Table 2.
Top 20 DE genes between control and M. vaccae groups
| Gene name | P-value fold change and regulation | GenBank accession | Relationship with TB | |||
|---|---|---|---|---|---|---|
| P-value a | FDR b | FCAbsolute c | Regulation | |||
| Retnlg | 5.2646E-11 | 3.00721E-07 | 6.762246 | Up | NM_181596 | Unknown |
| Tiprl | 6.7691E-11 | 3.00721E-07 | 2.3434467 | Up | NM_145513 | Unknown |
| Gyg | 1.0686E-10 | 3.00721E-07 | 2.590874 | Up | NM_013755 | Unknown |
| Ptgs2 | 1.1782E-10 | 3.00721E-07 | 33.16254 | Up | NM_011198 | Decreased transcription of PTGS2 was beneficial to the survival of M. tuberculosis |
| Zfp281 | 1.9767E-10 | 3.00721E-07 | 3.3773346 | Up | NM_177643 | Unknown |
| Gbp2 | 2.162E-10 | 3.00721E-07 | 8.493201 | Up | NM_010260 | One of prominent hubs in a highly active common core in TB |
| Cxcl2 | 2.2714E-10 | 3.00721E-07 | 176.0849 | Up | NM_009140 | Blocking of CXCL2 can significantly reduce the M. tuberculosis-induced IL-1β production |
| Ear6 | 2.4307E-10 | 3.00721E-07 | 30.299973 | Up | NM_053111 | Unknown |
| Ighv1–77 | 4.1282E-10 | 4.21673E-07 | 4.998427 | Up | AF045501 | Unknown |
| Slpi | 5.6974E-10 | 4.97498E-07 | 3.1604574 | Up | NM_011414 | Exposure of murine peritoneal macrophages to M. tuberculosis led to an increase in SLPI secretion accelerating both the phagocytosis and killing of the pathogen |
| Azin1 | 5.9447E-10 | 4.97498E-07 | 2.5270393 | Up | NM_018745 | Unknown |
| S100a8 | 7.0447E-10 | 4.97498E-07 | 9.958652 | Up | NM_013650 | A major pathologic role for S100A8/A9 proteins in decreasing lung tissue damage without impacting protective immunity against TB |
| Ccrl2 | 7.0963E-10 | 4.97498E-07 | 10.672567 | Up | NM_017466 | Unknown |
| Igj | 8.5416E-10 | 5.25022E-07 | 4.127778 | Up | NM_152839 | Unknown |
| Tnf | 9.694E-10 | 5.66345E-07 | 156.13841 | Up | NM_013693 | TNF-α has a prominent role in defense and pathological responses to TB and its production in TB patients was higher than that in the control group |
| Prkcd | 1.1807E-09 | 6.28255E-07 | 2.054293 | Up | NM_011103 | Unknown |
| Marcksl1 | 1.2759E-09 | 6.28255E-07 | 11.7962 | Up | NM_010807 | Unknown |
| Prss34 | 1.3143E-09 | 6.28255E-07 | 11.188594 | Up | NM_178372 | Unknown |
| Cct6a | 1.4218E-09 | 6.40172E-07 | 2.9756305 | Up | NM_009838 | Unknown |
| Il1a | 1.5183E-09 | 6.40172E-07 | 48.50243 | Up | NM_010554 | The expression of the IL1A gene was increased in both the TB-infected and the healthy cattle to M. bovis stimulation |
| Afp | 2.4759E-11 | 3.00721E-07 | 5.7038527 | Down | NM_007423 | Only a few literatures reported that AFP was normal in TB patients, but increased significantly in TB patients with hepatocellular carcinoma |
| Pcdhga9 | 8.4144E-11 | 3.00721E-07 | 2.3555577 | Down | NM_033592 | Unknown |
| Cdc42ep5 | 1.2007E-10 | 3.00721E-07 | 3.3431478 | Down | NM_021454 | Unknown |
| Hrsp12 | 1.5283E-10 | 3.00721E-07 | 2.9907024 | Down | NM_008287 | Unknown |
| Rnasek | 1.5763E-10 | 3.00721E-07 | 2.0300574 | Down | NM_173742 | Unknown |
| Nprl3 | 1.6254E-10 | 3.00721E-07 | 2.5463195 | Down | NM_001284359 | Unknown |
| 4932443I19Rik | 1.9509E-10 | 3.00721E-07 | 6.6056542 | Down | NM_001101519 | Unknown |
| Ly6g6c | 2.3228E-10 | 3.00721E-07 | 3.6154532 | Down | NM_023463 | Unknown |
| Kdr | 2.6218E-10 | 3.06341E-07 | 4.521906 | Down | NM_010612 | Unknown |
| 2810416G20Rik | 3.0664E-10 | 3.39439E-07 | 4.7047515 | Down | XM_003945668 | Unknown |
| Tubb2a | 4.3967E-10 | 4.21673E-07 | 3.6115813 | Down | NM_009450 | Unknown |
| Triqk | 4.4108E-10 | 4.21673E-07 | 4.918867 | Down | NM_173746 | Unknown |
| Slc6a16 | 6.2508E-10 | 4.97498E-07 | 4.1382565 | Down | XM_355900 | Unknown |
| Cxx1c | 8.1855E-10 | 5.25022E-07 | 3.0826645 | Down | NM_028375 | Unknown |
| Fez2 | 8.6019E-10 | 5.25022E-07 | 2.6090815 | Down | NM_001285940 | Unknown |
| 1810058I24Rik | 8.7371E-10 | 5.25022E-07 | 4.307958 | Down | NR_027875 | Unknown |
| Egfbp2 | 1.0983E-09 | 6.07878E-07 | 4.641702 | Down | NM_010115 | Unknown |
| Efna5 | 1.2336E-09 | 6.28255E-07 | 2.744601 | Down | NM_207654 | Unknown |
| Cd151 | 1.2898E-09 | 6.28255E-07 | 3.2171504 | Down | NM_009842 | CD9High classical monocytes expressed higher levels of tetraspanin CD151 compared to CD9Low classical monocytes |
| 2210013O21Rik | 1.4572E-09 | 6.40172E-07 | 3.4838674 | Down | NM_027327 | Unknown |
a, P-value calculated from t-test; b, FDR calculated from Benjamini Hochberg FDR; c, FCAbsolute, the absolute ratio (no log scale) of normalized intensities between two groups. Notes: mRNA with expression fold change > 2 and with FDR adjusted P-value < 0.05 was considered statistically significant. Here we show the expression fold change > 10