Fig. 6

Results from re-analysis dataset 2 [21] (ENA ID: PRJEB9942). Comparison between Control, RITA, CPI, and RITA plus CPI (Combo) treated Chronic myeloid leukemia (CML) haemopoietic stem cells (HSCs). Three differential comparisons were used RITA versus Control, CPI versus Control and Combo versus Control. Significance for differential expression was adjusted p < 0.05 and absolute log2 fold > 1. a PCA scatterplot showing PC1 versus PC2. The percent variation is given. b Gene expression heatmap combining all 2237 significant genes from the three comparisons. Colour denotes row scaled (Z-score) expression values, with darkest blue as lowest expression and darkest red as highest. The Y-axis has been hierarchically clustered using Spearman Correlations. c As (b) however showing the 329 genes in differential expression signature 4. d Differential expression signature four meta-gene violin with jitter values. The mean expression (Z-score) across all genes in the signature is given on the Y-axis. Black dots denote individual samples. The red dot and whisker denote mean and standard deviation respectively. e Bar chart of the five most enriched (adjusted p < 0.05) gene-sets (GO Biological Processes) for signature four. f Bar chart of the five most enriched (adjusted p < 0.05) upstream regulators (TRRUST) for Combo versus Control. g Network plot of the significantly enriched (adjusted p < 0.05) upstream regulators for Combo versus Control. Nodes denote regulators and edges join nodes where > 50% of the regulated genes are shared. Colour intensity represents significance (− log10p) and node size the number of genes that are potentially being regulated. h Bar chart of the five most activated upstream regulators (TRRUST) for Combo versus Control. Significantly activated regulators (activation Z-score > 2) are red. i Gene expression boxplot for each gene in the enriched upstream regulator TP53. Expression levels are given as per gene Z-scores