Table 5.
Functional category enrichment of differentially expressed genes between wild-type LA1589 and MIR167 transgenic lines
| MapMan BinCode | Category | Alla | Commonb | Uniquec | Genomed | P-valuef | P-value (common) | P-value (unique) | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| nume | Freq | num | freq | num | freq | num | freq | ||||||
| Regulation of transcription | 27.3.50 | General transcription (GRF family) | 4 (0) | 0.57% | 0 | 0 | 4 (0) | 0.78% | 31 | 0.09% | 0.011 | 0.263 | 0.010 |
| 27.3.24 | MADS box transcription factor family | 7 (6) | 0.99% | 2 (1) | 1.05% | 5 (5) | 0.97% | 101 | 0.28% | 0.016 | 0.060 | 0.039 | |
| 27.3.4 | Auxin response factor family | 3 (2) | 0.43% | 2 (2) | 1.05% | 1 (0) | 0.19% | 26 | 0.07% | 0.016 | 6.02E–03 | 0.138 | |
| 27.3.40 | Aux/IAA family | 3 (3) | 0.43% | 1 (1) | 0.52% | 2 (2) | 0.39% | 25 | 0.07% | 0.016 | 0.037 | 0.039 | |
| 27.3.26 | MYB-related transcription factor family | 3 (1) | 0.43% | 0 | 0 | 3 (1) | 0.58% | 49 | 0.14% | 0.059 | 0.332 | 0.039 | |
| 27.3.21 | GRAS transcription factor family | 3 (0) | 0.43% | 0 | 0 | 3 (0) | 0.58% | 53 | 0.15% | 0.069 | 0.340 | 0.047 | |
| 27.3.35 | bZIP transcription factor family | 4 (3) | 0.57% | 2 (1) | 1.05% | 2 (2) | 0.39% | 82 | 0.23% | 0.071 | 0.042 | 0.232 | |
| Cell wall | 10.6 | Cell wall degradation | 10 (9) | 1.42% | 3 (3) | 1.57% | 7 (6) | 1.36% | 181 | 0.51% | 0.016 | 0.060 | 0.039 |
| 10.8.1 | Pectinesterases | 6 (6) | 0.85% | 3 (3) | 1.57% | 3 (3) | 0.58% | 87 | 0.24% | 0.016 | 0.012 | 0.111 | |
| 10.1 | Cell wall precursor synthesis | 5 (4) | 0.71% | 2 (2) | 1.05% | 3 (2) | 0.58% | 68 | 0.19% | 0.019 | 0.030 | 0.070 | |
| 10.7 | Cell wall modification | 4 (4) | 0.57% | 3 (3) | 1.57% | 1 (1) | 0.19% | 81 | 0.23% | 0.071 | 0.010 | 0.437 | |
| 10.2 | Cellulose synthesis | 3 (3) | 0.43% | 2 (2) | 1.05% | 1 (1) | 0.19% | 66 | 0.19% | 0.100 | 0.028 | 0.354 | |
| Transport | 34.2 | Transport of sugars | 5 (2) | 0.71% | 2 (1) | 1.05% | 3 (1) | 0.58% | 80 | 0.23% | 0.029 | 0.042 | 0.091 |
| 34.1 | p- and v-ATPases | 3 (3) | 0.43% | 2 (2) | 1.05% | 1 (1) | 0.19% | 62 | 0.17% | 0.084 | 0.027 | 0.334 | |
| 34.15 | Potassium transport | 3 (2) | 0.43% | 2 (1) | 1.05% | 1 (1) | 0.19% | 62 | 0.17% | 0.084 | 0.027 | 0.334 | |
| Lipid metabolism | 11.1 | Fatty acid synthesis and elongation | 7 (6) | 0.99% | 2 (2) | 1.05% | 5 (4) | 0.97% | 132 | 0.37% | 0.029 | 0.100 | 0.060 |
| 11.8 | Lipid metabolism (steroids, squalene etc) | 6 (5) | 0.85% | 0 | 0 | 6 (5) | 1.17% | 114 | 0.32% | 0.039 | 0.503 | 0.023 | |
| Hormone metabolism | 17.6 | Gibberellin | 3 (1) | 0.43% | 2 (0) | 1.05% | 1 (1) | 0.19% | 53 | 0.15% | 0.069 | 0.021 | 0.289 |
