Table 2.
List of GO categories hypothesized to be related to aginga.
| GOb | Name | n | Ka/Ks | p-value highc | p-value lowc |
|---|---|---|---|---|---|
| Biological Process GO categories related to DNA repair or processing | |||||
| 0006974 | response to DNA damage stimulus | 148 | 0.27 | 9.0E−07 | 1 |
| 0006281 | DNA repair | 121 | 0.26 | 1.1E−04 | 1 |
| 0042770 | DNA damage response, signal transduction | 15 | 0.38 | 3.2E−04 | 1 |
| 0006306 | DNA methylation | 11 | 0.087 | 1 | 1.8E−04 |
| 0006471 | protein amino acid ADP-ribosylation | 10 | 0.36 | 3.3E−03 | 1 |
| 0006298 | mismatch repair | 9 | 0.32 | 5.8E−03 | 1 |
| 0006282 | regulation of DNA repair | 5 | 1.1 | 4.6E−08 | 1 |
| 0030330 | DNA damage response, signal transduction by p53 class mediator | 3 | 1.4 | 1.3E−13 | 1 |
| Other Biological Process GO categories | |||||
| 0006950 | response to stress | 594 | 0.27 | 1.1E−17 | 1 |
| 0006118 | electron transport | 216 | 0.23 | 0.039 | 0.96 |
| 0006511 | ubiquitin-dependent protein catabolism | 82 | 0.20 | 0.65 | 0.38 |
| 0006512 | ubiquitin cycle | 70 | 0.10 | 1 | 4.6E−11 |
| 0006979 | response to oxidative stress | 27 | 0.16 | 0.95 | 0.066 |
| 0007254 | JNK cascade | 23 | 0.12 | 1 | 2.6E−04 |
| 0006120 | mitochondrial electron transport, NADH to ubiquinone | 12 | 0.12 | 0.97 | 0.054 |
| 0001666 | response to hypoxia | 5 | 0.043 | 1 | 0.014 |
| Molecular Function GO categories | |||||
| 0005179 | hormone activity | 77 | 0.37 | 1.2E−08 | 1 |
| 0004840 | ubiquitin conjugating enzyme activity | 44 | 0.094 | 1 | 5.1E−06 |
| 0003773 | heat shock protein activity | 29 | 0.080 | 1 | 4.4E−08 |
| 0003684 | damaged DNA binding | 24 | 0.37 | 8.5E−05 | 1 |
| 0005184 | neuropeptide hormone activity | 15 | 0.39 | 4.8E−03 | 1 |
| 0004364 | glutathione transferase activity | 14 | 0.50 | 4.5E−04 | 1 |
| 0004407 | histone deacetylase activity | 8 | 0.14 | 0.95 | 0.082 |
Although the topic remains highly contentious, and the mechanisms of aging in primates are largely unknown, we selected GO categories encompassing mechanisms or functions typically associated with aging in model systems or hypothesized to be related to aging (see Materials and Methods).
Subcategories without evidence of positive selection or rapid evolution were omitted unless they were deemed as potentially relevant to aging.
This binomial probability is not used to directly reject the null hypothesis of a given GenAge category not undergoing rapid (probability high) or slow (probability low) evolution but provides a metric to identify categories potentially undergoing rapid or slow evolution. The test statistic threshold was set at 0.001 (see Materials and Methods).