Table I. Functional classification of DEGs in developing seeds of myb89-1 plants at 12 DAP.
Functional classification of DEGs was performed using the biological process category of Arabidopsis Gene Ontology (http://www.geneontology.com). Percentage refers to the ratio of genes of each functional category relative to total up-regulated or down-regulated DEGs identified in the RNA-seq experiment. The DEGs with log2 ratios greater than 1 or less than −1 (only GO Slim identifiers with P ≤ 0.05 and false discovery rate ≤ 0.05) are listed.
| Category |
Up-Regulated DEGs |
Down-Regulated DEGs |
|||||||
|---|---|---|---|---|---|---|---|---|---|
| ≥2 |
1 to 2 |
Total |
Percentage |
≤−2 |
−2 to −1 |
Total |
Percentage |
||
| log2 ratio | log2 ratio | ||||||||
| Metabolism | |||||||||
| Photosynthesis | 3 | 14 | 17 | 2.6 | 3 | 2 | 5 | 1.0 | |
| Cell wall | 4 | 11 | 15 | 2.3 | 1 | 3 | 4 | 0.8 | |
| Oil metabolism | 4 | 30 | 34 | 5.2 | 4 | 17 | 21 | 4.0 | |
| Carbohydrate metabolism | 4 | 67 | 71 | 10.9 | 16 | 38 | 54 | 10.3 | |
| Nucleic acid | 3 | 16 | 19 | 2.9 | 3 | 24 | 27 | 5.2 | |
| Amino acid and protein | 8 | 37 | 45 | 6.9 | 5 | 11 | 16 | 3.1 | |
| Growth and development | |||||||||
| Leaf and root development | 0 | 12 | 12 | 1.8 | 1 | 9 | 10 | 1.9 | |
| Shoot development | 2 | 2 | 4 | 0.6 | 0 | 0 | 0 | 0 | |
| Embryo/seed development | 1 | 11 | 12 | 1.8 | 1 | 9 | 10 | 1.9 | |
| Flower development | 5 | 7 | 12 | 1.8 | 2 | 3 | 5 | 1.0 | |
| Cell growth | 5 | 42 | 47 | 7.2 | 5 | 6 | 11 | 2.1 | |
| Hormone | 5 | 15 | 20 | 3.1 | 13 | 12 | 25 | 4.8 | |
| Stress/defense response | 9 | 40 | 49 | 7.6 | 27 | 76 | 103 | 19.7 | |
| Cell regulation | |||||||||
| Transcriptional regulation | 0 | 15 | 15 | 2.3 | 1 | 4 | 5 | 1.0 | |
| Signaling transduction | 6 | 34 | 40 | 6.2 | 10 | 23 | 33 | 6.3 | |
| Transport facilitation | 3 | 28 | 31 | 4.8 | 8 | 27 | 35 | 6.7 | |
| Others | 30 | 176 | 206 | 31.7 | 45 | 113 | 158 | 30.3 | |