Table 3.

Qualitative Comparison of the Diurnal Changes of Sets of Diagnostic Genes That Respond to Glucose, Sucrose, Light, Nitrogen Metabolite, and Water Deficit and the Diurnal Changes of Sugars, Light, Nitrogen Metabolites, and Water Deficit

	Wild-Type Col-0				pgm
	(%)				(%)
Treatment	Good Fit	Weak Fit	No Change	Negative	Good Fit	Weak Fit	No Change	Negative
Glucose	63	4	31	4	88	5	9	1
Sucrose	35	9	53	4	62	0	23	10
Carbon fixation	48	16	31	3	88	12	0	0
Photomorphogenesis	3	24	49	24	23	0	55	21
Light	23	20	40	17	38	16	28	17
N 30 min	7	19	45	27	26	8	47	19
N 3 h	22	17	48	11	15	28	65	15
Water deficit	26	27	41	5	22	31	42	5

Sets of 400 genes corresponding to the 200 most strongly induced and the 200 most strongly repressed genes were identified in published or in-house profiles showing the global changes of expression 3 h after adding 15 mM glucose or 15 mM sucrose to 9-d-old seedlings in liquid culture that had been starved of carbon for 2 d (D. Osuna, R. Morcuende, W.-R. Scheible, Y. Gibon, O. Bläsing, O. Thimm, M. Höhne, M. Günther, B. Usadel, M. Udvardi, B. Kamlage, R. Trethewey, and M. Stitt, unpublished data), from 5-week-old plants illuminated for 4 h under ambient (450 ppm) or low (<50 ppm) [CO₂], from dark-grown seedlings 4 h after exposure to weak white light (AtGenExpress), from 5-week-old plants exposed to low (<50 ppm) [CO₂] under 4 h of illumination or 4 h of prolonged darkness, 30 min and 3 h after adding 3 mM nitrate to 9-d-old seedlings that had been depleted of nitrogen for the previous 2 d (Scheible et al., 2004), and 3 h after adding 100 mM mannitol to 9-d-old seedlings (W.-R. Scheible, unpublished data). The lists of genes and responses are provided in Supplemental Table 6 online. The diurnal changes of the eight sets of 200 induced genes and the eight sets of 200 repressed genes were subjected to k-means clustering (see Figures 5A and 5B for the glucose-responsive genes and Supplemental Figure 3 online for the genes responsive to sucrose, carbon fixation, photomorphogenesis, light, nitrogen, and mannitol). They were compared with the diurnal changes of glucose and sucrose (Figure 1), light, nitrate, and amino acids (Figure 1), and water deficit (it was assumed that the water deficit increases in the light) to identify clusters where the diurnal change was in good or weak agreement with the physiological input contributing to the diurnal change in expression, clusters where there was no diurnal change, and clusters where the diurnal changes were opposed to those expected if that particular physiological input were contributing to the diurnal changes in gene expression. The average value for the signal at each time point was used to generate the clusters (Figures 5 and 6; see supplemental data online), which are the basis of the calculations for this table.