Table 1 State transitions obtained through Boolean model simulation using 'GINsim’

From: Understanding the sequential activation of Type III and Type VI Secretion Systems in Salmonella typhimurium using Boolean modeling

(A)
	Nodes
State Transition	Glucose	Iron	Magnesium	Calcium	Osmolarity	Stationary phase	Mlc	HilE	HilD	HilC	RtsA	HilA	Ihf	SirA-BarA	CsrBC	CsrA	Fur	H-NS	PhoP	SlyA	SsrAB	Fis	EnvZ	OmpR	YfhA	MviA	RcsB	PmrA	SciS	VrgS	SciG	SPI -1	SPI -2	T6SS
1	0	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	0	0	0	0	0
2	0	1	1	1	1	1	1*	1*	0	0	0	0	1*	1*	0	1*	1*	1*	0	0	0	1*	1*	1*	1*	0	0	0	0	0	0	0	0	0
3	0	1	1	1	1	1	1	0*	0	0	0	0	1	1	1*	1	1	1	0	0	0	1	1	0*	0*	1*	1*	0	0	0	0	0	0	0
4	0	1	1	1	1	1	1	0	0	0	0	0	1	1	1	0*	1	1	0	0	0	1	1	0	0	1	0*	0	0	0	0	0	0	0
5	0	1	1	1	1	1	1	0	1*	0	0	0	1	1	1	0	1	1	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0
6	0	1	1	1	1	1	1	0	1	1*	1*	0	1	1	1	0	1	1	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0
7	0	1	1	1	1	1	1	0	1	1	1	1*	1	1	1	0	1	1	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0
8	0	1	1	1	1	1	1	0	1	1	1	1	1	1	1	0	1	1	0	0	0	1	1	0	0	1	0	0	0	0	0	1*	0	0
(B)
	Nodes
State Transition	Glucose	Iron	Magnesium	Calcium	Osmolarity	Stationary phase	Mlc	HilE	HilD	HilC	RtsA	HilA	Ihf	SirA-BarA	CsrBC	CsrA	Fur	H-NS	PhoP	SlyA	SsrAB	Fis	EnvZ	OmpR	YfhA	MviA	RcsB	PmrA	SciS	VrgS	SciG	SPI -1	SPI -2	T6SS
1	1	1	0	0	0	1	0	0	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
2	1	1	0	0	0	1	0	1*	1	1	1	1	0	0	0	1*	1*	1*	1*	1*	0	1*	0	1*	1*	0	0	0	0	0	0	1	0	0
3	1	1	0	0	0	1	0	1	0*	1	1	0*	0	0	0	1	1	1	1	1	1*	1	0	1	1	0	1*	1*	0	0	0	1	0	0
4	1	1	0	0	0	1	0	1	0	1	1	0	0	0	0	1	1	1	1	1	0*	1	0	1	1	0	1	1	0	1*	1*	0*	1*	0
5	1	1	0	0	0	1	0	1	0	1	1	0	0	0	0	1	1	1	1	1	0	1	0	1	1	0	1	1	1*	1	1	0	0*	0
6	1	1	0	0	0	1	0	1	0	1	1	0	0	0	0	1	1	1	1	1	0	1	0	1	1	0	1	1	1	1	1	0	0	1*

The rows represent the dynamic behavior of the network (constituting 34 nodes) under study. ′0′ represents inactive state and ′1′ represents active state. Row 1 represents the values specified as the initial states for simulation. A node’s transit from an inactive state to an active state (0 → 1) or vice-versa (1 → 0) has been marked with asterisks (*). (A) Simulation considering the distal intestinal lumen environment, which is the site of infection by S. typhimurium. The 8th row corresponds to the steady state attained by the network (representing an activated SPI-1) (B) Simulation considering the intra-macrophageal environment faced by S. typhimurium after it has been engulfed by the macrophage. The 6th row corresponds to the steady state attained by the network (representing an activated T6SS).

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