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Table 1 AMBIENT modules differentially regulated in response to nitrogen stress

From: Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules

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
  1. 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.