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 |
[i] Pairs of biological processes that were classified to the same gene for at least 11 different genes are shown.
[ii] 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. TheP-value appears in column F. All but two pairs (transcription–intracellular signaling cascade and transcription–lipid metabolism) were significant at the 0.0001 level.