Expression landscape. (A) Fusion genes found in 7 AP, BP, or CP samples. Fusions were classified into 4 categories: known fusions, fusions including genes without a known protein product, unannotated fusions, and readthroughs. Blue (left) indicates detection of the fusion, and numbers indicate the number of unique reads supporting the fusion. The methods employed to validate the fusions are shown (right). (B) Depiction of the main molecular pathways with altered expression between healthy and CP cases, healthy and AP/BP cases, and CP and AP/BP cases. Upregulated pathways (top) and downregulated pathways (middle) in comparison with healthy cases. Deregulated pathways (bottom) in AP/BP vs CP cases. Pathways with P = .00 were set to the minimum P of all pathways divided by 2 in the visualization. (C) Venn diagram showing the number of differentially expressed genes between AP/BP and healthy (light blue), CP and healthy (light red), and AP/BP and CP. Differentially expressed genes relevant for CML pathogenesis are highlighted in the figure. Upregulated genes are highlighted with arrows pointing upward and downregulated genes with arrows pointing downward. *Genes significantly differentially expressed in AP/BP in comparison with healthy, but borderline significance (Q > .05 and Q < .10) in CP, in comparison with healthy cases.