Identification of c-ALL/pre–B-ALL samples with or without t(9;22). Analysis of 82 c-ALL/pre–B-ALL samples based on a supervised identification of differentially expressed genes among 42 patients demonstrating a t(9;22)/BCR-ABL and 40 patients without t(9;22). The labels and coloring of the classes were added after the analysis of means for better visualization. (A) In the hierarchical cluster analysis, the normalized expression value for each gene (given in rows) is coded by color (SD from mean). Red cells indicate high expression, and green cells indicate low expression. Most (61 of 82; 74%) patients were in the branch of c-ALL/pre–B-ALL without t(9;22) (left branch) or in the branch of c-ALL/pre–B-ALL with t(9;22) (right branch). The remaining 21 (26%) patients were in a third branch characterized by a gene expression profile clearly different from the 2 other groups (middle branch). (B) In 3-dimensional PCA, the c-ALL/pre–B-ALL samples were projected into the feature space consisting of the top 100 differentially expressed genes when comparing t(9;22)–positive (red) with t(9;22)–negative (purple) patients. Data points with similar characteristics cluster together. A single color-coded sphere represents each patient's expression pattern.