Skip to main content

Table 3 State vectors used for reconstructing the phosphate regulatory network

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

Exp. # 1 2 3 4 5 6 7   8
  State vectors (compiled from time-series)
Vector # 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34
pi-pp 1 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
pi-cp 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
po-pp 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 1 1 0 0 0 0 0
Pst-P 1 1 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 0 0
Pst 0 0 1 1 1 1 1 1 1 0 0 0 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 0 0 0 0 1 0 1 1
PhoU-I 1 1 1 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 1 1 0 0 0 0 1 1 1 0 0 1 1 0
PhoU-A 0 0 0 1 1 1 1 1 1 1 0 0 0 0 1 1 1 1 1 1 1 0 0 1 1 1 1 0 0 0 0 0 0 0 1
PhoR 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 1 0 1 0 1 1 1 1 1 0 0 0
PhoR-P 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 1 0 0 0 0 0 0 0 0
PhoR-S 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
PhoB 1 1 1 1 1 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 1 1 1 1 0 0 1 1 1 1 1 1 1 1
PhoB-P 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 1 1 1 1 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0
PhoB-S 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
PhoA-T 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 1 1 1 1 1 1 1 1
PhoA 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
PhoA-pp 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Term. state                      T       T T T T   T    T
  1. States are assigned to the experiments during which they occurred. The state vectors of experiments 1 to 8 are shown in this table, the state vectors of experiments 9 to 11 are shown in Table 4. States of Pst, PhoU, PhoR, and PhoB were considered as P-invariants. Phosphate, PhoR, PhoRP and the cytoplasmic PhoA protein were excluded as catalytic factors based on biological knowledge.