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

Table 4 State vectors used for reconstructing the phosphate regulatory network, difference vectors and additional decomposed reactions as obtained in the course of network reconstruction

Exp. #	9				10			11
	State vectors (compiled from time-series)											Difference vectors											Additional decomposed reactions
Vector #	35	36	37	38	39	40	41	42	43	44	45	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19
pi-pp	0	0	0	0	0	0	0	0	0	0	0	-1							+1				-1							+1
pi-cp	0	0	0	0	0	0	0	0	0	0	0	+1												+1
po-pp	0	0	0	0	0	0	0	0	0	0	0								-1										-1
Pst-P	1	0	0	0	1	0	0	1	0	0	0		-1							+1
Pst	0	1	1	1	0	1	1	0	1	1	1		+1							-1
PhoU-I	1	1	0	0	1	1	0	1	1	0	0			-1							+1
PhoU-A	0	0	1	1	0	0	1	0	0	1	1			+1							-1
PhoR	1	1	1	0	1	1	1	1	1	1	0				-1	+1									+1
PhoR-P	0	0	0	1	0	0	0	0	0	0	1				+1	-1									-1
PhoR-S	1	1	1	1	0	0	0	1	1	1	1
PhoB	0	0	0	0	1	1	1	1	1	1	1					-1						+1				-1
PhoB-P	0	0	0	0	0	0	0	0	0	0	0					+1						-1				+1
PhoB-S	1	1	1	1	1	1	1	0	0	0	0
PhoA-T	1	1	1	1	1	1	1	1	1	1	1
PhoA	0	0	0	0	0	0	0	0	0	0	0						+1	-1									-1
PhoA-pp	0	0	0	0	0	0	0	0	0	0	0							+1										+1
Term. state				T			T				T

States are assigned to the experiments during which they occurred. The state vectors of experiments 1 to 8 are shown in Table 3. Difference vectors and additional decomposed reactions that appeared in more than one experiment are listed only once. 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.

ISSN: 1752-0509