Table 8.
Pairs of Biological Processes With High Frequency of Coclassifications to the Same Gene
| Pairs of processes | A Genes with coclassification | B Genes with coclassification and coannotation | C Genes with coclassification, but no coannotation | D Genes with coannotation but no coclassification | E Genes without coclassification and coannotation | F P-value |
| DNA metabolism–cell cycle | 25 | 12 | 13 | 0 | 219 | 7.36E-14 |
| Transcription–oncogenesis | 22 | 5 | 17 | 2 | 220 | 7.08E-05 |
| Cell organization and biogenesis–cell cycle | 18 | 13 | 5 | 3 | 223 | 3.58E-15 |
| Transcription–cell proliferation | 18 | 10 | 8 | 2 | 224 | 1.59E-11 |
| Transcription–cell cycle | 18 | 7 | 11 | 2 | 224 | 1.13E-07 |
| Cell motility–defense (immune) response | 16 | 11 | 5 | 2 | 226 | 9.00E-14 |
| DNA metabolism–transcription | 15 | 9 | 6 | 1 | 228 | 6.72E-12 |
| Oncogenesis–cell proliferation | 14 | 5 | 9 | 3 | 227 | 1.47E-05 |
| Defense (immune) response–cell proliferation | 13 | 7 | 6 | 4 | 227 | 5.52E-08 |
| Transcription–intracellular signaling cascade | 13 | 2 | 11 | 3 | 228 | 2.40E-02 |
| Cell motility–cell adhesion | 12 | 10 | 2 | 1 | 231 | 4.21E-15 |
| Protein metabolism and modification–stress response | 12 | 5 | 7 | 0 | 232 | 1.15E-07 |
| Protein metabolism and modification–cell organization and biogenesis | 11 | 6 | 5 | 0 | 233 | 1.68E-09 |
| Cell motility–cell proliferation | 11 | 6 | 5 | 2 | 231 | 4.53E-08 |
| Cell proliferation–intracellular signaling cascade | 11 | 4 | 7 | 1 | 232 | 1.12E-05 |
| Transcription–lipid metabolism | 11 | 1 | 10 | 0 | 233 | 4.51E-02 |
Pairs of biological processes that were classified to the same gene for at least 11 different genes are shown.
The dependence between the coannotations and the coclassifications was tested with Fisher's exact test (see, e.g., Everitt 1992). A 2 × 2 contingency table was constructed for each process pair, and values in this table appear in columns B–F. The number of genes without a coannotation and a coclassification for a pair was computed by subtracting numbers in the other three columns from the total number of genes with at least 2 annotations or classifications. The P-value appears in column F. All but two pairs (transcription–intracellular signaling cascade and transcription–lipid metabolism) were significant at the 0.0001 level.