Table 2.
Functional Classification of Rapidly and Slowly Evolving Nematode Genes
| GO description (hierarchical biological function) | Fraction | P-value | GO term |
|---|---|---|---|
| Rapidly evolving genes (upper 10%) | |||
| Regulation of transcription, DNA-dependent | 45/753 | 4.27E-005 | GO:0006355 |
| Regulation of transcription | 45/753 | 5.72E-005 | GO:0045449 |
| Transcription, DNA-dependent | 45/753 | 7.63E-005 | GO:0006351 |
| Nucleobase, nucleoside, nucleotide and nucleic acid metabolism | 53/753 | 0.036752 | GO:0006139 |
| Slowly evolving genes (lower 10%) | |||
| Embryogenesis and morphogenesis | 107/753 | 9.30E-018 | GO:0007345 |
| Physiological processes | 268/753 | 4.04E-012 | GO:0007582 |
| Protein biosynthesis | 48/753 | 1.82E-011 | GO:0006412 |
| Cellular process | 132/753 | 4.89E-011 | GO:0009987 |
| Biosynthesis | 63/753 | 5.25E-011 | GO:0009058 |
| Small GTPase-mediated signal transduction | 23/753 | 7.89E-011 | GO:0007264 |
| Cell growth and/or maintenance | 94/753 | 3.33E-008 | GO:0008151 |
| Intracellular protein transport | 15/753 | 9.92E-006 | GO:0006886 |
| Development | 89/753 | 1.31E-005 | GO:0007275 |
| Metabolism | 189/753 | 2.17E-005 | GO:0008152 |
| Protein metabolism | 92/753 | 3.01E-005 | GO:0019538 |
| Cell organization and biogenesis | 20/753 | 8.09E-005 | GO:0016043 |
| Transport | 68/753 | 0.000318 | GO:0006810 |
| Reproduction | 43/753 | 0.000377 | GO:0000003 |
| Nucleosome assembly | 8/753 | 0.001020 | GO:0006334 |
| Intracellular signaling cascade | 30/753 | 0.001910 | GO:0007242 |
| Signal transduction | 38/753 | 0.002579 | GO:0007165 |
| Two-component signal transduction system (phosphorelay) | 7/753 | 0.002746 | GO:0000160 |
| Main pathways of carbohydrate metabolism | 11/753 | 0.003427 | GO:0006092 |
| Energy derivation by oxidation of organic compounds | 12/753 | 0.004455 | GO:0015980 |
| Energy pathways | 12/753 | 0.004455 | GO:0006091 |
| DNA packaging | 8/753 | 0.010077 | GO:0006323 |
| Establishment and/or maintenance of chromatin architecture | 8/753 | 0.010077 | GO:0006325 |
| Chromatin assembly/disassembly | 8/753 | 0.010077 | GO:0006333 |
| Cell communication | 40/753 | 0.012676 | GO:0007154 |
| mRNA splicing | 5/753 | 0.016747 | GO:0006371 |
Upper and lower 10% is scaled according to dN. Note the entire hierarchy of Gene Ontology terms for each gene was used when assessing functional overrepresentation; therefore, categories often contain the same sets of genes. All P-values are Bonferroni-corrected.