Table 1.
Neutrophil signatures in DEGs and IPA USRs.
| DEG (q < 0.05) | Fold change | FDR | Activity | |
|---|---|---|---|---|
| Cxcl2 | 2.42 | 3.1E-02 | ↑ neut. recruitment (91, 92) | |
| IL-6 | 1.93 | 4.9E-02 | ↑ neut. survival and migration (93, 94) | |
| IL-1β | 1.71 | 4.0E-04 | ↑ neut. recruitment, survival, and activity (95–98) | |
| Cyr61 | 1.52 | 1.2E-03 | ↑ neut. infiltration (99) | |
| Ccr1 | 1.37 | 1.5E-02 | ↑ neut. migration/recruitment (100, 101) | |
| Ccl7 | 1.37 | 2.7E-02 | ↑ neut. chemotaxis (102) | |
| RORα | 1.30 | 1.8E-02 | ↑ Th17 development (103) | |
| IPA USR (direct only) | Activation z-score | p-value | Activity | |
| CEBPA | 3.26 | 2.36E-05 | ↑ granulopoiesis (90, 104) | |
| HMGB1 | 1.755 | 2.00E-03 | ↑ neut. mediated injury (105) | |
| SMAD3 | 1.688 | 1.45E-04 | ↑ neut. activation (106) | |
| IRF-1 | 1.482 | 1.07E-02 | ↑ granulopoiesis (107) | |
| STAT4 | 1.136 | 1.04E-04 | ↑ neut. activation (108) | |
| EGR1 | 1.158 | 1.98E-04 | Activated neuts. (109) | |
| HIF1A | 1.052 | 2.74E-04 | ↑ neut. survival (110) | |
| DLX3 | −2 | 3.39E-04 | Dlx3−/−↑ skin IL-17 (111) | |
| TP73 | −2.809 | 2.69E-04 | p73−/−↑ neut. infiltration and edema (112) | |
| IPA diseases or functions annotation (direct only) | Activation z-score | p-value | ||
| Accumulation of neutrophils | 1.969 | 1.22E-03 | ||
| Th17 immune response | 1.698 | 2.18E-05 | ||
| Polyarthritis | 1.574 | 2.87E-06 | ||
| Inflammation of joint | 1.085 | 8.39E-04 | ||
| Infiltration by neutrophils | 0.528 | 2.78E-04 | ||
| IPA USR (direct and indirect) | Activation z-score | p-value | Activity | |
| IL-1β | 2.962 | 4.84E-03 | ↑ neut. recruitment/survival/activity (95–98) | |
| PI3K/ERK | 2.7/2.1 | 2.7E-03 | ↑ neut. SCFA-induced chemotaxis (113) and survival (114) | |
| 3.1E-04 | ||||
| IL-17A | 1.946 | 5.33E-06 | ↑ neut. recruitment and survival (114, 115) | |
| IL-10 | −0.818 | 1.22E-03 | ↓ anti-inflammatory (116) | |
DEGs from RNA-Seq analysis of feet of CHIKV-infected mice (day 6.5 post infection) comparing high fiber diet with no fiber diets (Supplementary Table 1b), were analyzed by Ingenuity Pathway Analysis (IPA) upstream regulator (USR) feature (Supplementary Tables 1c,d). Selected DEGs and USRs associated with neutrophils (neuts.) are listed. FDR, false discovery rate (or q-value); ↑, increased; ↓, decreased.