Table 3.
Expression and phosphorylation of proteins associated with the non-canonical nuclear factor κB (NF-κB) pathway or involved in the negative regulation of NF-κB. Expression and phosphorylation of regulatory proteins were assessed in TNF long term-incubated and naïve monocytes using microarray (mRNA; derived from analyses presented in [7]) and LC-MS/MS (protein, phosphorylation) analyses. Significantly increased ratios among TNF long term-incubated (48 h TNF) and naïve (48 h medium) cells are shown. Among the microarray and the phosphopeptide ratios, multiple values indicated different probes for one gene or different phosphopeptides of one protein (phosphoproteome).
| Protein Name | Microarray Ratio | Proteome Ratio | Phosphopeptide Ratio |
|---|---|---|---|
| IDO1 | 55.9 | 19.4 | - |
| SIGLEC10 | 133.3 | 16.3 | 6.2 |
| NFKB2 | 4; 4.1; 4.2; 4.3 | 15.8 | 4.6 |
| KYNU | 4.8; 6.3 | 8.1 | - |
| RELB | 8.1 | 7 | 16.8 |
| CAST | 0.7; 0.9; 1; 1.2 | 4.6 | 13.2; 12.2; 3.4 |
| TNFAIP2 | 3.1 | 3.75 | - |
| C/EBPB | 1.7; 1.8; 1.9; 2.9 | 3.4 | - |
| TRAFD1/FLN29 | 4.5 | 3 | 2 |
| USP15 | 0.9; 1; 1.4 | 2.6 | - |
| NFKB1 | 1.8; 1.9; 2 | 2.5 | - |
| TRAF1 | 6.6; 11.2 | - | 16 |
| NCOR1 | 0.7; 1; 1.2; 1.7 | - | 12.9; 7.75 |
| SIRT1 | 0.7 | - | 10.2; 5.4 |
| PML | 2.4; 2.5; 2.6; 2.9; 3.9; 6 | - | 8.25 |
| DCP1A | 1.4 | - | 7.9 |
| NCOR2/SMRT | 8.8 | - | 7.4; 7.4 |
| NDRG1 | 4.8; 10.6 | - | 6.2; 4.7; 4.2; 4.0 |
| HSF1 | 1 | - | 4.0; 4.0 |
| TP53BP1 | 1.2 | - | 2.1 |