Table 3.
Functional annotation cluster (FAC) of genes up- or down-regulated (>2-fold change) in Luna Rossa and AVG cultivars that have a significant P value (≤0.05). Gene ontology, enrichment score, P value, fold enrichment, and statistical significance using Bonferroni, Benjamini, FDR
| Cultivar | Cluster | Gene expression | Term | Enrichment score (ES) | P value | Fold enrichment | Bonferroni | Benjamini | FDR |
|---|---|---|---|---|---|---|---|---|---|
| Luna Rossa | 1 | down | GO:0009835~ripening | 1.2 | 0.05 | 6.81 | 0.96 | 0.42 | 43.03 |
| Luna Rossa | 2 | down | GO:0019748~secondary metabolic process | 1.2 | 0.01 | 7.27 | 0.43 | 0.43 | 9.08 |
| Luna Rossa | 2 | down | GO:0008610~lipid biosynthetic process | 1.2 | 0.02 | 5.59 | 0.71 | 0.46 | 18.90 |
| Luna Rossa | 2 | down | GO:0016108~tetraterpenoid metabolic process; GO:0016109~tetraterpenoid biosynthetic process; GO:0016116~carotenoid metabolic process; GO:0016117~carotenoid biosynthetic process. |
1.2 | 0.02 | 10.90 | 0.71 | 0.34 | 19.34 |
| Luna Rossa | 2 | down | carotenoid biosynthesis | 1.2 | 0.02 | 10.32 | 0.78 | 0.78 | 22.38 |
| Luna Rossa | 2 | down | GO:0042440~pigment metabolic process GO:0046148~pigment biosynthetic process |
1.2 | 0.03 | 9.08 | 0.84 | 0.37 | 27.02 |
| Luna Rossa | 2 | down | GO:0006720~isoprenoid metabolic process; GO:0006721~terpenoid metabolic process; GO:0008299~isoprenoid biosynthetic process; GO:0016114~terpenoid biosynthetic process |
1.2 | 0.04 | 7.79 | 0.92 | 0.40 | 35.03 |
| Luna Rossa | 3 | down | GO:0008610~lipid biosynthetic process | 0.8 | 0.02 | 5.59 | 0.71 | 0.46 | 18.90 |
| Luna Rossa | 4 | down | active site:Proton donor | 0.8 | 0.03 | 5.07 | 0.67 | 0.67 | 23.82 |
| AVG | 2 | up | GO:0005576~extracellular region | 0.7 | 0.04 | 3.87 | 0.48 | 0.48 | 26.08 |
| AVG | 3 | up | nucleus | 0.6 | 0.05 | 3.09 | 0.98 | 0.98 | 44.21 |
| AVG | 1 | down | GO:0019748~secondary metabolic process | 2.1 | 0.00 | 7.58 | 0.00 | 0.00 | 0.00 |
| AVG | 1 | down | transit peptide | 2.1 | 0.00 | 3.55 | 0.00 | 0.00 | 0.02 |
| AVG | 1 | down | GO:0006720~isoprenoid metabolic process; GO:0006721~terpenoid metabolic process; GO:0008299~isoprenoid biosynthetic process; GO:0016114~terpenoid biosynthetic process. |
2.1 | 0.00 | 8.12 | 0.02 | 0.01 | 0.14 |
| AVG | 1 | down | transit peptide:Chloroplast | 2.1 | 0.00 | 3.27 | 0.03 | 0.03 | 0.34 |
| AVG | 1 | down | GO:0008610~lipid biosynthetic process | 2.1 | 0.00 | 5.10 | 0.07 | 0.02 | 0.66 |
| AVG | 1 | down | GO:0016108~tetraterpenoid metabolic process; GO:0016109~tetraterpenoid biosynthetic process; GO:0016116~carotenoid metabolic process; GO:0016117~carotenoid biosynthetic process. |
2.1 | 0.01 | 7.58 | 0.62 | 0.22 | 8.72 |
| AVG | 1 | down | carotenoid biosynthesis | 2.1 | 0.01 | 7.64 | 0.53 | 0.32 | 8.44 |
| AVG | 1 | down | GO:0042440~pigment metabolic process; GO:0046148~pigment biosynthetic process. |
2.1 | 0.01 | 6.32 | 0.84 | 0.31 | 15.72 |
| AVG | 1 | down | Isoprene biosynthesis | 2.1 | 0.03 | 9.56 | 0.93 | 0.59 | 26.46 |
| AVG | 2 | down | transferase | 1.1 | 0.05 | 2.39 | 0.99 | 0.59 | 40.62 |