TABLE 4.
Enrichment analysis of metabolic pathways.
| Treatment (h) | Number of rice homolog genes | Super-class | Pathway | P-value | Number of genes |
| (A) Up-regulated genes | |||||
| 6 up | 153 | Amino acids degradation | Glycine cleavage complex | 2.37E-03 | 2 |
| Cofactors, prosthetic groups, electron carriers biosynthesis | Chlorophyllide a biosynthesis | 1.96E-02 | 2 | ||
| 24 up | 349 | Amino acids biosynthesis | Cysteine biosynthesis | 5.19E-04 | 4 |
| Cofactors, prosthetic groups, electron carriers biosynthesis | Branched-chain α-keto acid dehydrogenase complex | 7.37E-03 | 3 | ||
| 96 up | 323 | Carbohydrates biosynthesis/Cell structures biosynthesis | Cellulose biosynthesis | 2.83E-02 | 4 |
| UDP-D-xylose biosynthesis | 9.98E-03 | 2 | |||
| dTDP-L-rhamnose biosynthesis I | 2.40E-02 | 3 | |||
| Nucleosides and nucleotides biosynthesis | Purine nucleotides de novo biosynthesis | 1.86E-02 | 4 | ||
| 6 and 24 up | 385 | Cofactors, prosthetic groups, electron carriers biosynthesis | γ-glutamyl cycle (glutathione) | 6.49E-03 | 4 |
| Nucleosides and nucleotides biosynthesis | Purine nucleotides de novo biosynthesis | 2.69E-02 | 4 | ||
| Secondary metabolites biosynthesis | Flavonoid biosynthesis | 4.23E-02 | 2 | ||
| 6 and 96 up | 190 | Carbohydrates biosynthesis/Cell structures biosynthesis | Cellulose biosynthesis | 2.24E-03 | 4 |
| Secondary metabolites biosynthesis | Flavonoid biosynthesis | 8.87E-03 | 2 | ||
| 24 and 96 | 253 | Carbohydrates biosynthesis/Cell structures biosynthesis | Cellulose biosynthesis | 4.00E-03 | 5 |
| Nucleosides and nucleotides biosynthesis | Purine nucleotides de novo biosynthesis | 1.41E-02 | 4 | ||
| Secondary metabolites biosynthesis/Hormones biosynthesis | Jasmonic acid biosynthesis | 2.90E-02 | 3 | ||
| Divinyl ether biosynthesis II (13-LOX) | 1.56E-03 | 3 | |||
| Secondary metabolites biosynthesis | Mevalonate pathway (terpenes) | 4.02E-02 | 2 | ||
| All up | 3,785 | Amines and polyamines degradation | Carnitine degradation | 3.99E-02 | 3 |
| Amino acids biosynthesis | Arginine biosynthesis II (acetyl cycle) | 1.51E-03 | 9 | ||
| Homocysteine biosynthesis | 3.03E-02 | 2 | |||
| Asparagine biosynthesis | 3.54E-02 | 4 | |||
| Proline biosynthesis (from arginine) | 3.99E-02 | 3 | |||
| Proline biosynthesis (from glutamate) | 4.54E-02 | 6 | |||
| Amino acids degradation | Tryptophan degradation (side chain pathway) | 3.99E-02 | 3 | ||
| Carboxylates degradation/Secondary metabolites degradation | β-D-glucuronide degradation | 1.83E-02 | 3 | ||
| Cell structures biosynthesis | Peptidoglycan biosynthesis I | 3.99E-02 | 3 | ||
| Carbohydrates biosynthesis/Cell structures biosynthesis | Chlorophyllide a biosynthesis | 1.54E-02 | 11 | ||
| Phylloquinone biosynthesis | 3.03E-02 | 2 | |||
| Pantothenate biosynthesis (coenzyme A) | 4.28E-02 | 5 | |||
| Generation of precursor metabolites and energy | Pentose phosphate pathway (non-oxidative branch) | 2.90E-02 | 5 | ||
| Inorganic nutrients metabolism | Urea cycle | 1.02E-02 | 4 | ||
| Nucleosides and nucleotides biosynthesis | Purine nucleotides de novo biosynthesis I | 1.52E-03 | 20 | ||
| De novo biosynthesis of pyrimidine deoxyribonucleotides | 1.97E-02 | 8 | |||
| Secondary metabolites biosynthesis | Canavanine biosynthesis | 3.93E-03 | 4 | ||
