Fig. 5

Genome-wide differential mRNA expression among drug and gene therapy treatments in CF cells. a Differentially expressed genes (FDR < 0.01, |log₂ fold-change| > 0.5, mean TPM > 1) between all pairs of treatments displayed as a heatmap (9750 total). Genes are mean centered and scaled (i.e. z-scored) across conditions and are colored according to the colorbar legend (lower left, blue underexpressed, red overexpressed). Colored matrix below heatmap indicates treatment condition and cell type. b Differentially expressed genes between non-digitoxin treated samples, including TNFα, VX drug (mono and combination) and gene therapy treatments, displayed as heatmap (4569 total genes). c Heatmap of all 2003 differentially expressed genes commonly modulated by digitoxin treatment and gene therapy. Digitoxin-treated and control IB3–1 cell samples are shown along with gene therapy S9 cells. Vertical colorbars on the left-hand axis indicate directional expression groups: up-regulated by digitoxin treatment but down-regulated by gene therapy (purple, 476 genes), up-regulated by both conditions (red, 410 genes), down-regulated by both conditions (blue, 611 genes), and up-regulated by gene therapy but down-regulated by digitoxin (green, 506 genes)