Table 5. Clusters of ontological categories regulated by antibodies targeting EGFR.
| Antibodies | By antibodies only | Both antibodies and kinase inhibitors | ||||||
| Suppressed | 255 genes | 112 genes | ||||||
| Enrichment Score: 9.80 | p-Val | Enrichment Score: 7.39 | p-Val | Enrichment Score: 3.85 | p-Val | |||
| intermediate filament cytoskeleton. | 1.E-08 | Intermediate filament protein, | 2.E-13 | response to steroid hormone stimulus. | 1.E-05 | |||
| Enrichment Score: 4.94 | ** | keratin filament. | 5.E-08 | S | response to hormone stimulus. | 1.E-04 | ||
| response to hormone stimulus. | 1.E-06 | Enrichment Score: 4.48 | Enrichment Score: 3.08 | |||||
| Enrichment Score: 4.08 | regulation of hair cycle. | 8.E-06 | regulation of cell migration. | 6.E-04 | ||||
| regulation of hair follicle development. | 2.E-05 | ** | regulation of epidermis development. | 6.E-04 | M | regulation of locomotion. | 1.E-03 | |
| Enrichment Score: 3.52 | Enrichment Score: 3.71 | Enrichment Score: 2.45 | ||||||
| hemopoiesis. | 2.E-04 | female gonad development. | 1.E-04 | hemopoiesis. | 2.E-03 | |||
| Enrichment Score: 3.24 | ** | sex differentiation. | 1.E-04 | immune system development. | 5.E-03 | |||
| P | regulation of phosphorylation. | 1.E-03 | Enrichment Score: 3.47 | Enrichment Score: 2.42 | ||||
| Enrichment Score: 3.22 | ovulation cycle process. | 1.E-04 | extracellular matrix binding. | 2.E-04 | ||||
| M | regulation of cell migration. | 3.E-04 | ** | ovulation cycle. | 1.E-04 | integrin binding. | 2.E-03 | |
| Enrichment Score: 3.11 | Enrichment Score: 3.47 | Enrichment Score: 2.34 | ||||||
| M | Cell structure and motility. | 6.E-03 | hair follicle development. | 3.E-04 | regulation, phosphate metabolic process. | 3.E-03 | ||
| Enrichment Score: 3.02 | ** | molting cycle process. | 3.E-04 | P | regulation of phosphorylation. | 1.E-02 | ||
| female gonad development. | 5.E-04 | Enrichment Score: 3.42 | Enrichment Score: 2.15 | |||||
| Enrichment Score: 3.01 | response to hormone stimulus. | 9.E-05 | positive regulation of cell migration. | 5.E-03 | ||||
| M | cell migration. | 5.E-04 | response to endogenous stimulus. | 2.E-04 | M | positive regulation of cell motion. | 7.E-03 | |
| Enrichment Score: 2.99 | Enrichment Score: 3.23 | Enrichment Score: 2.13 | ||||||
| hair cycle process. | 9.E-04 | reproductive process. | 3.E-04 | Intermediate filament protein. | 2.E-03 | |||
| ** | gamete generation. | 3.E-03 | Type II keratin. | 4.E-03 | ||||
| Enrichment Score: 2.51 | ||||||||
| hemopoiesis. | 2.E-03 | |||||||
| ** | immune system development. | 5.E-03 | ||||||
| Enrichment Score: 2.14 | ||||||||
| cell migration. | 5.E-03 | |||||||
| M | cell motility. | 8.E-03 | ||||||
| Enrichment Score: 2.08 | ||||||||
| blood vessel morphogenesis. | 5.E-03 | |||||||
| ** | vasculature development. | 1.E-02 | ||||||
| Enrichment Score: 2.04 | ||||||||
| erythrocyte differentiation. | 4.E-03 | |||||||
| ** | erythrocyte homeostasis. | 6.E-03 | ||||||
| Induced | 640 genes | 122 genes | ||||||
| Enrichment Score: 10.27 | Enrichment Score: 10.03 | Enrichment Score: 1.44 | ||||||
| contractile fiber. | 3.E-12 | contractile fiber. | 5.E-12 | tissue regeneration. | 1.E-02 | |||
| Enrichment Score: 4.98 | ∼∼ | myofibril. | 1.E-10 | regeneration. | 4.E-02 | |||
| glycosaminoglycan binding. | 3.E-04 | Enrichment Score: 5.57 | Enrichment Score: 1.40 | |||||
| Enrichment Score: 2.53 | polysaccharide binding. | 4.E-07 | apoptosis. | 7.E-02 | ||||
| myosin filament. | 8.E-04 | glycosaminoglycan binding. | 1.E-04 | A | programmed cell death. | 7.E-02 | ||
| Enrichment Score: 2.41 | Enrichment Score: 5.12 | Enrichment Score: 1.24 | ||||||
| lung development. | 5.E-03 | muscle myosin complex. | 2.E-06 | response to nutrient. | 3.E-02 | |||
| Enrichment Score: 2.14 | ∼∼ | myosin II complex. | 4.E-06 | response to extracellular stimulus. | 9.E-02 | |||
| E | neural crest cell differentiation. | 5.E-03 | Enrichment Score: 3.64 | |||||
| Enrichment Score: 2.05 | locomotory behavior. | 2.E-04 | ||||||
| skeletal muscle contraction. | 2.E-03 | M | chemotaxis. | 2.E-04 | ||||
| Enrichment Score: 1.96 | Enrichment Score: 3.64 | |||||||
| myofibril assembly. | 9.E-03 | blood vessel development. | 6.E-05 | |||||
| Enrichment Score: 1.86 | vasculature development. | 8.E-05 | ||||||
| M | cell migration. | 1.E-02 | Enrichment Score: 2.52 | |||||
| Myosin tail. | 1.E-05 | |||||||
| ∼∼ | Heavy chain of myosin. | 9.E-04 | ||||||
| Enrichment Score: 2.19 | ||||||||
| anterior/posterior pattern formation. | 5.E-03 | |||||||
| pattern specification process. | 1.E-02 | |||||||
| Enrichment Score: 2.17 | ||||||||
| skeletal muscle contraction. | 1.E-03 | |||||||
| ∼∼ | troponin complex. | 1.E-02 | ||||||
| Enrichment Score: 2.10 | ||||||||
| myofibril assembly. | 7.E-03 | |||||||
| ∼∼ | actomyosin structure organization. | 2.E-02 |
Panels pertain to the 255 and 640 genes specifically regulated by the antibodies, and to 72+40 and 64+58 genes shared by the antibodies and kinase inhibitors (see Fig. 3). Asterisks mark the ontological categories related to tissue development, tildes the categories related to contractility, specifically induced by the antibodies. The letter markings are as in the legend of Table 2.