Table 2.
Functional Classification by COG Analysis of Genes That Are Upregulated or Downregulated at Least Twofold in the udt1-1 Anthers
| Function | Down | I | II | III | Up | VI | V | Total |
|---|---|---|---|---|---|---|---|---|
| Information storage and processing | ||||||||
| Translation/ribosomal structure/biogenesis | 14 | 0 | 3 | 11 | 2 | 0 | 2 | 16 |
| RNA processing/modification | 14 | 2 | 5 | 7 | 4 | 2 | 2 | 18 |
| Transcriptional regulation | 62 | 10 | 31 | 21 | 6 | 1 | 5 | 68 |
| Replication/recombination/repair | 12 | 3 | 4 | 5 | 3 | 0 | 3 | 15 |
| Chromatin structure/dynamics | 5 | 2 | 0 | 3 | 0 | 0 | 0 | 5 |
| Cellular processing and signaling | ||||||||
| Cell cycle/cell division/chromosome partitioning | 8 | 5 | 3 | 0 | 2 | 0 | 2 | 10 |
| Defense mechanisms | 20 | 0 | 13 | 7 | 5 | 3 | 2 | 25 |
| Signal transduction mechanisms | 52 | 6 | 23 | 23 | 19 | 6 | 13 | 71 |
| Cell wall/membrane/envelope biogenesis | 9 | 1 | 3 | 5 | 7 | 0 | 7 | 16 |
| Cytoskeleton | 4 | 3 | 0 | 1 | 2 | 1 | 1 | 6 |
| Extracellular structure | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 1 |
| Intracellular trafficking/secretion/vesicular transport | 12 | 1 | 3 | 8 | 1 | 0 | 1 | 13 |
| Posttranslational modification/protein turnover/chaperones | 67 | 10 | 36 | 21 | 21 | 8 | 13 | 98 |
| Metabolism | ||||||||
| Energy production/conversion | 12 | 2 | 4 | 6 | 4 | 0 | 4 | 16 |
| Carbohydrate transport/metabolism | 34 | 5 | 22 | 7 | 14 | 5 | 9 | 48 |
| Amino acid transport/metabolism | 11 | 4 | 5 | 2 | 8 | 3 | 5 | 19 |
| Nucleotide transport/metabolism | 5 | 3 | 2 | 0 | 0 | 0 | 0 | 5 |
| Coenzyme transport/metabolism | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 1 |
| Lipid transport/metabolism | 41 | 3 | 20 | 18 | 5 | 1 | 4 | 46 |
| Inorganic ion transport/metabolism | 13 | 0 | 7 | 6 | 6 | 5 | 1 | 19 |
| Secondary metabolites/biosynthesis/transport/metabolism | 26 | 8 | 11 | 7 | 10 | 3 | 7 | 36 |
| Poorly characterized | ||||||||
| General function prediction only | 68 | 15 | 32 | 21 | 27 | 9 | 18 | 89 |
| Hypothetical protein | 469 | 78 | 273 | 118 | 119 | 34 | 85 | 588 |
| Total | 958 | 157 | 402 | 299 | 267 | 82 | 185 | 1225 |
COGs (http://www.ncbi.nlm.nih.gov/COG/old/) were delineated by comparing protein sequences encoded in 43 complete genomes. I, II, III, IV, and V are groups I to V in Figure 8.