Table 3.
Computational analysis of proteins that can interact with σC. (A) Results compiled from the program STRING (32) and (B). Analysis of co-expression levels of known σ / anti σ pairs in M. tuberculosis.
| (A) | ||||||
|---|---|---|---|---|---|---|
| Gene- name |
Neighborhood | Gene fusion |
Co-occurence | Text mining |
Homology | Score |
| SigM | − | − | + | + | − | 0.726 |
| Rv0093c | − | + | − | − | − | 0.693 |
| RpoE | − | − | + | + | + | 0.390 |
| SigE | − | − | + | + | + | 0.352 |
| Upk | − | − | − | + | − | 0.267 |
| LepA | + | − | − | − | − | 0.256 |
| DapF | − | − | + | − | − | 0.226 |
| Rv3676 | − | − | + | − | − | 0.223 |
| SigG | − | − | + | − | + | 0.222 |
| Rv1318c | − | − | + | − | − | 0.222 |
| (B) | |||||
|---|---|---|---|---|---|
| Name | Stationary | Low oxygen | 7h9 | Balb | Scid |
| Rv3416(whiB3) | −0.69 (−1.9) | 0.64 (1.7) | −0.96 (−6.9) |
−0.87 (−3.9) |
0.89 (3.9) |
| Rv3413(anti-σD) | 0.92 (4.7) | −0.67(−1.8) | 0.55 (1.3) | −0.38 (−0.8) | −0.34 (−0.7) |
| Rv3287(anti-σF) | 0.50 (1.2) |
0.41 (0.9) |
0.99 (14.0) |
−0.63 (−1.6) |
−0.66 (−1.8) |
| Rv3229(anti-σH) | 0.28 (0.6) |
0.99 (14.0) |
0.43 (1.0) |
0.34 (0.7) |
−0.28 (−0.6) |
| Rv0736(anti-σL) |
0.98 (9.8) |
0.96 (8.9) |
−0.98 (9.8) |
−0.67 (−1.8) |
0.96 (6.9) |
| Rv0093c | −0.76 (−2.3) |
−0.81 (−2.8) |
0.92 (4.7) |
−0.42 (−0.9) |
−0.64 (−1.6) |
Legend: Expression levels are correlated under different conditions. Stationary: stationary phase of growth; Low oxygen:anaerobic conditions; 7h9: growth in 7H9 medium; Balb: M. tuberculosis isolated from immune competent Balb/c mice; scid: M. tuberculosis isolated from severe combined immune-defecient (SCID) mice.