CPP-SOM of microarray data. (A) Illustration of self-organizing map outputs of microarray data by component plane presentations. Each presentation illustrates a sample specific global map in which all up-regulated units (red), down-regulated units (blue), and moderately regulated units (yellow and green) are well delineated, permitting direct comparison of regulatory status/biologic significance of clustered genes within and between treatment series (that is, imatinib mesylate treatment series (S series), ATO treatment series (A series), and imatinib mesylate plus ATO treatment series (A+S series), respectively, shown in rows 1, 2 and 3). Color index stands for log ratio with base 2. The brighter the color, the higher the ratio. (B) An enlarged grid ideogram summarizing modulated gene clusters shown on the component plane presentations. Seven major regulatory categories are recognizable. Each category appears to be associated with characteristic features: 1, regulators/players of cell cycle and survival; 2, members of BCR-ABL signaling and mitochondria respiration complexes; 3, regulators/players of cell cycle and negative regulators of the intrinsic apoptotic pathway; 4, members of BCR-ABL signaling and RNA splicing; 5, regulators/players of the intrinsic apoptotic pathway and erythroid differentiation; 6, transcription factors associated with cell apoptosis and erythroid differentiation; 7, molecules associated with oxidative stress; and 8, regulators/players of the extrinsic apoptotic pathway and negative regulators of cell survival/antiapoptosis.