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Table 1 In silico experiments performed to obtain time series data sets on wild-type cells and deletion mutants by following the token flow through the Petri net of Figure 8a

From: Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks

Experiment Genetic background Experimental perturbation Petri net implementation
Exp #1 Wild-type Addition of organic and inorganic phosphate token in pi_pp and po_pp
Exp #2 Wild-type Absence of organic and inorganic phosphate Petri net as shown in Figure 8
Exp #3 Wild-type Inhibition of transcription/translation no token in phoA, token in po_pp
Exp #4 Δ pstSCAB Absence of organic and inorganic phosphate no token in Pst-P
Exp #5 Δ pstSCAB Addition of organic phosphate no token in Pst-P, token in po_pp
Exp #6 Δ pstSCAB Addition of organic and inorganic phosphate no token in Pst-P, token in pi_pp and po_pp
Exp #7 Δ phoU Absence of organic and inorganic phosphate no token in PhoU-I
Exp #8 Δ phoR Absence of organic and inorganic phosphate no token in PhoR
Exp #9 Δ phoB Absence of organic and inorganic phosphate no token in PhoB
Exp #10 phoR Δ Psite Absence of organic and inorganic phosphate no token in PhoR-S
Exp #11 phoB Δ Psite Absence of organic and inorganic phosphate no token in PhoB-S
  1. For each experiment, the type of experimental perturbation and the implementation of this perturbation in the form of the intitial marking of the Petri net of Figure 8a is indicated. Genetic background column: ΔphoR means that the phoR gene is deleted and that the PhoR protein is absent accordingly, etc. ΔPsite means that the phosphorylation site in the respective protein is deleted, while the protein as such is present.