Table 2.
Assignment of Diurnally Regulated Genes to Different Functional Categories
| Amplitude Limit |
|||||||
|---|---|---|---|---|---|---|---|
| No. of Genes |
Percentage of Genes |
||||||
| Functional Category | Total | >0.8 | >1 | >2 | >0.8 | >1 | >2 |
| Polyamine metabolism | 9 | 4 | 4 | 1 | 41.2 | 41.2 | 11.8 |
| N-metabolism | 23 | 9 | 6 | 2 | 39.1 | 26.1 | 8.7 |
| Major CHO metabolism | 100 | 39 | 32 | 16 | 38.7 | 32.2 | 16.1 |
| S-assimilation | 13 | 5 | 4 | 1 | 38.5 | 30.8 | 7.7 |
| Metal handling | 69 | 25 | 16 | 3 | 35.3 | 23.4 | 4.0 |
| Fermentation | 12 | 4 | 2 | 1 | 33.3 | 16.7 | 8.3 |
| Amino acid metabolism | 225 | 68 | 48 | 11 | 30.1 | 21.5 | 4.7 |
| Redox regulation | 178 | 50 | 38 | 10 | 27.9 | 21.4 | 5.6 |
| Hormone metabolism | 474 | 113 | 91 | 31 | 23.9 | 19.3 | 6.5 |
| Cofactor and vitamins | 36 | 9 | 6 | 2 | 23.6 | 16.7 | 4.2 |
| Photosynthesis | 153 | 35 | 19 | 6 | 22.7 | 12.6 | 3.9 |
| Transport | 849 | 191 | 136 | 30 | 22.5 | 16.0 | 3.5 |
| Lipid metabolism | 347 | 78 | 51 | 7 | 22.5 | 14.7 | 2.0 |
| Tetrapyrrole synthesis | 33 | 7 | 6 | 5 | 22.4 | 19.3 | 15.3 |
| Nucleotide metabolism | 127 | 28 | 13 | 2 | 22.1 | 9.9 | 1.6 |
| Secondary metabolism | 358 | 79 | 58 | 10 | 21.9 | 16.1 | 2.9 |
| C1 metabolism | 24 | 5 | 3 | 0 | 21.9 | 13.7 | 0.0 |
| Minor CHO metabolism | 105 | 23 | 17 | 9 | 21.5 | 15.8 | 8.6 |
| Gluconeogenesis/glyoxylate | 9 | 2 | 1 | 0 | 21.4 | 10.7 | 0.0 |
| Stress | 764 | 158 | 114 | 39 | 20.7 | 14.9 | 5.2 |
| Development | 402 | 81 | 56 | 19 | 20.1 | 13.9 | 4.7 |
| Miscellaneous | 1110 | 210 | 160 | 38 | 18.9 | 14.4 | 3.4 |
| Protein postmodification | 948 | 175 | 112 | 28 | 18.5 | 11.8 | 2.9 |
| Signaling | 760 | 137 | 85 | 19 | 18.0 | 11.1 | 2.4 |
| RNA regulation | 2274 | 406 | 280 | 73 | 17.9 | 12.3 | 3.2 |
| Glycolysis | 61 | 11 | 10 | 2 | 17.4 | 15.7 | 3.3 |
| Cell wall | 463 | 80 | 61 | 12 | 17.3 | 13.2 | 2.5 |
| Oxidative pentose phosphate | 28 | 5 | 3 | 0 | 16.4 | 10.9 | 0.0 |
| Cell | 557 | 84 | 48 | 8 | 15.0 | 8.7 | 1.4 |
| TCA/organic acid metabolism | 71 | 10 | 7 | 1 | 14.2 | 9.2 | 1.4 |
| Not assigned | 8653 | 1149 | 765 | 139 | 13.3 | 8.8 | 1.6 |
| RNA transcription | 62 | 8 | 4 | 1 | 12.9 | 6.5 | 1.6 |
| Protein degradation | 1058 | 122 | 70 | 16 | 11.5 | 6.6 | 1.5 |
| Mitochondrial electron transport | 112 | 11 | 6 | 1 | 10.1 | 5.6 | 0.9 |
| Protein targeting | 173 | 16 | 10 | 0 | 9.0 | 5.8 | 0.0 |
| RNA processing | 201 | 17 | 8 | 0 | 8.2 | 4.0 | 0.0 |
| DNA | 977 | 63 | 29 | 3 | 6.4 | 3.0 | 0.3 |
| Protein synthesis | 474.2 | 30 | 16 | 1 | 6.4 | 3.4 | 0.2 |
Subsets of genes that show increasingly large diurnal changes in transcript levels were identified by filtering out all genes called “absent” at all six time points and all genes where the average correlation coefficient between three pair-wise comparisons of the biological triplicates was <0.5 and then applying three increasingly stringent filters of a diurnal change with a maximum:minimum ratio of >0.8, >1, or >2 on a log2 scale. The genes were grouped using the functional categories defined in MapMan (Thimm et al., 2004; version 1.4.3, http://gabi.rzpd.de/projects/MapMan/). The functional categories are ordered according to their frequency in the gene set with the smallest diurnal cycle. The average response for an amplitude >0.8, >1, or >2 was 16, 11, and 2.4%, respectively. Classes of genes that show a twofold higher, a higher, and a lower frequency of diurnal changes than the average are shown in bold, normal, and italic type, respectively, in the columns giving the percentage of response. CHO, carbohydrate; TCA, tricarboxylic acid.