Two types of normalization were performed on the raw intensity scores derived from the GenePix Pro analysis. First, for a given experiment, the average intensity of all the spots in the weaker of the two channels (Cy3 or Cy5) was normalized to those in the stronger channel. Second, in a given set of experiments done in triplicate at a particular time point, the two experiments with the weaker average signal intensity over all spots were normalized to those in the third microarray with the strongest average signal intensity. All spots with signal levels equal to or below background were removed from the analysis. The resulting files contained on average about 6,000 spots. These files were then sorted according to Cy3/Cy5 signal intensity, and those spots with the 10% highest and 10% lowest intensity ratios (approximately 600 spots/experiment) were compared across the three experiments at a given time point using custom Perl scripts (available upon request from JCC). All spots which were present in the top 10% most up- or down-regulated genes in two out of three or three out of three experiments were recorded (the latter are listed in Table S3).