Fig. 3
From: RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery
Breast cancer subtype identification of ER+ and ER- cases in global RNA-seq from FFPE and Fresh specimens. a Schematic of experimental design. RNA expression from ER+ (n = 3, red) and ER- (n = 3, blue) breast cancers from FFPE (bright green) specimens were compared to clinically verified ER+ (n = 10, red) and ER- (n = 10, blue) cases from a publicly available data set derived from fresh (dark green) tissue specimens. b Sequence alignment parameters of clipping (no = light blue, soft = light purple) and allowed nucleotide mismatches (mm) of 3–15 were evaluated for the 6 FFPE samples. c Unsupervised clustering based upon Pearson correlation values determined from global gene expression in 6 original FFPE samples and 3 samples whose libraries were resequenced (r) showing tight clustering of repeats and originals and clustering based upon ER status. d Unsupervised clustering based upon Pearson correlation plot of global gene expression correlation in 6 FFPE samples (light green) and 20 fresh samples (dark green) with clear separations firstly based upon sample type (FFPE vs. Fresh) and secondly based upon ER status (ER+ = red, ER- = blue). e Principal component analysis of the 6 FFPE (circle) and 20 Fresh (triangle) samples confirms separation based upon sample type (PC1) and ER status (PC2)