Figure 3

Hierarchical clustering of differentially expressed genes occurring in ras knockout cell lines after stimulation with serum. (a) After stimulation with serum for 1 hour; (b) after stimulation with serum for 8 hours. Heatmaps generated by cluster analysis of absolute expression values of a selected group of gene probesets showing the highest levels of differential expression (induction or repression; stringent cutoff parameters set as FDR = 0.05 and P-value < 0.003) in the lists of differentially expressed genes corresponding to starved control WT fibroblasts and H-ras^-/-, N-ras^-/-and H-ras^-/-/N-ras^-/- fibroblasts cultured after starvation in the presence of serum for 1 hour (a) (267 different probesets) or 8 hours (b) (239 different probesets). Horizontal rows represent individual gene probesets and vertical columns depict results from single microarray hybridizations. The intensity of color saturation in each probeset box (ranging from 2 to 14 in a log2 scale) provides a quantitative estimation of its expression level. Red color denotes over-expression, increasing in brightness with higher values. Green color denotes repression, increasing in brightness with lower values. Black color denotes unchanged expression signals relative to controls. Cluster blocks numbered on the right side of each heatmap identify gene sets sharing common expression behavior under the genotypes and experimental conditions indicated.