Figure 3

GSEA reveals similarities between genes upregulated in ETV6/RUNX1 positive ALL and those upregulated in normal Pro-B cells. A) Heat map generated within GSEA of the top ranked 50 up- and downregulated genes in ETV6/RUNX1-positive leukemia as compared to the remaining ALLs. B) Enrichment plot showing the enrichment of genes upregulated in Pro-B cells among the top ranked upregulated genes in ALLs with ETV6/RUNX1. The lower portion of the figure shows the rank ordered genes for ETV6/RUNX1-positive ALL when compared to other ALL, with genes being highly expressed to the far left and downregulated genes to the right. Each black line represents a hit from the gene set being investigated in the rank ordered gene list. The more hits among the top up- or downregulated genes, the more likely you are to get a significant gene set enrichment score. The upper part of the figure shows the enrichment score, which is calculated by walking down the ranked ordered gene list and increasing the score when a gene from the rank ordered gene list is in the gene set and decreasing it when it is not. C) Heat map of the core enrichment genes in the ETV6/RUNX1 positive ALL and the remaining ALLs. D) Heat map of the same core enrichment genes in the normal flow sorted hematopoietic cells. The order of the core enrichment genes is the same as in C. From figure C and D, the similarity of the ETV6/RUNX1 and the Pro-B cell gene expression profiles can be easily appreciated and clearly shows that there are transcriptional programs that are shared between this specific leukemia and its normal counterpart.