Fig. 3. Global gene expression analysis upon oncogene-activation.

a Principal component analysis (PCA) of transcriptional profiles of sorted human myeloid cells (CD33⁺) GFP⁺ and GFP⁻ fractions from control mice, transplanted with human HSPCs transduced with GFP (light pink for GFP⁻ and dark pink for GFP⁺), wtBRAF (light red for GFP⁻ and dark red for GFP⁺) or untransduced cells (salmon), and mice transplanted with BRAF^V600E-expressing HSPCs at 16 days post-transplantation (green for GFP⁺ and blu for GFP⁻ cells). b Unsupervised clustering analysis of DEGs in the different experimental groups. c, d Volcano plots highlighting significant downregulated (green) and upregulated (red) genes in sorted human myeloid cells (CD33⁺) from the BRAF^V600E mice group (both GFP⁺/⁻ fractions) compared to controls. The gene symbols of the top 15 upregulated and the top ten downregulated genes based on adjusted p-value are indicated. Statistical test: two-sided exact test for negative-binomial distribution, the Benjamini and Hochberg’s approach has been used for controlling the false discovery rate (FDR). e Venn Diagram representation of upregulated and downregulated DEGs in GFP⁺ and GFP⁻ CD33⁺ cells of the BRAF^V600E group showing that about 90% of the DEGs in the GFP⁻ fraction were also deregulated in the GFP⁺ fraction. f Gene set enrichment analysis (GSEA) of sorted CD33⁺/GFP⁺ and CD33⁺/GFP⁻ cells from the BRAF^V600E group. Normalized enrichment score (NES) is indicated.