Table 3.

Simple Regulatory Rules

Regulator presence	Regulator function	DNA binding conformation	Effector presence (i)		Discrete expression level
		P	Absent	→	Off
	Positive		Present	→	Off
		P-i	Absent	→	Off
Absence			Present	→	Off
		P	Absent	→	On
	Negative		Present	→	On
		P-i	Absent	→	On
			Present	→	On
		P	Absent	→	On
	Positive		Present	→	Off
Presence		P-i	Absent	→	Off
			Present	→	On
		P	Absent	→	Off
	Negative		Present	→	On
		P-i	Absent	→	On
			Present	→	Off

This table describes the rules determining gene expression when a single protein regulates genes. The rules show the regulatory protein complexes (protein and effector-metabolite), when present. We distinguish two types of conformation of regulators notated as P when they bind to their DNA-binding site with no effector, and as P-i regulators when they bind to DNA with the effector present. In the case of an absent protein, we assume that the expression state depends on the promoter strength.

Regulatory Network of Escherichia coli: Consistency Between Literature Knowledge and Microarray Profiles