Fig. 4
From: RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery
Breast cancer subtype identification in FFPE samples utilizing clinically relevant gene panels. a) Schematic of overlapping target genes in four clinically relevant gene panels; Oncotype DX, Mammaprint, Endopredict and PAM50. Size of gene panel is indicated in parentheses and genes whose protein products (IHC) or DNA amplification (ISH) are evaluated by clinical histological examination are underlined. Unsupervised hierarchical Pearson correlation clustering based upon RNA-seq gene expression values for targeted expressed genes from b) Oncotype Dx, c) Mammaprint and d) PAM50. ER+ cases are indicated in red and ER- in blue for both FFPE (light green) and Fresh (dark green specimens). Breast cancer intrinsic subtype assessment from PAM50 gene signature is displayed as Luminal A-dark purple, Luminal B-pink, Basal-orange and HER2-teal. PAM50 gene expression values were z-score transformed prior to clustering in alignment with protocols for subtype allocation