Table 1.
Pruned KEGG hierarchy used for our classification model
| Level 1 | Level 2 | Level 3 |
|---|---|---|
| Metabolism | — | — |
| Genetic Inf.Proc. | Transcription (–) | — |
| Translation | — | |
| Folding, sorting, degradation | — | |
| Env. Inf. Proc. | Membrane transport (–) | — |
| Signal transduction | MAPK pathway | |
| ErbB pathway (2, 0) | ||
| Wnt pathway (2) | ||
| Notch pathway | ||
| Hedgehog pathway | ||
| TGF-β pathway (3, 2) | ||
| VEGF pathway | ||
| Jak-STAT pathway | ||
| Calcium signaling (4) | ||
| Phosphatidylinositol system | ||
| mTOR signaling (–) | ||
| Signaling molecules and interaction | Neuroactive ligand-receptor interaction | |
| Cytokine–cytokine receptor interaction | ||
| ECM–receptor interaction | ||
| Cell adhesion molecules | ||
| Cellular Processes | Cell motility | — |
| Cell growth and death | Cell cycle | |
| Apoptosis | ||
| p53pathway | ||
| Cell communication | Focal adhesion | |
| Adherens junction | ||
| Tight junction | ||
| Gap junction | ||
| Endocrine system | Insulin pathway | |
| Adipocytokine pathway | ||
| PPAR pathway | ||
| GnRH pathway | ||
| Melanogenesis | ||
| Immune system | Hematopoietic cell lineage | |
| Complement and coagulation cascades | ||
| Toll-like receptor pathway | ||
| Natural killer cell-mediated cytotoxicity | ||
| Antigen processing and presentation | ||
| T-cell receptor signaling | ||
| B-cell receptor signaling | ||
| Fc-ɛ RI pathway | ||
| Leukocyte transendothelial migration | ||
| Nervous system | Long-term potentiation | |
| Long-term depression | ||
| Sensory system | Olfactory transduction (–) | |
| Taste transduction (–) | ||
| Development | — |
Hierarchy branches marked with ‘–’ are left out in the cross-validation procedure, but are included in the final model. For signaling pathways the number in brackets indicate the number of connected pathway components. The first number refers to the number of connected pathway components used in the final model, and the second (italic) to the number used in the cross-validation procedure.