Table 2.
Functional enrichment of Calu-3 clusters.
| Cluster | Top biological functions enrichment within each cluster | Predictive abilitya | ||||
|---|---|---|---|---|---|---|
| Functional Pathways | p-valueb | # molecules | Calu-3 | Macaque | Mouse | |
| 1 | None | 0.89* | 0.23 | 0.98* | ||
| 2 | cell surface receptor linked signal transduction | 1.56E-02 | 6 | 0.88* | -0.44 | 0.28 |
| activation of eukaryotic cells | 1.56E-02 | 9 | ||||
| developmental process of antigen presenting cells | 1.56E-02 | 5 | ||||
| aggregation of blood cells | 3.09E-02 | 4 | ||||
| growth of leukocytes | 3.09E-02 | 4 | ||||
| replication of virus | 3.09E-02 | 6 | ||||
| 3 | binding of blood cells | 5.22E-07 | 16 | 0.96* | 0.44 | 0.98* |
| activation of granulocytes | 5.28E-07 | 11 | ||||
| stimulation of normal cells | 6.52E-07 | 13 | ||||
| inflammatory response | 6.56E-07 | 23 | ||||
| maturation of leukocytes | 6.98E-07 | 14 | ||||
| chemotaxis of cells | 9.01E-07 | 20 | ||||
| activation of monocytes | 9.65E-07 | 9 | ||||
| activation of phagocytes | 9.65E-07 | 13 | ||||
| activation of T lymphocytes | 1.09E-06 | 16 | ||||
| immune response | 2.82E-06 | 28 | ||||
| 4 | developmental process of blood cells | 2.38E-04 | 41 | 0.99* | -0.13 | -0.99* |
| function of lymphatic system cells | 1.95E-03 | 5 | ||||
| recruitment of normal cells | 4.40E-03 | 14 | ||||
| differentiation of lymphocytes | 4.47E-03 | 20 | ||||
| function of leukocytes (including function of granulocytes) | 5.51E-03 | 9 | ||||
| quantity of leukocytes | 5.76E-03 | 25 | ||||
| 5 | development of intercellular junctions | 8.80E-04 | 10 | 0.83 | -0.21 | 0.92* |
| 6 | cell division process | 2.98E-03 | 253 | 0.96 | 0.25 | -0.97* |
| metabolism of carbohydrate | 3.52E-02 | 80 | ||||
| transactivation | 3.52E-02 | 127 | ||||
| cell death of connective tissue cells | 3.83E-02 | 66 | ||||
| modification of DNA | 5.02E-02 | 58 | ||||
| 7 | secretion of cytokine/recognition of cells | 2.97E-02 | 1 | 0.64 | 0.32 | 0.58 |
| methylation of protein or DNA | 2.97E-02 | 1 | ||||
| 8 | accumulation of calcium | 3.13E-02 | 6 | 0.97* | 0.68* | -0.86 |
| contraction of tissue | 3.69E-02 | 16 | ||||
| neurotransmission | 3.78E-02 | 20 | ||||
| blood pressure | 3.78E-02 | 13 | ||||
| response of cells | 3.78E-02 | 24 | ||||
| synthesis of cyclic AMP | 3.78E-02 | 7 | ||||
| 9 | None | 0.72 | 0.25 | 0.86 | ||
| 10 | transcription | 1.67E-08 | 150 | 0.99* | 0.72* | 0.33 |
| protein kinase cascade (including IKKB/NFkB cascades) | 4.25E-03 | 33 | ||||
| activation of cyclin-dependent protein kinase | 5.06E-03 | 11 | ||||
| developmental process of organism | 1.62E-02 | 81 | ||||
| cell cycle progression | 2.79E-02 | 67 | ||||
| activation of protein | 4.00E-02 | 20 | ||||
a asterisk indicates statistical significance versus random for predictive ability
b Benjamini-Hochberg adjusted