TABLE 1.
Top 30 DEGs common to chickens exposed or infected with Rlow or LAV strainsa
| Gene symbol | Log2 fold change | Q value |
|---|---|---|
| Day 1 | ||
| MMP7 | 10.7134 | 0.000757872 |
| NOXO1 | 6.65159 | 0.00811598 |
| IL13RA2 | 6.5396 | 0.000757872 |
| EX-FABP | 5.90677 | 0.000757872 |
| TLR-4 | 5.56618 | 0.000757872 |
| ENPP3 | 5.33232 | 0.000757872 |
| AVD | 5.33025 | 0.000757872 |
| IL-1β | 5.30879 | 0.000757872 |
| IL-22 | 5.27032 | 0.00441529 |
| CA4 | 5.26316 | 0.000757872 |
| CXCL1 | 5.14426 | 0.000757872 |
| ENSGALG00000004041 | 5.07205 | 0.000757872 |
| IRG1 | 4.98928 | 0.000757872 |
| MB | −4.74018 | 0.000757872 |
| IL8-L1 | 4.73203 | 0.000757872 |
| TLR-15 | 4.70932 | 0.000757872 |
| IL-22RA2 | 4.55899 | 0.000757872 |
| ENSGALG00000016556 | 4.54609 | 0.0231227 |
| SEMA3G | 4.47905 | 0.0102995 |
| CSF3R | 4.46757 | 0.000757872 |
| LYG2 | 4.4458 | 0.000757872 |
| MYL2 | −4.34357 | 0.00521464 |
| ENSGALG00000002343 | 4.25019 | 0.0437935 |
| CCL4 | 4.22887 | 0.00137722 |
| NOX1 | 4.20915 | 0.000757872 |
| SERPINE2 | 4.18123 | 0.000757872 |
| IL-4I1 | 4.14185 | 0.000757872 |
| IL-8-L2 | 4.09163 | 0.000757872 |
| GGT1 | 4.04279 | 0.000757872 |
| MYL3 | −4.08948 | 0.000757872 |
| Day 2 | ||
| MMP7 | 11.5514 | 0.000502174 |
| NOXO1 | 7.782 | 0.0180061 |
| AVD | 7.09226 | 0.000502174 |
| ENSGALG00000005099 | 6.57039 | 0.000502174 |
| ENSGALG00000004041 | 6.57034 | 0.000502174 |
| MMP7 | 11.5514 | 0.000502174 |
| OGCHI | 6.54007 | 0.000502174 |
| IL13RA2 | 6.36389 | 0.000502174 |
| ENSGALG00000024484 | 6.26863 | 0.000502174 |
| OLFM4 | 6.05065 | 0.000502174 |
| IL8-L1 | 5.94985 | 0.000502174 |
| CA4 | 5.80822 | 0.000502174 |
| EX-FABP | 5.55622 | 0.000502174 |
| ENSGALG00000006295 | −5.47359 | 0.000502174 |
| CSF3R | 5.45562 | 0.000502174 |
| CALCA | 5.45036 | 0.000502174 |
| ENPP3 | 5.43387 | 0.000502174 |
| MMP9 | 5.23091 | 0.000502174 |
| IL8-L2 | 4.99823 | 0.000502174 |
| ENSGALG00000023578 | −4.89811 | 0.000926417 |
| TLR15 | 4.75184 | 0.000502174 |
| PCDH1 | 4.74193 | 0.000502174 |
| IL1R2 | 4.63499 | 0.000502174 |
| ENSGALG00000021025 | 4.61934 | 0.000502174 |
| NOX1 | 4.58002 | 0.000502174 |
| IL-4I1 | 4.44538 | 0.000502174 |
| RARRES1 | 4.43871 | 0.000502174 |
| IRG1 | 4.41293 | 0.000502174 |
| SOCS3 | 4.39838 | 0.000502174 |
| SLC6A14 | 4.39808 | 0.000502174 |
| SEMA3G | 4.37535 | 0.000502174 |
a
DEGs were determined by Cuffdiff and ranked based on the log2 fold change values in the Rlow infection group.