Differentially expressed genes and subnetworks in ROR1^Posvs ROR1^NegCLL cells. (A) Unsupervised clustering of ROR1^Pos (n = 12, red) and ROR1^Neg (n = 12, blue) CLL cases using log₂ effective count z scores for 2000 genes expressed in all samples (effective count >0) with the largest coefficients of variation. Each column represents a separate case. (B) z scores from Ingenuity Pathway Analysis depicting the subnetwork–gene expression differences between ROR1^Pos vs ROR1^Neg CLL cases. The z score heat map depicts the top 10 most upregulated and top 10 most downregulated subnetworks. Each row represents the data for the subnetwork indicated at the right margin. (C) The z score of each of the 14 subnetworks that are expressed differentially by ROR1^Pos (n = 12) vs ROR1^Neg (n = 12) CLL cases that also were expressed differentially by the leukemia cells of ROR1xTCL1 (n = 4) vs TCL1 transgenic mice (n = 4). The color of the bar indicates whether the subnetwork is expressed at higher or lower level by ROR1^Pos CLL relative to ROR1^Neg CLL, or by ROR1xTCL1 leukemia cells relative to TCL1 leukemia cells, as indicated in the legend at the bottom of the figure. (D) Immunoblot analyses of whole cell lysates of ROR1^Neg and ROR1^Pos CLL as indicated at the top of the panel. Each lane represents a separate case. The membranes were probed with mAb-specific phospho-AKT (p-AKT Ser473) or total AKT (t-AKT) as indicated on the left margin. The ratios of the band densities for each case of p-AKT/t-AKT are provided in the dot plot on the right for ROR1^Neg CLL cases vs ROR1^Pos CLL cases, as indicated at the bottom. The horizontal bar provides the median ratio observed for each group. The Mann-Whitney U test was used to calculate the P value, indicating the significance of the difference in median values between the 2 groups.