Fig. 4: RNA profiling analysis of Study biopsy #2 showing intrinsic subtyping and gene expression of hormone receptors and identified copy alterations.

a Hormone receptor gene expression: distribution of batch corrected gene expression values, z-scaled within each cohort, filtered by subtype, and depicted as a density histogram. Y-axis shows the frequency, X-axis represents the log transformed transcripts per million (TPM), mean centered and scaled within each cohort: TCGA Breast Cancer cohort (n = 1227), in blue, and a SMMART-program metastatic breast cancer cohort (n = 40), in orange. Black line marks the patient’s RNA expression for ERBB2 (HER2), ESR1 (ER), PGR (PR), and AR. b PAM50 intrinsic subtyping analysis of RNA expression related to five breast cancer subtypes: Basal, HER2, Luminal A (LumA), Luminal B (LumB), and Normal. Y-axis is the Spearman Correlation. c TNBC-specific intrinsic subtyping: analysis of RNA expression that identifies four basal subtypes: basal-like immune-activated (BLIA), basal-like immunosuppressed (BLIS), mesenchymal (MES) and luminal androgen receptor (LAR). Y-axis is the Spearman Correlation. d Additional RNA expression profiles of genes found to be altered by genomic or proteomic assays, processed and displayed as in (a).