure S5. NMF of both datasets (discovery and validation, renormalized together) of study data using feature set of 2188 genes utilized in Lehmann et al. (2010) and comparison of resulting clusters t Figure S6. ESR1 expression for ER-positive breast cancers, LAR TNBCs, and all other TNBCs. Figure S7. Expression of common differentially expressed genes in claudin-low tumors selected for their role in luminal differentiation from Prat et al. (2010). Figure S8. Aberrant fraction and ploidy of ASCAT derived copy number estimates. Figure S9. ASCAT derived copy number events reveals distinctive gains and losses that segregate LAR subtype tumors from remaining subtypes.