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Table 2 Scenarios used in the flood minimization of E. coli regulatory network

From: A flood-based information flow analysis and network minimization method for gene regulatory networks

Scenario Inputs Reporter gene selection Genes in a sub-network Reporter genes Total flood in a network with the flood threshold equals to
      0.00 0.35 0.70
Stationary phase σ38 Stationary phase specific genes under control of σ38 (22) 1,254 10 185 50 33
Exponential growth / GO groups σ70, σ54, σ28 Genes based on GO terms (amino acid synthesis, translation, protein folding, protein modification, glycolysis, tricarboxylic acid cylce) 1,584 168 242 49 48
Exponential growth / expression data σ70, σ54, σ28 Genes expressed in the exponential phase (microarray expression data (23) 1,584 54 232 96 40
Heat shock / GO groups σ38, σ54, σ32 Genes expressed in the exponential phase (microarray expression data (23) 1,314 13 173 46 33
Transition phase / expression data σ70, σ38 Genes expressed in the transition from the exponential to the stationary phase (microarray expression data (23) 1,595 34 241 102 52
  1. Total number of genes is shown for a sub-network regulated by the selected inputs. Total flood is shown for full and minimized networks with three different flood thresholds (the maximum flood through a link is 1.0).