Supplemental Data

Files in this Data Supplement:

• Supplemental Figure 1 - Supplemental Figure 1. Supporting material to the statistical analysis in Table 1. For a description of the analysis, see Material and Methods.
• Supplemental Table 2
• Supplemental Table 3
• Supplemental Table 12
• Supplemental Figure 2 - Supplemental Figure 2. MapMan screenshots of the diurnal rhythm. Screenshots were taken for selected pathways and functional categories showing diurnal amplitudes and timing in Col-0 wild-type and pgm.
• Supplemental Figure 3 - Supplemental Figure 3.Clustering of sets of diagnostic genes, based on their diurnal response in wild-type Col-0. The plots provide background documentation for the summary shown in Table 3 of the hard copy. They show the clusters generated from the diurnal response in Col-0 wild-type for the sets of the 200 most induced and 200 most strongly repressed genes for different challenges.
• Supplemental Figure 4 - Supplemental Figure 4. Comparison of the average transcript level across the entire diurnal cycle in Col-0 wild-type and in pgm. This panel shows genes that showed highly significant differences in average diurnal expression between pgm and Col-0. They were identified from 6+6+6 time points in the wild-type experiments and 6+2 times from the pgm experiments which were combined for the subsequent RMA normalisation. Of the 16559 analysed genes, 2173 (13%) were found to be significantly differing in pgm when compared to wild-type after t-testing (FDR controlled p-value < 0.05). For the vast majority of these genes, the shift matches that expected if the dominating difference between pgm and Col-0 is low sugar during the night, viz. genes that are induced and repressed by sugars had, respectively, higher and lower average transcript levels in pgm.
• Supplemental Figure 5 - Supplemental Figure 5. Clustering of sets of diagnostic genes, based on their diurnal responses in a combined data set for wild-type Col-0 and pgm. The plots provide background documentation for the summary shown in Table 3 of the hardcopy. They show the 7 clusters generated from the diurnal response in Col-0 wild-type and pgm for the sets of the 200 most induced and 200 most strongly repressed genes for different challenges.
• Supplemental Figure 6 - Supplemental Figure 6. Phase shift between a free-running and a diurnal cycle for genes that peak at 6 different times during the diurnal cycle and relation to the sugar-sensitivity of the genes. This plot shows the 373 circadian clock-responsive genes identified from Harmer et al. (2000). Genes peaking at 0, 4, 8, 12, 16, and 20 h into the free-running cycle are shown in separate panels (CT0, CT4, CT8, CT12, CT16, CT20, respectively). For each gene peaking at that time in the free-running cycle, the panel shows (i) the peaking time in a light / dark cycle on the x-axis and (ii) the sugar sensitivity of the gene on the y-axis. The arrows show genes that peak at the same time in the diurnal cycle at the same time as in a free-running cycle. For other genes there is a small (4 h) or larger (8 or 12 h) shift in the timing of the peak.
• Supplemental Figure 7 - Supplemental Figure 7. Comparison of the amplitudes of the diurnal changes of sucrose-responsive, photomorphogenetic light-responsive and glucose-responsive genes to the background amplitudes of all measured genes on the ATH1 array. This plot provides additional information to Fig. 9 in the hardcopy. It shows the relation for further sets of diagnostic genes (sucrose-responsive, photomorphogenesis-responsive and a set of glucose-responsive genes extracted from Price et al. (2000) that were omitted from Fig. 11. For more details of the calculations see the legend to Fig. 11.
• Supplemental Figure 8 - Supplemental Figure 8. MapMan screenshots displaying the first and second principle component separating wild-type Col-0 samples collected at different times of the diurnal cycle in MapMan. This plot shows the weightings of genes in the first and second principle components of Fig. 12, showing the separation of samples during the diurnal cycle of wild-type Col-0. Genes with an increasingly high weighting are colored increasingly intensely, and genes with a negative and positive weighting are colored red or blue. Files for downloading and visualisation in Mapman are provied as part of the supplementary material.
• Supplemental Figure 9 - Supplemental Figure 9. Weightings in the first and second principle components of genes that are responsive to glucose, carbon fixation, light, nitrogen, water stress and circadian regulation. (A) This Figure is identical to Fig. 13 in the hardcopy, except that the analysis has been modified to minimise bias in the choice of the genes depicted. It shows the weightings of all genes whose expression is changed by >2-fold in response to a particular input (blue = induced and red = repressed). Genes belonging to the 200 most strongly induced and the 200 most strongly repressed genes are identified as blue and red crosses. (B) These panels show the weightings in the first and second components of genes in further sets of diagnostic genes, that are omitted from Fig. 13 in the hardcopy.
• Supplemental Table 1
• Supplemental Table 4
• Supplemental Table 5
• Supplemental Table 6
• Supplemental Table 7
• Supplemental Table 8
• Supplemental Table 9
• Supplemental Table 10
• Supplemental Table 11