(A) The Principal Component Analysis (PCA) graph of global miRNA expression data was computed using GenEx software version 6; CML Lin-CD34-CD38- are shown as blue cubes; CML Lin-CD34+CD38− are shown as green cubes, Normal Donor Lin-CD34-CD38- are shown as yellow cubes; CML Lin-CD34+CD38− are shown as red cubes. (B) Venn diagram showing the intersection of the lists of differentially expressed miRNAs (DEMs) in the comparison CML Lin-CD34-CD38- vs Normal Donor Lin-CD34-CD38- and CML Lin-CD34+CD38- vs Normal Donor Lin-CD34+CD38-. (C) Normalized MIF of intracellular p-CrkL levels in K562 cells after IM treatment. Untreated control pCRKL MIF was set to 1 to compare K562 before and after treatment with IM. The results are expressed as mean values ±SEM (n = 3), *p < 0.05, **p < 0.01 in untreated versus IM-treated cells. p-value from one-way ANOVA is 0.00002 (D) Real-Time PCR results showing expression levels of CML up-regulated miRNAs in K562 cells after IM treatment. (E) Real-Time PCR results showing expression levels of CML down-regulated miRNAs in K562 cells after IM treatment. Data are presented as Fold Change (FC) ± SEM (n = 3). FC of the untreated control was set to 1 to compare K562 before and after treatment with IM. BCR-ABL- independent miRNAs were identified as miRNAs with FC < 1.5 and > 0.67. (F) Relative expression level expressed as Fold Change (FC) of selected BCR-ABL-independent miRNAs in the comparisons CML Lin-CD34-CD38- vs Normal Donor Lin-CD34-CD38- (black bars) and CML Lin-CD34+CD38- vs Normal Donor Lin-CD34+CD38- (striped bars). Abbreviations: MIF indicates Mean Fluorescence Intensity; IM, Imatinib Mesylate; NT, Not Treated.