Table 2.
Overrepresented pathways in upregulated (UP) and downregulated (DOWN) genes across growth conditions and genotypes
| Patterna | Pathway id | Pathway name | In group | In all genes | Bh_p_val |
|---|---|---|---|---|---|
| D1_COLD_UP | PWY-2902 | cytokinins-O-glucoside biosynthesis | 37 | 72 | 0.0002 |
| PWY-3781 | aerobic respiration -- electron donor IIa | 7 | 106 | 0.0012 | |
| D1_CG60_DOWN | PWY-695 | abscisic acid biosynthesis | 9 | 12 | 0.0013 |
| PWY-6299 | aldehyde oxidation I | 6 | 8 | 0.0354 | |
| PWY-6446 | benzoate biosynthesis III (CoA-dependent, non- β -oxidative) | 8 | 15 | 0.0354 | |
| PWY-6444 | benzoate biosynthesis II (CoA-independent, non- β -oxidative) | 8 | 15 | 0.0354 | |
| PWYQT-4429 | CO2 fixation into oxaloacetate | 4 | 4 | 0.0354 | |
| D4_COLD_DOWN | PWY-282 | cuticular wax biosynthesisb | 0 | 5 | 0.0057 |
| D4_COLD_UP | PWY-282 | cuticular wax biosynthesis | 3 | 5 | 0.0115 |
| D4_CG60_DOWN | PWY-6446 | benzoate biosynthesis III (CoA-dependent, non- β -oxidative) | 10 | 15 | 0.0091 |
| PWY-6444 | benzoate biosynthesis II (CoA-independent, non- β -oxidative) | 10 | 15 | 0.0091 | |
| PWY-724 | superpathway of lysine, threonine and methionine biosynthesis II | 23 | 59 | 0.0168 | |
| PWY-6457 | trans-cinnamoyl-CoA biosynthesis | 6 | 7 | 0.0220 | |
| PWY-5156 | superpathway of fatty acid biosynthesis II (plant) | 18 | 44 | 0.0332 | |
| PWY-1081 | homogalacturonan degradation | 18 | 45 | 0.0332 | |
| TRPSYN-PWY | tryptophan biosynthesis | 11 | 22 | 0.0332 | |
| PWY1F-467 | phenylpropanoid biosynthesis, initial reactions | 6 | 8 | 0.0332 | |
| PWY-5172 | acetyl-CoA biosynthesis (from citrate) | 6 | 8 | 0.0332 | |
| PWY0–162 | pyrimidine ribonucleotides de novo biosynthesis | 14 | 33 | 0.0391 | |
| PWY-5670 | epoxysqualene biosynthesis | 4 | 4 | 0.0429 |
aThe code for the gene expression pattern is “day”, main effect factor level, direction of the main effect. D1 refers to samples harvested during cold exposure and their controls. D4 refers to samples harvested 24 h after cold exposure and their controls. CG60_UP indicates a significant, positive effect of CG60. CG60_DOWN indicates a significant, negative effect of CG60
bPathways with b at the end of the description were underrepresented amongst the gene set