Fig. 2: Identification of pediatric leukemia-enriched signature and gene sets.

a Combined heatmap showing normalized, scaled expression of top significant (Bonferroni adj. p < 0.05) differentially expressed genes (DEGs) derived from comparing blast cells and healthy BM cells for each leukemia type (two-sided Wilcoxon rank sum test). Top 10 genes were identified based on log2FC values. b Heatmap showing similarity in DEGs for each leukemia’s blast cells as the Jaccard Similarity/Index, calculated as the number of intersecting genes divided by the size of the union of genes between two leukemia types. c Dot plot with gene sets which are common or specific to leukemia types that were identified by comparing enrichment scores (from gene set enrichment analysis) in blast and healthy BM cells (two-sided t-tests). The top significantly enriched (Benjamini-Hochberg adj. p < 0.05) gene sets were selected based on T-statistic. d Volcano plot showing differential expression analysis results from comparing different leukemias versus normal BM samples in bulk RNA-seq datasets (moderated two-sided t-test, limma). Genes significantly over-expressed (log2FC > 0.25, Benjamini-Hochberg adj. p < 0.05) in leukemia types are shown in red, genes significantly under-expressed (log2FC <−0.25, Benjamini-Hochberg adj. p < 0.05) are shown in blue, and non-significant genes are shown in grey. The shapes of the points represent the results of the differential expression analysis for different leukemia types. e A dot plot illustrating a summary of bulk RNA-seq DEG analysis (moderated two-sided t-test, limma) across different leukemias, with the color of the dots representing the log2FC, the shape representing whether the gene is over- (triangle) or under-expressed (circle) in leukemia compared to normal, and the Benjamini-Hochberg adjusted p-value represented as asterisks on the dots (*, < 0.05; **, <0.01; ***, <0.001; ****, <0.0001). AML acute myeloid leukemia, B-ALL b-cell acute lymphoblastic leukemia, B/My MPAL b-cell/myeloid mixed phenotype acute leukemia, T-ALL t-cell acute lymphoblastic leukemia, T/My MPAL t-cell/myeloid mixed phenotype acute leukemia, FC fold change. Source data are provided as a Source Data file.