Table 3 |
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|
State vectors used for reconstructing the phosphate regulatory network |
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|
Exp. # |
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
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|
State vectors (compiled from time-series) |
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|
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 |
|
|
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|
Term. state |
T |
T |
T |
T |
T |
T |
T |
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|
|
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|
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. |
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|
Durzinsky et al. BMC Systems Biology 2011 5:113 doi:10.1186/1752-0509-5-113 |
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