Gene probe distance on the microarray surface as a function of the genes' chromosomal distance. Shown is a distance matrix of the probes for the first 100 genes of chromosome 4 for each microarray design. Proximal and periodically-spaced genes are printed in proximity in each of the microarray designs shown. (A) the UHN design. (B) the UMC design. (C-D) the designs used in Spellman et al., 1998  for the α-factor (C; SMD1; same as that used in figure 1) and cln3 (D; SMD2) arrest and release experiments. Distances are shown in probes except for the UHN design in which they are shown in pixels because in this design there are large spaces between the different subarray blocks, making the presentation in probes less clear. The pattern in the SMD2 design is a result of a single transformation of the exact order of the genes on the chromosome region shown.