| 17.2.3 | Auxin-induced-regulated- responsive-activated | 7 (4) | 0.99% | 4 (2) | 2.09% | 3 (2) | 0.58% | 218 | 0.61% | 0.140 | 0.032 | 0.479 | |
| Others | 29.7 | Protein glycosylation | 6 (6) | 0.85% | 2 (2) | 1.05% | 4 (4) | 0.78% | 49 | 0.14% | 6.6E–03 | 0.021 | 0.016 |
| 26.22 | Short chain dehydrogenase/ reductase | 7 (6) | 0.99% | 1 (1) | 0.52% | 6 (5) | 1.17% | 86 | 0.24% | 0.011 | 0.169 | 0.011 | |
| 30.6 | MAP kinases | 3 (3) | 0.43% | 3 (3) | 1.57% | 0 | 0 | 17 | 0.05% | 0.011 | 1.24E–04 | 0.331 | |
| 16.2 | Phenylpropanoids metabolism. | 10 (3) | 1.42% | 1 (0) | 0.52% | 9 (3) | 1.75% | 179 | 0.50% | 0.016 | 0.340 | 0.011 | |
| 26.6 | O-methyl transferases | 3 (3) | 0.43% | 3 (3) | 1.57% | 0 | 0 | 20 | 0.06% | 0.016 | 1.66E–04 | 0.354 | |
| 8 | TCA | 6 (6) | 0.85% | 6 (6) | 3.14% | 0 | 0 | 87 | 0.24% | 0.016 | 6.39E–05 | 0.778 | |
| 26.3 | Gluco-, galacto- and mannosidases | 5 (4) | 0.71% | 1 (1) | 0.52% | 4 (3) | 0.78% | 71 | 0.20% | 0.022 | 0.131 | 0.039 | |
| 5 | Fermentation | 3 (3) | 0.43% | 0 | 0 | 3 (3) | 0.58% | 32 | 0.09% | 0.025 | 0.266 | 0.022 | |
| 31.3 | Cell cycle | 7 (4) | 0.99% | 1 (1) | 0.52% | 6 (3) | 1.17% | 130 | 0.37% | 0.028 | 0.263 | 0.039 | |
| na | SUN-like proteins | 3 (2) | 0.44% | 1 (1) | 0.54% | 2 (1) | 0.40% | 34 | 0.10% | 0.028 | 0.055 | 0.060 | |
| 21.2 | Ascorbate and glutathione | 4 (2) | 0.57% | 2 (1) | 1.05% | 2 (1) | 0.39% | 61 | 0.17% | 0.038 | 0.027 | 0.144 | |
| 24 | Biodegradation of xenobiotics | 4 (2) | 0.57% | 3 (1) | 1.57% | 1 (1) | 0.19% | 64 | 0.18% | 0.042 | 6.02E-03 | 0.346 | |
| 21.1 | Thioredoxin | 4 (4) | 0.57% | 0 | 0 | 4 (4) | 0.78% | 75 | 0.21% | 0.060 | 0.423 | 0.039 | |
| 26.28 | GDSL-motif lipase | 5 (5) | 0.71% | 4 (4) | 2.09% | 1 (1) | 0.19% | 112 | 0.32% | 0.072 | 6.02E–03 | 0.571 | |
| 19 | Tetrapyrrole synthesis | 3 (2) | 0.43% | 3 (2) | 1.57% | 0 | 0 | 58 | 0.16% | 0.075 | 6.02E–03 | 0.641 | |
| 26.2 | UDP glucosyl and glucoronyl transferases | 10 (10) | 1.42% | 7 (7) | 3.66% | 3 (3) | 0.58% | 338 | 0.95% | 0.149 | 7.03E–03 | 0.778 | |
P-values in bold indicate significant enrichment. a, All 687 differentially expressed genes between wild-type tomato and MIR167 transgenic lines. b, The 185 genes that were differentially expressed both owing to overexpression of MIR167 in tomato and in the Arabidopsis arf6 arf8 double mutant. c, The 502 differentially expressed genes unique in tomato. d, Number of genes in the GO category in the entire tomato genome. e, Numbers in the parentheses are the numbers of down-regulated genes. f, Hypergeometric tests were performed in R using ‘phyper’. FDR method was used for P-value correction.