TABLE 3.
Biological processes specifically associated with KCl response genes
| GO term annotationa | No. of genes | Frequency (%)b |
|---|---|---|
| Genes with increased expression after 15 min | ||
| Cytoplasm organization and biogenesis (184) | 4 | 13 |
| Ribosome biogenesis (148) | 4 | 13 |
| rRNA processing (122) | 4 | 13 |
| Transcription from RNA Pol II promoter (24) | 2 | 7 |
| Genes with reduced expression after 15 min | ||
| ATP synthesis coupled electron transport (17) | 2 | 3 |
| Electron transport (117) | 4 | 5 |
| Energy derivation by oxidation of organic compounds (101) | 5 | 6 |
| Generation of precursor metabolites and energy (249) | 9 | 12 |
| Nitrogen compound metabolism (249) | 3 | 4 |
| Genes with increased expression after 60 min | ||
| Carbohydrate metabolism (184) | 11 | 14 |
| Cation transport (101) | 5 | 6 |
| Cell communication (258) | 9 | 11 |
| Generation of precursor metabolites and energy (249) | 7 | 9 |
| M phase (309) | 9 | 11 |
| Meiosis (143) | 8 | 10 |
| Negative regulation of cellular metabolism (86) | 5 | 6 |
| Nicotinamide metabolism (24) | 3 | 4 |
| Nucleotide metabolism (107) | 5 | 6 |
| Oxidoreduction coenzyme metabolism (39) | 4 | 5 |
| Positive regulation of biological process (44) | 2 | 3 |
| Protein-mitochondrial targeting (42) | 3 | 4 |
| Regulation of enzyme activity (46) | 2 | 3 |
| Regulation of transcription by glucose (10) | 2 | 3 |
| Response to abiotic stimulus (102) | 5 | 6 |
| Response to nutrients (16) | 3 | 4 |
| Response to stimulus (388) | 13 | 16 |
| Signal transduction (232) | 8 | 10 |
| Genes with reduced expression after 60 min | ||
| Carbohydrate transport (24) | 2 | 5 |
| Cell separation during cytokinesis (22) | 2 | 5 |
| Cytokinesis (125) | 5 | 13 |
| Monosaccharide transport (7) | 2 | 5 |
| Transport (747) | 12 | 30 |
a
Biological-process GO terms specifically associated with genes with a ≥3-fold reproducible change in expression compared to the expression in untreated cells (P ≤ 0.05). The number of S. pombe genes annotated with each term is shown in parentheses. Pol, polymerase.
b
Percentage of GO-process annotated genes in each expression group that are annotated with each specific GO term. The numbers of GO process-annotated genes analyzed for each expression group were 30 and 77 and 80, and 40 for the increased and decreased expression groups at 15 and 60 min, respectively.