Fig. 5

Pathway Validation of FFPE RNA-seq. Fresh and FFPE data sets were independently evaluated for differential gene expression based upon sample ER status. a Gene Set Enrichment Analysis (GSEA) determined significant enrichment for Estrogen Response genes (left) in ER+ samples and E2F-Proliferation associated genes in ER- samples for both FFPE and fresh specimens. b Venn-Diagram displaying overlapping and unique statistically significant differentially expressed genes (p ≤ 0.05, Fisher’s exact test using all input genes (n =14,330) as background results in p < 2.2e-16) between ER+ (red) and ER- (blue) samples from FFPE (gray) and fresh (green) specimens. Small numbers depict numbers of differentially expressed genes in the respective region. Shaded green represents genes identified in both FFPE and fresh data sets. 1. and 2. denote gene pools used for subsequent custom gene set analyses c) Gene set enrichment plots for FFPE samples derived from custom gene sets composed of 928 genes found significantly upregulated in ER+ fresh but not in FFPE samples, and 1099 genes significantly downregulated in ER+ fresh, but not in FFPE samples. d Hallmark GSEA enrichment plots of UV response and Unfolded Protein Response genes sets from analysis comparing all FFPE to all fresh specimens