Table 1. Top 10 gene ontology (GO) terms in the biological process category affected by gamma irradiation.
| GO-ID | GO-term | ka | P Value | Cb |
|---|---|---|---|---|
| Up-regulation | ||||
| GO:0016042 | Lipid catabolic process | 21/1151 (1.8%) | 0.0001 | 275/27416 (1%) |
| GO:0019953 | Sexual reproduction | 6/1151 (0.5%) | 0.0017 | 227/ 27416 (0.8%) |
| GO:0071281 | Cellular response to iron ion | 7/1151 (0.6%) | 0.0018 | 35/27416 (0.1%) |
| GO:0031146 | SCF-dependent proteasomal ubiquitin-dependent protein catabolic process | 13/1151 (1.1%) | 0.0036 | 16/27416 (0.1%) |
| GO:0050832 | Defense response to fungus | 25/1151 (2.2%) | 0.0060 | 561/27416 (2%) |
| GO:0055114 | Oxidation-reduction process | 61/1151 (5.3%) | 0.0078 | 5166/27416 (18.8%) |
| GO:0006417 | Regulation of translation | 7/1151 (0.6%) | 0.0327 | 252/27416 (0.9%) |
| GO:0019745 | Pentacyclic triterpenoid biosynthetic process | 3/1151 (0.3%) | 0.0407 | 13/27416 (0.05%) |
| GO:0071281 | Cellulose catabolic process | 4/1151 (0.3%) | 0.0524 | 27/27416 (0.1%) |
| GO:0043086 | Negative regulation of catalytic activity | 6/1151 (0.5%) | 0.0558 | 401/27416 (1.5%) |
| Down-regulation | ||||
| GO:0000165 | MAPK cascade | 12/1089 (1.1%) | 0.0001 | 129/27416 (0.5%) |
| GO:0009607 | Response to biotic stimulus | 10/1089 (0.9%) | 0.0001 | 1983/27416 (7.2%) |
| GO:0016042 | Lipid catabolic process | 16/1089 (1.5%) | 0.0019 | 275/27416 (1%) |
| GO:0007166 | Cell surface receptor signaling pathway | 8/1089 (0.7%) | 0.0028 | 375/27416 (1.4%) |
| GO:0006468 | Protein phosphorylation | 51/1089 (4.7%) | 0.0043 | 3184/27416 (11.6%) |
| GO:0006855 | Drug transmembrane transport | 9/1089 (0.8%) | 0.0059 | 100/27416 (0.4%) |
| GO:0009308 | Amine metabolic process | 4/1089 (0.4%) | 0.0078 | 274/27416 (1.0%) |
| GO:0006351 | Transcription, DNA-templated | 95/1089 (8.7%) | 0.0084 | 5502/27416 (20.1%) |
| GO:0050832 | Defense response to fungus | 30/1089 (2.8%) | 0.0093 | 561/27416 (2%) |
| GO:0032259 | Methylation | 17/1089 (1.6%) | 0.0094 | 907/27416 (3.3%) |
Gene ontology analysis was performed using radiation-responsive transcripts showing a more than 2-fold difference in expression between the WT and ddm1-2 mutant after gamma irradiation. GO terms in the table were selected based on P values in each GO category.
aCluster frequency of a given GO term in the differentially expressed genes selected. Numbers in parentheses indicate percentages.
bThe total frequency of a given GO term in all annotations in the Arabidopsis genome.