TABLE 4.
Pathways enriched with genes uniquely regulated in RAW264.7 and TGEM cells upon KLA treatment at 4 h and 24 h
| KEGG Pathway Name | Total Number | Number Regulated | UP | DOWN | EF | p | Number Regulated | UP | DOWN | EF | p |
| RAW264.7 cells | 4 h (Regulated genes: 275) | 24 h (Regulated genes: 1,435) | |||||||||
| CAMs | 144 | 7 | 3 | 4 | 3.70 | 2.99E-03 | 13 | 8 | 5 | 1.32 | 1.89E-01 |
| Cell cycle | 122 | 7 | 2 | 5 | 4.37 | 1.16E-03 | 33 | 7 | 26 | 3.95 | 4.76E-12 |
| DNA replication | 35 | 4 | 0 | 4 | 8.70 | 1.11E-03 | 22 | 1 | 21 | 9.17 | 1.32E-17 |
| Glutathione metabolism | 53 | 1 | 1 | 0 | 1.44 | 5.04E-01 | 10 | 4 | 6 | 2.75 | 2.88E-03 |
| Lysosome | 122 | 3 | 2 | 1 | 1.87 | 2.16E-01 | 16 | 11 | 5 | 1.91 | 9.19E-03 |
| Mismatch repair | 22 | 3 | 0 | 3 | 10.38 | 2.87E-03 | 10 | 1 | 9 | 6.63 | 6.70E-07 |
| Pyrimidine metabolism | 93 | 3 | 0 | 3 | 2.46 | 1.24E-01 | 17 | 2 | 15 | 2.67 | 1.76E-04 |
| Systemic lupus erythematosus | 93 | 3 | 1 | 2 | 2.46 | 1.24E-01 | 26 | 13 | 13 | 4.08 | 3.91E-10 |
| TGEM cells | 4 h (Regulated genes: 1,303) | 24 h (Regulated genes: 969) | |||||||||
| Chemokine signaling pathway | 172 | 13 | 8 | 5 | 1.21 | 2.75E-01 | 19 | 12 | 7 | 2.39 | 4.02E-04 |
| ECM-receptor interaction | 84 | 8 | 5 | 3 | 1.53 | 1.51E-01 | 10 | 2 | 8 | 2.57 | 5.35E-03 |
| Focal adhesion | 197 | 25 | 19 | 6 | 2.04 | 5.57E-04 | 19 | 8 | 11 | 2.08 | 2.06E-03 |
| Glycerophospholipid metabolism | 78 | 13 | 8 | 5 | 2.68 | 9.90E-04 | 7 | 3 | 4 | 1.94 | 6.91E-02 |
| Jak-STAT signaling pathway | 145 | 15 | 14 | 1 | 1.66 | 3.67E-02 | 16 | 14 | 2 | 2.38 | 1.13E-03 |
| Lysosome | 122 | 12 | 5 | 7 | 1.58 | 7.76E-02 | 15 | 2 | 13 | 2.66 | 5.18E-04 |
| Phagosome | 161 | 15 | 11 | 4 | 1.50 | 7.71E-02 | 22 | 15 | 7 | 2.95 | 5.32E-06 |
| PPAR signaling pathway | 76 | 11 | 5 | 6 | 2.33 | 7.18E-03 | 15 | 7 | 8 | 4.26 | 1.73E-06 |
| Proteasome | 44 | 6 | 6 | 0 | 2.19 | 5.37E-02 | 12 | 12 | 0 | 5.89 | 4.84E-07 |
| Toll-like receptor signaling pathway | 96 | 17 | 14 | 3 | 2.84 | 8.19E-05 | 11 | 9 | 2 | 2.48 | 4.80E-03 |
EF: the enrichment factor of uniquely regulated genes for a pathway is the ratio of the fraction of such genes among all genes in this pathway over the fraction in the 20,932 genes examined. All selected pathways have a p-value less than 0.01 and the number of regulated genes in the pathway is at least 10 or the fold-change for RAW264.7 or TGEM cells is at least five (at 4 h or 24 h). ECM, extracellular matrix.