Table 1. Gene ontology (GO) annotation of differentially expressed genes (DEGs) assigned to the biological process (BP) category after cold treatment and recovery in shoots.
The bars show the numbers of genes in each GO Slim category. GO enrichment analysis was conducted using agriGO (http://bioinfo.cau.edu.cn/agriGO/), and GO terms with a p < 0.05 were considered to have significantly enriched expression in the cluster.
| Shoot | |||||||
| TNG67 | TCN1 | ||||||
| Up-regulated | |||||||
| 3/0 hr | |||||||
| Term | Count | % | P-value | Term | Count | % | P-value |
| cellular process | 228 | 40.86% | 4.10E-19 | biosynthetic process | 94 | 20.94% | 2.40E-14 |
| biosynthetic process | 118 | 21.15% | 6.40E-18 | generation of precursor metabolites and energy | 23 | 5.12% | 8.00E-14 |
| nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 92 | 16.49% | 3.40E-15 | cellular process | 175 | 38.98% | 1.40E-13 |
| metabolic process | 235 | 42.11% | 1.30E-13 | photosynthesis | 13 | 2.90% | 7.60E-11 |
| photosynthesis | 8 | 1.43% | 5.70E-05 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 69 | 15.37% | 1.40E-10 |
| protein modification process | 49 | 8.78% | 8.50E-05 | metabolic process | 182 | 40.53% | 7.20E-10 |
| generation of precursor metabolites and energy | 11 | 1.97% | 0.0012 | cellular component organization | 14 | 3.12% | 8.10E-05 |
| cellular component organization | 13 | 2.33% | 0.002 | transport | 28 | 6.24% | 0.019 |
| death | 12 | 2.15% | 0.013 | carbohydrate metabolic process | 18 | 4.01% | 0.021 |
| protein metabolic process | 71 | 12.72% | 0.016 | ||||
| response to stress | 18 | 3.23% | 0.017 | ||||
| 24/0 hr | |||||||
| Term | Count | % | P-value | Term | Count | % | P-value |
| cellular process | 510 | 39.66% | 1.60E-38 | cellular process | 409 | 39.56% | 7.00E-31 |
| metabolic process | 557 | 43.31% | 8.50E-33 | biosynthetic process | 211 | 20.41% | 3.20E-29 |
| biosynthetic process | 249 | 19.36% | 2.80E-31 | metabolic process | 453 | 43.81% | 1.10E-27 |
| nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 199 | 15.47% | 2.90E-28 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 166 | 16.05% | 3.10E-25 |
| protein modification process | 127 | 9.88% | 2.70E-13 | generation of precursor metabolites and energy | 29 | 2.80% | 7.80E-11 |
| protein metabolic process | 192 | 14.93% | 1.80E-08 | Photosynthesis | 15 | 1.45% | 2.50E-08 |
| generation of precursor metabolites and energy | 27 | 2.10% | 1.30E-07 | protein modification process | 91 | 8.80% | 9.70E-08 |
| transport | 84 | 6.53% | 2.40E-05 | catabolic process | 27 | 2.61% | 9.80E-06 |
| cellular component organization | 25 | 1.94% | 0.00033 | protein metabolic process | 143 | 13.83% | 3.70E-05 |
| catabolic process | 27 | 2.10% | 0.00033 | cellular component organization | 22 | 2.13% | 0.00023 |
| photosynthesis | 10 | 0.78% | 0.00093 | carbohydrate metabolic process | 41 | 3.97% | 0.00098 |
| carbohydrate metabolic process | 48 | 3.73% | 0.0013 | Transport | 61 | 5.90% | 0.0029 |
| lipid metabolic process | 24 | 1.87% | 0.0049 | lipid metabolic process | 18 | 1.74% | 0.025 |
| response to stress | 34 | 2.64% | 0.022 | ||||
| signal transduction | 17 | 1.32% | 0.031 | ||||
| re24/0 hr | |||||||
| Term | Count | % | P-value | Term | Count | % | P-value |
| carbohydrate metabolic process | 13 | 7.39% | 0.00041 | metabolic process | 342 | 44.02% | 1.8E-21 |
| metabolic process | 66 | 37.50% | 0.00087 | carbohydrate metabolic process | 56 | 7.21% | 8.8E-13 |
| catabolic process | 6 | 3.41% | 0.0097 | cellular process | 217 | 27.93% | 3.9E-06 |
| biosynthetic process | 25 | 14.20% | 0.0087 | biosynthetic process | 102 | 13.13% | 7.9E-06 |
| nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 19 | 10.80% | 0.019 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 82 | 10.55% | 8.3E-06 |
| transport | 53 | 6.82% | 0.00028 | ||||
| protein metabolic process | 106 | 13.64% | 0.00053 | ||||
| generation of precursor metabolites and energy | 13 | 1.67% | 0.0019 | ||||
| protein modification process | 54 | 6.95% | 0.0057 | ||||
| catabolic process | 16 | 2.06% | 0.0061 | ||||
| lipid metabolic process | 16 | 2.06% | 0.0085 | ||||
| response to stress | 22 | 2.83% | 0.032 | ||||
| Down-regulated | |||||||
| 3/0 hr | |||||||
| Term | Count | % | P-value | Term | Count | % | P-value |
| metabolic process | 130 | 43.05% | 1.2E-08 | protein modification process | 23 | 11.79% | 0.00016 |
| cellular process | 108 | 35.76% | 2E-07 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 27 | 13.85% | 0.00024 |
| nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 45 | 14.90% | 4.5E-07 | metabolic process | 75 | 38.46% | 0.00023 |
| protein modification process | 37 | 12.25% | 9.1E-07 | biosynthetic process | 32 | 16.41% | 0.00042 |
| biosynthetic process | 52 | 17.22% | 2.6E-06 | cellular process | 57 | 29.23% | 0.0061 |
| protein metabolic process | 50 | 16.56% | 0.00045 | protein metabolic process | 30 | 15.38% | 0.013 |
| lipid metabolic process | 8 | 2.65% | 0.015 | ||||
| response to stress | 11 | 3.64% | 0.026 | ||||
| 24/0 hr | |||||||
| Term | Count | % | P-value | Term | Count | % | P-value |
| metabolic process | 386 | 36.28% | 1.80E-13 | metabolic process | 444 | 37.19% | 1.10E-16 |
| protein modification process | 101 | 9.49% | 5.50E-10 | cellular process | 362 | 30.32% | 8.30E-13 |
| lipid metabolic process | 32 | 3.01% | 1.70E-07 | transport | 104 | 8.71% | 2.70E-12 |
| transport | 81 | 7.61% | 1.60E-07 | protein modification process | 114 | 9.55% | 3.10E-11 |
| response to stress | 42 | 3.95% | 5.30E-06 | reproduction | 18 | 1.51% | 2.60E-10 |
| reproduction | 11 | 1.03% | 3.10E-05 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 123 | 10.30% | 1.70E-07 |
| carbohydrate metabolic process | 46 | 4.32% | 8.10E-05 | protein metabolic process | 167 | 13.99% | 4.90E-06 |
| protein metabolic process | 144 | 13.53% | 8.60E-05 | response to stress | 45 | 3.77% | 7.70E-06 |
| cellular process | 269 | 25.28% | 0.00013 | pollination | 11 | 0.92% | 1.10E-05 |
| nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 90 | 8.46% | 0.003 | lipid metabolic process | 29 | 2.43% | 3.30E-05 |
| pollination | 7 | 0.66% | 0.0033 | biosynthetic process | 140 | 11.73% | 3.50E-05 |
| death | 28 | 2.35% | 4.80E-05 | ||||
| carbohydrate metabolic process | 45 | 3.77% | 0.0015 | ||||
| cell communication | 11 | 0.92% | 0.004 | ||||
| re24/0 hr | |||||||
| Term | Count | % | P-value | Term | Count | % | P-value |
| metabolic process | 53 | 41.73% | 0.00039 | metabolic process | 231 | 40.53% | 4.2E-12 |
| cellular process | 43 | 33.86% | 0.0019 | cellular process | 192 | 33.68% | 2.8E-10 |
| nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 18 | 14.17% | 0.0019 | carbohydrate metabolic process | 36 | 6.32% | 2.2E-07 |
| protein modification process | 14 | 11.02% | 0.005 | protein modification process | 56 | 9.82% | 1.4E-06 |
| transport | 12 | 9.45% | 0.0077 | response to stress | 27 | 4.74% | 0.000013 |
| nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 60 | 10.53% | 0.00013 | ||||
| lipid metabolic process | 16 | 2.81% | 0.00043 | ||||
| biosynthetic process | 70 | 12.28% | 0.00099 | ||||
| transport | 38 | 6.67% | 0.0027 | ||||
| pollination | 5 | 0.88% | 0.0039 | ||||
| generation of precursor metabolites and energy | 10 | 1.75% | 0.0044 | ||||
| reproduction | 5 | 0.88% | 0.0096 | ||||
| protein metabolic process | 73 | 12.81% | 0.013 | ||||
| death | 12 | 2.11% | 0.015 | ||||