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Table 2 (metabolite, regulator) sets inferred from the model.

From: A joint model of regulatory and metabolic networks

length

set

net explained

pval

1

 

1

1.0

2

 

1

1.0

3

(glucose, ArcA) (acetate, ArcA)

34

< 10-5

4

(g6p, ArcA) (acetyl-CoA, ArcA)

38

< 10-5

4

(g6p, ArcA) (acetylphosphate, ArcA)

38

< 10-5

4

(g6p, ArcA) (acetate, ArcA)

38

< 10-5

4

(g6p, ArcA) (pyrophosphate, ArcA)

38

< 10-5

5

(g6p, ArcA) (pyruvate, ArcA)

65

< 10-5

6

(g6p, ArcA) (pyruvate, ArcA)

66

< 10-5

6

(g6p, ArcA) (acetyl-CoA, ArcA)

66

< 10-5

6

(g6p, ArcA) (malate, ArcA)

66

< 10-5

6

(g6p, ArcA) (2k3d6pg, ArcA)

66

< 10-5

7

(g6p, ArcA) (pyruvate, ArcA) (pepyruvate, FruR)

74

< 10-5

8

(f6p, ArcA) (pepyruvate, ArcA) (2pg, FruR)

78

< 10-5

9

(f6p, ArcA) (pepyruvate, ArcA) (6pg, FruR)

72

< 10-5

  1. The explanatory power (net explained) is (# explained responses – # contradicted responses). The p-value of the explanatory power is calculated by randomly permuting the perturbation responses over genes or fluxes. No feedback links are added to the network when the maximum path length ≤ 2, since short paths containing feedback links can not explain the data. Abbreviation of metabolites: g6p: glucose-6-phosphate, pepyruvate: phosphoenolpyruvate, f6p: fructose-6-phosphate, 6pg: 6-phospho-gluconate, 2pg: 2-phosphoglycerate, 2k3d6pg: 2-keto-3-deoxy-6-phospho-gluconate.