Table 2.
Differentially expressed genes selected from AmpliSeq analysis of hMDMs 12-h post infection with pathogenic (M. bovis BCG, M. tb R179) and nonpathogenic (M. smegmatis) mycobacteria.
|
M. smegmatis |
M. bovis BCG |
M. tb R179 |
|||||||
|---|---|---|---|---|---|---|---|---|---|
| Gene name | Fold change | p value | FDR | Fold change | p value | FDR | Fold change | p value | FDR |
| IFIT1 | 6.3 | 3.36E-19 | 2.02E-15 | 1.6 | 1.16E-18 | 4.64E-15 | 1.8 | 6.09E-18 | 1.83E-14 |
| IFIT2 | 4 | 2.27E-11 | 1.01E-08 | 1.6 | 2.5E-11 | 1.07E-08 | 1.8 | 3.76E-11 | 1.56E-08 |
| IFIT3 | 6.9 | 2.53E-09 | 4.75E-07 | 2.8 | 2.95E-09 | 5.46E-07 | 2.5 | 3.87E-07 | 6.99E-07 |
| MX1 | 4.6 | 6.05E-11 | 2.27E-08 | 1.6 | 6.51E-11 | 2.37E-08 | 1.7 | 6.7E-11 | 2.39E-08 |
| MX2 | 3.4 | 1.85E-17 | 3.18E-14 | 1.9 | 1.45E-16 | 2.06E-13 | 1.8 | 1.54E-16 | 2.06E-12 |
| IFI44 | 4 | 2.19E-08 | 3.29E-06 | 1.6 | 2.42E-08 | 3.59E-06 | 1.6 | 2.58E-08 | 3.78E-06 |
| IFI44L | 9 | 7.49E-11 | 2.58E-08 | 2.3 | 1.1E-10 | 3.69E-08 | 1.7 | 1.49E-10 | 4.7E-08 |
| ISG15 | 3.5 | 7.23E-10 | 1.64E-07 | 1.7 | 8.71E-10 | 1.94E-07 | 1.9 | 1.08E-09 | 2.36E-07 |
| IL12B | 178.1 | 1.11E-13 | 8.38E-11 | 57.3 | 1.55E-13 | 1.1E-10 | 29.7 | 2.58E-13 | 1.73E-10 |
| IL23A | 9.1 | 6.86E-10 | 1.62E-07 | 3.2 | 7.03E-10 | 1.63E-07 | 1.7 | 5.92E-10 | 1.43E-07 |
| IL6 | 12.4 | 5.64E-05 | 0.00029 | 6.5 | 5.89E-05 | 0.00023 | 4.6 | 6.07E-05 | 0.00023 |
| IL8 | 8.7 | 2.45E-06 | 0.00021 | 7.2 | 2.46E-06 | 0.00021 | 5.9 | 2.83E-06 | 0.000238 |
| RSAD2 | 7.9 | 5.62E-07 | 5.64E-05 | 3.1 | 6.75E-07 | 6.71E-05 | 2.6 | 6.8E-08 | 6.71E-05 |
| TRIB3 | −7.5 | 3.12E-07 | 0.00031 | −7 | 4.4E-07 | 0.00041 | −1.9 | 5.23E-07 | 0.00051 |
| MT1A | −32 | 1.42E-05 | 0.00053 | −41 | 1.42E-05 | 0.00041 | −1.8 | 1.52E-05 | 0.00053 |
| IDO1 | 12.6 | 1.79E-05 | 0.00015 | 6.6 | 1.8E-05 | 0.00011 | 5 | 1.81E-05 | 0.00014 |
| EIF2AK2 | 2.3 | 4.11E-34 | 4.94E-30 | 1.6 | 8.47E-18 | 1.91E-14 | 1.6 | 9.51E-18 | 1.91E-14 |
| IFN-γ | 14.4 | 7.08E-07 | 6.93E-05 | 3.9 | 7.29E-07 | 7.08E-05 | 3.4 | 7.53E-07 | 7.25E-05 |
Abbreviations: BCG, Bacillus Calmette–Guerin; EIF2AK2, eukaryotic translation initiation factor 2 alpha kinase 2; FDR, false discovery rate; IDO, indoleamine 2,3-dioxygenase; hMDMs, human monocyte-derived macrophages; IFI, interferon-induced protein; IFIT, interferon-induced protein with tetratricopeptide; IFN, interferon gamma; IL, interleukin; ISG, interferon-stimulated gene; MTA, metastasis-associated protein; MX, interferon-induced GTP binding protein; RSAD, radical S-adenosyl methionine domain-containing protein 2; TRIB, trible homolog; UBC, polyubiquitin-C. Figure 3 is the pictorial heat-map of these results.