Table 1.
Functional Categorization of Cold-Regulated Genes
| Cold Upregulated
|
Cold Downregulated
|
|||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ETU
|
ECU
|
LU
|
Subtotal
|
ETD
|
ECD
|
LD
|
Subtotal
|
Total
|
||||||||||
| Functional Category | No. | % | No. | % | No. | % | No. | % | No. | % | No. | % | No. | % | No. | % | No. | % |
| Metabolism | 6 | 7.5 | 19 | 12.0 | 67 | 13.7 | 92 | 12.6 | 2 | 10.0 | 1 | 20.0 | 67 | 24.1 | 70 | 23.1 | 162 | 15.7 |
| Energy | 1 | 1.3 | 5 | 3.2 | 18 | 3.7 | 24 | 3.3 | 0.0 | 0.0 | 6 | 2.2 | 6 | 2.0 | 30 | 2.9 | ||
| Storage protein | 0.0 | 0.0 | 1 | 0.2 | 1 | 0.1 | 0.0 | 0.0 | 0.0 | 0 | 0.0 | 1 | 0.1 | |||||
| Cell cycle and DNA processing | 0.0 | 0.0 | 9 | 1.8 | 9 | 1.2 | 0.0 | 1 | 20.0 | 6 | 2.2 | 7 | 2.3 | 16 | 1.6 | |||
| Transcription | 19 | 23.8 | 26 | 16.5 | 68 | 13.9 | 113 | 15.5 | 1 | 5.0 | 0.0 | 19 | 6.8 | 20 | 6.6 | 133 | 12.9 | |
| Protein synthesis | 0.0 | 0.0 | 4 | 0.8 | 4 | 0.5 | 2 | 10.0 | 0.0 | 2 | 0.7 | 4 | 1.3 | 8 | 0.8 | |||
| Protein fate (folding, modification, and destination) | 1 | 1.3 | 8 | 5.1 | 22 | 4.5 | 31 | 4.3 | 3 | 15.0 | 1 | 20.0 | 13 | 4.7 | 17 | 5.6 | 48 | 4.7 |
| Protein with binding function or cofactor requirement | 0.0 | 1 | 0.6 | 4 | 0.8 | 5 | 0.7 | 0.0 | 0.0 | 5 | 1.8 | 5 | 1.7 | 10 | 1.0 | |||
| Cellular transport, transport facilitation, and transport routes | 4 | 5.0 | 8 | 5.1 | 26 | 5.3 | 38 | 5.2 | 0.0 | 0.0 | 13 | 4.7 | 13 | 4.3 | 51 | 4.9 | ||
| Cellular communication/signal transduction mechanism | 12 | 15.0 | 11 | 7.0 | 40 | 8.2 | 63 | 8.7 | 0.0 | 1 | 20.0 | 18 | 6.5 | 19 | 6.3 | 82 | 8.0 | |
| Cell rescue, defense, and virulence | 6 | 7.5 | 22 | 13.9 | 39 | 8.0 | 67 | 9.2 | 0.0 | 0.0 | 13 | 4.7 | 13 | 4.3 | 80 | 7.8 | ||
| Interaction with the cellular environment | 0.0 | 1 | 0.6 | 0.0 | 1 | 0.1 | 0.0 | 0.0 | 0.0 | 0 | 0.0 | 1 | 0.1 | |||||
| Interaction with the environment (systemic) | 0.0 | 1 | 0.6 | 4 | 0.8 | 5 | 0.7 | 0.0 | 0.0 | 5 | 1.8 | 5 | 1.7 | 10 | 1.0 | |||
| Transposable elements and viral and plasmid proteins | 0.0 | 1 | 0.6 | 1 | 0.2 | 2 | 0.3 | 1 | 5.0 | 1 | 20.0 | 1 | 0.4 | 3 | 1.0 | 5 | 0.5 | |
| Cell fate | 0.0 | 0.0 | 7 | 1.4 | 7 | 1.0 | 0.0 | 0.0 | 0.0 | 0 | 0.0 | 7 | 0.7 | |||||
| Development (systemic) | 0.0 | 1 | 0.6 | 3 | 0.6 | 4 | 0.5 | 0.0 | 0.0 | 2 | 0.7 | 2 | 0.7 | 6 | 0.6 | |||
| Biogenesis of cellular components | 2 | 2.5 | 3 | 1.9 | 7 | 1.4 | 12 | 1.6 | 1 | 5.0 | 0.0 | 6 | 2.2 | 7 | 2.3 | 19 | 1.8 | |
| Subcellular localization | 4 | 5.0 | 6 | 3.8 | 14 | 2.9 | 24 | 3.3 | 0.0 | 0.0 | 6 | 2.2 | 6 | 2.0 | 30 | 2.9 | ||
| No clear classification/unclassified | 25 | 31.3 | 45 | 28.5 | 156 | 31.8 | 226 | 31.0 | 10 | 50.0 | 0.0 | 96 | 34.5 | 106 | 35.0 | 332 | 32.2 | |
| Total | 80 | 100.0 | 158 | 100.0 | 490 | 100.0 | 728 | 100.0 | 20 | 100.0 | 5 | 100.0 | 278 | 100.0 | 303 | 100.0 | 1031 | 100.0 |
Note that among 939 cold-responsive genes, 132 belong to multiple functional categories and 10 are missing in the Functional Catalogue. The missing 10 genes were manually grouped into different functional categories following database searches. ETU/D, early transiently upregulated/downregulated; ECU/D, early continually upregulated/downregulated; LU/D, late upregulated/downregulated.