Table 1.
AMBIENT modules differentially regulated in response to nitrogen stress
| Module | q-value | No. of reactions | No. of metabolites | Reactions with associated genes | Specific function(s) |
|---|---|---|---|---|---|
| Up | |||||
| u1 |
<0.004 |
8 |
2 |
8 |
Nitrate/nitrite uptake and assimilation |
| u2 |
0.00 |
3 |
2 |
3 |
Cytosine/uracil uptake and assimilation |
| u3 |
0.02 |
6 |
2 |
6 |
Ethanolamine uptake and assimilation |
| u4 |
0.02 |
4 |
2 |
4 |
Arginine/ornithine metabolism |
| u5 |
0.02 |
4 |
3 |
4 |
Histidine degradation |
| u6 |
0.01 |
1 |
1 |
1 |
Arginine metabolism |
| u7 |
0.02 |
1 |
1 |
1 |
Ammonium transport |
| u8 |
0.02 |
4 |
1 |
4 |
Cation transport |
| u9 |
0.02 |
1 |
1 |
1 |
Cyanate degradation |
| u10 |
0.02 |
5 |
4 |
5 |
Fatty acid metabolism |
| u11 |
0.02 |
1 |
1 |
1 |
Hydrogen peroxide metabolism |
| u12 |
0.02 |
1 |
1 |
1 |
Hydrogen peroxide metabolism |
| u13 |
0.02 |
1 |
1 |
1 |
Hydrogen peroxide metabolism |
| u14 |
0.03 |
3 |
2 |
3 |
Energy metabolism |
| u15 |
0.03 |
2 |
1 |
2 |
Thiamine transport and assimilation |
| u16 |
0.04 |
4 |
1 |
4 |
Galactose metabolism |
| u17 |
0.03 |
1 |
1 |
1 |
Allantoin transport |
| u18 |
0.03 |
1 |
1 |
1 |
Hydrogen peroxide metabolism |
| u19 |
0.04 |
3 |
1 |
3 |
Gluconate degradation |
| u20 |
0.04 |
2 |
1 |
1 |
Fatty acid metabolism |
| uHP |
<0.004 |
4 |
1 |
4 |
Hydrogen peroxide metabolism |
| Down | |||||
| d1 |
<.004 |
152 |
75 |
110 |
LPS, RNA and DNA synthesis, central carbon metabolism |
| d3 |
0.04 |
5 |
3 |
5 |
Pantothenate metabolism |
| d4 |
0.04 |
4 |
2 |
3 |
Fatty acid metabolism |
| d5 |
0.04 |
4 |
3 |
0 |
Isoprenoid utilization |
| d6 |
0.05 |
4 |
2 |
3 |
Fatty acid metabolism |
| d7 | 0.04 | 3 | 2 | 2 | Xylose uptake and assimilation |
Up- and down-regulated modules found using AMBIENT in nitrogen stress, in decreasing order of score, indicating the number of reactions and metabolites present in each. Scores are calculated by AMBIENT, taking into account the logarithm of the fold-change of the genes associated with each reaction and the connectivity in the metabolic network of each metabolite in the module. The number of genes associated with these reactions according to the Model SEED M. smegmatis model is also shown. Functional assignments are based on manual inspection of the exact function of the member reactions of the modules. Diagrams for each module are available as Additional files 3 (Up modules) and 4 (down modules), except for u11, u12, u13 and u18, which are combined in uHP.