Enrichment analyses of the CODEGs in AML. (A) A network of Gene Ontology biological processes that are enriched in upregulated (red nodes) and downregulated (blue nodes) genes. Node size is proportional to fold enrichment, and edge width and transparency are proportional to the number of shared CODEGs. (B) GSEA of CODEGs throughout normal myeloid differentiation (GSE24759 data set). A differentiation hierarchy representing analyzed hematopoietic populations (left); heat maps summarizing GSEA results on upregulated and downregulated CODEGs, respectively. For each square in the heat maps, a ranked list of DEGs between denoted populations A and B was generated, the enrichment of upregulated (middle) and downregulated (right) CODEG genes was examined against the ranked list, and an enrichment score was generated. Heat map colors correspond to the normalized enrichment score in population A vs B. *Significant enrichments with nominal P < .05 and false discovery rate <0.05. HSC1, CD133⁺ CD34dim HSCs; HSC2, CD38⁻ CD34⁺ HSCs; CMP, common myeloid progenitor; GMP, granulocyte/monocyte progenitor; MEP, megakaryocyte/erythroid progenitor; GRAN3, granulocyte (neutrophil); EOS, eosinophil; BASO, basophil; MONO2, monocyte, Ery5, CD34⁻ CD71⁻ GlyA⁺ erythroid; and MEGA2, megakaryocyte. (C) GSEA of upregulated and downregulated genes in leukemic stem cell positive (LSC⁺) vs negative (LSC⁻) populations (GSE76009 data set). (D) GSEA of upregulated and downregulated genes in AML samples at diagnosis vs relapse (GSE66525).