Table II.

Significant overlap between diurnal-, circadian-, and Suc-regulated genes and those contributing to variance between cold experiments

Following PCA (Fig. 1) to identify the major differences between independent experiments to identify cold-responsive genes, we extracted the top 500 genes contributing to PC 1 to PC 5. These genes were compared with diagnostic sets of diurnal-regulated (Blasing et al., 2005), circadian-regulated (Edwards et al., 2006), and Suc-regulated (Solfanelli et al., 2005) genes, and the significance of the overlap was calculated. Absolute numbers of genes as well as P values from Fisher's exact test are shown. The numbers of genes in parentheses indicate the size of each diagnostic gene set. Venn diagrams showing the overlap between gene lists are shown in Supplemental Figure S2.

PCDiurnal (3,409)Circadian (3,480)Suc (1,890)
PC 13034.4 × 10−882551.2 × 10−511371.5 × 10−23
PC 23421.2 × 10−1222409.4 × 10−432631.3 × 10−118
PC 32594.8 × 10−561612.4 × 10−091233.1 × 10−17
PC 43083.5 × 10−922451.2 × 10−451339.8 × 10−22
PC 52347.3 × 10−411524.3 × 10−071206.9 × 10−16