Table 2.

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

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

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).