Table 1.
Gene ontology categorization of common genes up- or down-regulated in buds of OFF-Crop and de-fruited (DEF) trees relative to buds of ON-Crop trees at Time 4
| General process | GO term | Description | Ref item | OFF | DEF | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Query item | P-value | FDR | Fold enrichmenta | Query item | P-value | FDR | Fold enrichmenta | ||||
| Up-regulated | |||||||||||
| Response to light | GO:0010218 | Response to far red light | 25 | 11 | 2.80E-07 | 0.00057 | 6.48 | 14 | 7.20E-11 | 9.40E-08 | 8.51 |
| GO:0010114 | Response to red light | 47 | 14 | 1.90E-06 | 0.00089 | 4.39 | 17 | 3.80E-09 | 3.00E-06 | 5.50 | |
| GO:0009639 | Response to red or far red light | r | 22 | 0.00023 | 0.024 | 2.31 | 22 | 0.00015 | 0.014 | 2.39 | |
| GO:0009416 | Response to light stimulus | 380 | 44 | 0.00055 | 0.047 | 1.70 | 59 | 2.20E-09 | 2.20E-06 | 2.36 | |
| GO:0009637 | Response to blue light | 27 | 7 | 8.20E-05 | 0.049 | 6.39 | 11 | 5.20E-07 | 0.00015 | 6.19 | |
| GO:0009644 | Response to high light intensity | 70 | 20 | 1.80E-08 | 8.90E-06 | 4.34 | |||||
| GO:0009642 | Response to light intensity | 88 | 23 | 1.10E-08 | 7.00E-06 | 3.97 | |||||
| GO:0009314 | Response to radiation | 404 | 59 | 2.10E-08 | 9.30E-06 | 2.22 | |||||
| Photosynthesis and carbon fixation | GO:0015977 | Carbon fixation | 7 | 6 | 6.60E-07 | 0.00068 | 12.62 | 5 | 2.40E-05 | 0.0031 | 10.85 |
| GO:0009773 | Photosynthetic electron transport in photosystem I | 12 | 7 | 4.00E-06 | 0.0013 | 8.59 | 5 | 0.00067 | 0.038 | 6.33 | |
| GO:0015979 | Photosynthesis | 128 | 33 | 2.90E-11 | 1.20E-07 | 3.80 | 47 | 9.80E-23 | 3.90E-19 | 5.58 | |
| GO:0009767 | Photosynthetic electron transport chain | 31 | 10 | 2.60E-05 | 0.0059 | 4.75 | 11 | 2.60E-06 | 0.00055 | 5.39 | |
| GO:0019684 | Photosynthesis, light reaction | 85 | 19 | 3.90E-06 | 0.0013 | 3.29 | 31 | 1.60E-15 | 3.10E-12 | 5.54 | |
| GO:0019685 | Photosynthesis, dark reaction | 5 | 5 | 1.50E-06 | 0.00087 | 14.72 | |||||
| GO:0010207 | Photosystem II assembly | 36 | 13 | 2.60E-07 | 8.50E-05 | 5.49 | |||||
| GO:0009765 | Photosynthesis, light harvesting | 13 | 8 | 3.50E-07 | 0.00011 | 9.35 | |||||
| Chloroplast | GO:0051667 | Establishment of plastid localization | 28 | 9 | 6.70E-05 | 0.011 | 4.73 | 8 | 0.00034 | 0.023 | 4.34 |
| GO:0051644 | Plastid localization | 28 | 9 | 6.70E-05 | 0.011 | 4.73 | 8 | 0.00034 | 0.023 | 4.34 | |
| GO:0009902 | Chloroplast relocation | 28 | 9 | 6.70E-05 | 0.011 | 4.73 | 8 | 0.00034 | 0.023 | 4.34 | |
| GO:0051656 | Establishment of organelle localization | 31 | 9 | 0.00016 | 0.02 | 4.27 | 8 | 0.00073 | 0.04 | 3.92 | |
| GO:0009658 | Chloroplast organization | 81 | 18 | 7.60E-06 | 0.002 | 3.27 | 14 | 0.00083 | 0.044 | 2.63 | |
| GO:0009657 | Plastid organization | 123 | 21 | 9.50E-05 | 0.014 | 2.51 | 20 | 0.00018 | 0.015 | 2.47 | |
| Response to carbohydrate stimulus | GO:0009744 | Response to sucrose stimulus | 47 | 12 | 5.60E-05 | 0.011 | 3.76 | 14 | 1.30E-06 | 0.00033 | 4.53 |
| GO:0034285 | Response to disaccharide stimulus | 48 | 12 | 7.10E-05 | 0.011 | 3.68 | 14 | 1.80E-06 | 0.00039 | 4.43 | |
