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 |