Table 2.
Functional enrichment of each network in Fig. 6 as per gene ontology (GO) using the whole genome as a statistical background
| Pathway ID | Pathway description | Observed gene count | False discovery rate |
|---|---|---|---|
| Time point 1: 1 day | |||
| Biological process (GO) | |||
| None | |||
| Cellular component (GO) | |||
| None | |||
| Time point 2: 3 days | |||
| Biological process (GO) | |||
| GO.0008152 | Metabolic process | 111 | 0.0154 |
| GO.0006807 | Nitrogen compound metabolic process | 73 | 0.0212 |
| GO.0034138 | Toll-like receptor 3 signalling pathway | 7 | 0.0212 |
| GO.0035666 | TRIF-dependent toll-like receptor signalling pathway | 7 | 0.0212 |
| GO.0044238 | Primary metabolic process | 100 | 0.0212 |
| GO.1901564 | Organonitrogen compound metabolic process | 32 | 0.0212 |
| GO.0002224 | Toll-like receptor signalling pathway | 8 | 0.0246 |
| GO.0071704 | Organic substance metabolic process | 100 | 0.0269 |
| GO.0006950 | Response to stress | 51 | 0.0299 |
| GO.0002221 | Pattern recognition receptor signalling pathway | 8 | 0.0404 |
| GO.0010033 | Response to organic substance | 40 | 0.0404 |
| GO.0034142 | Toll-like receptor 4 signalling pathway | 7 | 0.0404 |
| Cellular process (GO) | |||
| GO.0005576 | Extracellular region | 73 | 8.21E-06 |
| GO.0044421 | Extracellular region part | 62 | 8.63E-05 |
| GO.0031982 | Vesicle | 58 | 0.000291 |
| GO.0031988 | Membrane-bounded vesicle | 57 | 0.000291 |
| GO.0070062 | Extracellular exosome | 49 | 0.000291 |
| GO.0034663 | Endoplasmic reticulum chaperone complex | 3 | 0.0227 |
| GO.0016222 | Procollagen-proline 4-dioxygenase complex | 2 | 0.0385 |
| GO.0044444 | Cytoplasmic part | 86 | 0.0385 |
| GO.0042470 | Melanosome | 6 | 0.0421 |
| Time point 3: 7days | |||
| Biological process (GO) | |||
| GO.0001649 | Osteoblast differentiation | 8 | 0.00153 |
| GO.0044710 | Single-organism metabolic process | 40 | 0.00584 |
| GO.0001503 | Ossification | 9 | 0.0122 |
| GO.0008152 | Metabolic process | 65 | 0.0122 |
| GO.0044712 | Single-organism catabolic process | 16 | 0.0122 |
| GO.0006559 | L-phenylalanine catabolic process | 3 | 0.0222 |
| GO.0006570 | Tyrosine metabolic process | 3 | 0.0222 |
| GO.0071704 | Organic substance metabolic process | 60 | 0.0222 |
| GO.0048731 | System development | 33 | 0.0292 |
| GO.0031638 | Zymogen activation | 6 | 0.0318 |
| GO.0048856 | Anatomical structure development | 36 | 0.0318 |
| GO.0048513 | Organ development | 27 | 0.038 |
| GO.0051604 | Protein maturation | 8 | 0.038 |
| GO.0030099 | Myeloid cell differentiation | 7 | 0.0418 |
| Cellular process (GO) | |||
| GO.0005576 | Extracellular region | 41 | 0.000855 |
| GO.0005615 | Extracellular space | 20 | 0.000855 |
| GO.0044421 | Extracellular region part | 38 | 0.000855 |
| GO.0070062 | Extracellular exosome | 31 | 0.000855 |
| GO.0043227 | Membrane-bounded organelle | 73 | 0.00652 |
| GO.0031982 | Vesicle | 33 | 0.0112 |
| GO.0031988 | Membrane-bounded vesicle | 32 | 0.0139 |
| GO.0043226 | Organelle | 73 | 0.0367 |
| Time point 4: 14days | |||
| Biological process (GO) | |||
| GO.0042738 | Exogenous drug catabolic process | 4 | 0.0393 |
| GO.0044710 | Single-organism metabolic process | 42 | 0.0393 |
| Cellular process (GO) | |||
| None | |||