Table IV. Functional classification of DEGs in developing seeds of tt2-5 plants at 16 DAP.
Functional classification of the DEGs was performed using the biological process category of Arabidopsis Gene Ontology (http://www.geneontology.com). Percentage (far-right column) refers to the ratio of genes of each functional category relative to total up-regulated or down-regulated DEGs identified in the microarray experiment. The DEGs with log2 ratios greater than 1.00 or less than −1.00 (only GO Slim IDs with P values equal to or less than 0.5) were listed.
| Category | Up-regulated DEGs |
Down-regulated DEGs |
||||||
|---|---|---|---|---|---|---|---|---|
| ≥2 | 1–2 | Total | Percentage | ≤−2 | −2 to −1 | Total | Percentage | |
| Log2 ratio | ||||||||
| Metabolism | ||||||||
| Flavonoid metabolism | 0 | 4 | 4 | 1.3 | ||||
| Lipid metabolism | 2 | 21 | 23 | 8.0 | 1 | 6 | 7 | 1.5 |
| Carbohydrate metabolism | 0 | 24 | 24 | 8.4 | 9 | 39 | 48 | 10.5 |
| Nucleic acid | 0 | 7 | 7 | 2.4 | 4 | 28 | 32 | 7.0 |
| Amino acid and protein | 1 | 30 | 31 | 10.7 | 6 | 75 | 81 | 17.7 |
| Growth and development | ||||||||
| Leaf and root development | 0 | 1 | 1 | 0.3 | 0 | 9 | 9 | 2.0 |
| Embryo and seed development | 2 | 4 | 6 | 2.1 | 0 | 23 | 23 | 5.0 |
| Flower development | 0 | 6 | 6 | 2.1 | 1 | 11 | 12 | 2.6 |
| Cell growth | 1 | 19 | 20 | 6.9 | 2 | 18 | 20 | 4.4 |
| Cytoskeleton structure | 1 | 9 | 10 | 3.5 | 2 | 18 | 20 | 4.4 |
| Hormone | 0 | 11 | 11 | 3.8 | 4 | 13 | 17 | 3.7 |
| Stress/defense response | 5 | 66 | 71 | 24.6 | 13 | 65 | 78 | 17.1 |
| Cell regulation | ||||||||
| Transcriptional regulation | 0 | 2 | 2 | 0.7 | 2 | 40 | 42 | 9.2 |
| Signaling transduction | 0 | 15 | 15 | 5.2 | 1 | 27 | 28 | 6.1 |
| Transport facilitation | 0 | 39 | 39 | 13.5 | 1 | 12 | 13 | 2.8 |
| Other | 0 | 19 | 19 | 6.6 | 2 | 25 | 27 | 5.9 |