| GO:0009743 | Response to carbohydrate stimulus | 178 | 31 | 1.70E-06 | 0.00088 | 2.56 | 33 | 9.30E-08 | 3.30E-05 | 2.82 | |
| Cellular homeostasis | GO:0071704 | Organic substance metabolic process | 7 | 6 | 6.60E-07 | 0.00068 | 12.62 | 5 | 2.40E-05 | 0.0031 | 10.85 |
| GO:0019725 | Cellular homeostasis | 129 | 23 | 2.30E-05 | 0.0055 | 2.63 | 21 | 0.00012 | 0.012 | 2.47 | |
| GO:0055082 | Cellular chemical homeostasis | 57 | 12 | 2.90E-06 | 0.0037 | 5.19 | 16 | 5.90E-07 | 0.00016 | 4.26 | |
| Ion homeostasis | GO:0006873 | Cellular ion homeostasis | 52 | 12 | 0.00016 | 0.02 | 3.40 | 14 | 5.00E-06 | 0.00095 | 4.09 |
| GO:0030003 | Cellular cation homeostasis | 50 | 11 | 0.00046 | 0.043 | 3.24 | 13 | 1.60E-05 | 0.0023 | 3.95 | |
| GO:0055082 | Cellular chemical homeostasis | 57 | 15 | 4.70E-06 | 0.0014 | 3.87 | 41 | 0.00013 | 0.012 | 1.87 | |
| GO:0006812 | Cation transport | 333 | 43 | 6.00E-05 | 0.011 | 1.90 | 14 | 0.00037 | 0.023 | 2.84 | |
| GO:0006811 | Ion transport | 470 | 55 | 0.0001 | 0.014 | 1.72 | 52 | 0.00028 | 0.021 | 1.68 | |
| GO:0010155 | Regulation of proton transport | 11 | 6 | 3.40E-05 | 0.0075 | 8.03 | 7 | 1.40E-06 | 0.00033 | 9.67 | |
| GO:0055080 | Cation homeostasis | 64 | 13 | 0.00025 | 0.019 | 3.09 | |||||
| Pentose cycle | GO:0019253 | Reductive pentose-phosphate cycle | 5 | 5 | 1.50E-06 | 0.00087 | 14.72 | ||||
| GO:0006098 | Pentose-phosphate shunt | 65 | 13 | 0.0003 | 0.022 | 3.04 | |||||
| Response to biotic stress | GO:0010200 | Response to chitin | 90 | 16 | 0.00038 | 0.038 | 2.62 | 17 | 8.10E-05 | 0.0089 | 2.87 |
| GO:0050832 | Defence response to fungus | 123 | 20 | 0.00027 | 0.028 | 2.39 | 20 | 0.00018 | 0.015 | 2.47 | |
| Abiotic stress | GO:0009611 | Response to wounding | 128 | 20 | 0.00046 | 0.043 | 2.30 | 20 | 0.00031 | 0.022 | 2.37 |
| Down-regulated | |||||||||||
| Secondary metabolism | GO:0019748 | Secondary metabolic process | 467 | 58 | 5.80E-05 | 0.042 | 1.73 | 55 | 1.20E-06 | 0.0011 | 2.04 |
| GO:0006721 | Terpenoid metabolic process | 118 | 23 | 1.20E-05 | 0.016 | 2.72 | 18 | 0.00017 | 0.028 | 2.64 | |
| GO:0006720 | Isoprenoid metabolic process | 186 | 29 | 8.10E-05 | 0.049 | 2.17 | 8 | 0.00031 | 0.044 | 4.46 | |
| GO:0009699 | Phenylpropanoid biosynthetic process | 143 | 23 | 1.00E-05 | 0.0035 | 2.78 | |||||
| GO:0009698 | Phenylpropanoid metabolic process | 184 | 27 | 1.10E-05 | 0.0035 | 2.54 | |||||
| Various | GO:0055114 | Oxidation reduction | 1344 | 166 | 2.00E-10 | 7.40E-07 | 1.72 | 137 | 2.60E-09 | 7.50E-06 | 1.76 |
| GO:0042221 | Response to chemical stimulus | 1345 | 142 | 1.30E-05 | 0.016 | 1.47 | 120 | 1.00E-05 | 0.0035 | 1.54 | |
| GO:0010035 | Response to inorganic substance | 462 | 58 | 4.30E-05 | 0.039 | 1.75 | |||||
a Fold enrichment as calculated based on GO-annotated genes (777, 753, 821, 662 in OFF-Crop up-regulated, DEF up-regulated, OFF-Crop down-regulated, DEF down-regulated, respectively) in the list of genes (959, 920, 997, 797 in OFF-Crop up-regulated, DEF up-regulated, OFF-Crop down-regulated, DEF down-regulated, respectively) per GO-annotated genes (11445) in the reference list (14400 genes).