| (B) Down-regulated genes | |||||
| 6 down | 171 | Secondary metabolites biosynthesis | Phenylpropanoid biosynthesis, initial reactions | 1.56E-03 | 2 |
| Secondary metabolites biosynthesis/Cell structures biosynthesis | Suberin biosynthesis | 5.06E-03 | 2 | ||
| 24 down | 475 | Carbohydrates Biosynthesis | Gluconeogenesis | 3.57E-04 | 8 |
| Generation of precursor metabolites and energy | Calvin cycle | 5.54E-03 | 6 | ||
| Glycolysis | 4.07E-02 | 6 | |||
| Cofactors, prosthetic groups, electron carriers biosynthesis | Pyridoxal 5’-phosphate biosynthesis | 7.14E-03 | 2 | ||
| Nucleosides and nucleotides biosynthesis | Salvage pathways of purine and pyrimidine nucleotides | 4.77E-02 | 4 | ||
| 96 down | 307 | Secondary metabolites biosynthesis/Hormones biosynthesis | Divinyl ether biosynthesis II (13-LOX) | 9.26E-03 | 2 |
| 6 and 24 down | 394 | Carbohydrates biosynthesis | Gluconeogenesis | 7.09E-03 | 5 |
| Carbohydrates biosynthesis/Carbohydrates degradation | UDP-glucose conversion | 2.48E-02 | 4 | ||
| Carbohydrates degradation | sucrose degradation to ethanol and lactate (anaerobic) | 9.26E-03 | 8 | ||
| Fatty acid and lipid biosynthesis | Acyl-CoA thioesterase pathway | 2.15E-02 | 2 | ||
| Generation of precursor metabolites and energy | Glycolysis | 7.02E-03 | 6 | ||
| 6 and 96 down | 253 | Hormones biosynthesis | Cytokinins-O-glucoside biosynthesis | 3.74E-02 | 5 |
| Secondary metabolites biosynthesis/Hormones biosynthesis | Divinyl ether biosynthesis II (13-LOX) | 1.26E-02 | 2 | ||
| 24 and 96 down | 215 | Amino Acids biosynthesis | Histidine biosynthesis | 1.13E-02 | 2 |
| Methionine salvage pathway | 2.20E-02 | 2 | |||
| Hormones biosynthesis | Ethylene biosynthesis from methionine | 1.96E-02 | 2 | ||
| All down | 2,528 | Amino acids biosynthesis | Cysteine biosynthesis | 3.28E-02 | 6 |
| Methionine salvage pathway | 1.18E-02 | 9 | |||
| Amines and Polyamines Biosynthesis | Spermine biosynthesis | 3.67E-02 | 3 | ||
| Carbohydrates Biosynthesis | Trehalose biosynthesis | 3.60E-03 | 7 | ||
| Carbohydrates biosynthesis/Carbohydrates degradation | UDP-glucose conversion | 3.43E-02 | 14 | ||
| Carbohydrates biosynthesis/Cell structures biosynthesis | GDP-D-rhamnose biosynthesis | 3.96E-02 | 4 | ||
| dTDP-L-rhamnose biosynthesis | 4.65E-02 | 7 | |||
| Carbohydrates degradation | Mannose degradation | 2.29E-02 | 3 | ||
| Starch degradation | 1.66E-02 | 12 | |||
| Sucrose degradation | 7.65E-03 | 5 | |||
| Cofactors, prosthetic groups, electron carriers biosynthesis | Ascorbate biosynthesis | 2.87E-02 | 5 | ||
| Fatty acid and lipid biosynthesis | Glycolipid biosynthesis | 8.95E-06 | 8 | ||
| Generation of precursor metabolites and energy | Photorespiration | 2.32E-02 | 7 | ||
| Hormones biosynthesis | Cytokinins-O-glucoside biosynthesis | 4.34E-02 | 26 | ||
| Ethylene biosynthesis from methionine | 7.75E-03 | 4 | |||
| Inorganic Nutrients Metabolism | Ammonia assimilation cycle II | 3.67E-02 | 3 | ||
| Nitrate reduction II (assimilatory) | 8.13E-03 | 9 | |||
| Secondary metabolites biosynthesis/Hormones biosynthesis | Gibberellin biosynthesis III (early C-13 hydroxylation) | 8.13E-03 | 4 | ||
Gene expression patterns were sorted into up- and down-regulated genes upon 6, 24, and 96 h of aphid feeding on RTC-144 tef plants.