The table below reproduces a list of 42 feed-forward loops (FFLs) in Escherichia coli that was compiled by Alon and co-workers (http://www.weizmann.ac.il/mcb/UriAlon) [1,2]. However, annotation has been added (columns 2, 4, 5, and 7) to indicate 1) the transcription factors (TFs) that are encoded by the transcriptional units (TUs) in the FFLs and 2) the signals or conditions recognized by the TFs. Annotation is based largely on information available in electronic databases: EcoCyc [3], RegulonDB [4], and EcoTFs [5].

References:

[1] Shen-Orr, S. S., et al. (2002) Nat. Genet. 31, 64-68.
[2] Mangan, S. & Alon, U. (2003) Proc. Natl. Acad. Sci. USA 100, 11980-11985.
[3] Karp, P. D., et al. (2004) ASM News 70, 25-30
[4] Salgado, H., et al. (2004) Nucleic Acids Res. 32, D303-D306.
[5] Wall, M. E., et al. (2004) Nat. Rev. Genet. 5, 34-42.

Index	TF X	TU of X	Signal(s) recognized by X	TF Y	TU of Y regulated by X	Signal(s) recognized by Y	TU of Z regulated by X and Y	Type of FFL	Function of Z
1	ArcA	arcA	phosphorylation state of ArcB	AppY	appY	unknown, a metabolite of fermentation?	appCBA	Coh-1	Anaerobic/stationary phase
2	CRP	crp	cAMP	FucR	fucPIKUR	fuculose 1-phosphate	fucAO	Coh-1	Fucose utilization
3	CRP	crp	cAMP	Fur	fur	Fe2+	cirA	Inc-1	Iron citrate uptake
4	CRP	crp	cAMP	GalS	galS	&beta-D-galactose	mglBAC	Inc-1	Carbon utilization
5	CRP	crp	cAMP	MalI	malI	unknown, a sugar?	malXY	Coh-4	Maltose utilization
6	CRP	crp	cAMP	MelR	melR	melibiose	melAB	Coh-1	Melibiose utilization
7	CRP	crp	cAMP	CaiF	caiF	L-carnitine (putative) crotonobetaine (putative)	caiTABCDE	Coh-1	Carnitine metabolism
8	CRP	crp	cAMP	CaiF	caiF	L-carnitine (putative) crotonobetaine (putative)	fixABCX	Coh-1	Carnitine metabolism
9	CRP	crp	cAMP	NagC	nagBACD	N-acetylglucosamine 6-phosphate	manXYZ	Inc-1	Carbon utilization
10	CRP	crp	cAMP	NagC	nagBACD	N-acetylglucosamine 6-phosphate	nagE	Inc-1	Carbon utilization
11	CRP	crp	cAMP	MalT	malT	maltotriose + ATP	malEFG	Coh-1	Maltose utilization
12	CRP	crp	cAMP	MalT	malT	maltotriose + ATP	malK-lamB-malM	Coh-1	Maltose utilization
13	CRP	crp	cAMP	MalT	malT	maltotriose + ATP	malS	Coh-1	Maltose utilization
14	CRP	crp	cAMP	AraC	araC	L-arabinose	araBAD	Coh-1	Arabinose utilization
15	CRP	crp	cAMP	AraC	araC	L-arabinose	araE	Coh-1	Arabinose utilization
16	CRP	crp	cAMP	AraC	araC	L-arabinose	araFGH	Coh-1	Arabinose utilization
17	CRP	crp	cAMP	AraC	araC	L-arabinose	araJ	Coh-1	Arabinose utilization
18	FlhDC heterotetrameric complex	flhDC	protein-protein interactions	FliA (a.k.a. &sigma28 and &sigmaF)	fliAZY	anti-sigma factor FlgM	flgBCDEFGHIJK	Coh-1	Flagella system
19	FlhDC heterotetrameric complex	flhDC	protein-protein interactions	FliA (a.k.a. &sigma28 and &sigmaF)	fliAZY	anti-sigma factor FlgM	flhBAE	Coh-1	Flagella system
20	FlhDC heterotetrameric complex	flhDC	protein-protein interactions	FliA (a.k.a. &sigma28 and &sigmaF)	fliAZY	anti-sigma factor FlgM	fliE	Coh-1	Flagella system
21	FlhDC heterotetrameric complex	flhDC	protein-protein interactions	FliA (a.k.a. &sigma28 and &sigmaF)	fliAZY	anti-sigma factor FlgM	fliFGHIJK	Coh-1	Flagella system
22	FlhDC heterotetrameric complex	flhDC	protein-protein interactions	FliA (a.k.a. &sigma28 and &sigmaF)	fliAZY	anti-sigma factor FlgM	fliLMNOPQR	Coh-1	Flagella system
23	FNR	fnr	oxidation state of FNR	ArcA	arcA	phosphorylation state of ArcB	cydAB	Inc-3	Anaerobic metabolism
24	FNR	fnr	oxidation state of FNR	ArcA	arcA	phosphorylation state of ArcB	cyoABCDE	Coh-3	Anaerobic metabolism
25	FNR	fnr	oxidation state of FNR	ArcA	arcA	phosphorylation state of ArcB	focA-pflB	Coh-1	Anaerobic metabolism
26	FNR	fnr	oxidation state of FNR	ArcA	arcA	phosphorylation state of ArcB	glpACB	Inc-1	Anaerobic metabolism
27	FNR	fnr	oxidation state of FNR	ArcA	arcA	phosphorylation state of ArcB	icdA	Coh-3	Anaerobic metabolism
28	FNR	fnr	oxidation state of FNR	ArcA	arcA	phosphorylation state of ArcB	nuoABCEFGHIJKLMN	Coh-3	Anaerobic metabolism
29	FNR	fnr	oxidation state of FNR	ArcA	arcA	phosphorylation state of ArcB	sdhCDAB-b0725-sucABCD	Coh-3	Anaerobic metabolism
30	HimAD complex (a.k.a. IHF)	himA	DNA curvature	OmpR	ompR-envZ	phosphorylation states of BarA and EnvZ	ompC	Coh-2	Osmotic stress response
31	HimAD complex (a.k.a. IHF)	himA	DNA curvature	OmpR	ompR-envZ	phosphorylation states of BarA and EnvZ	ompF	Inc-4	Osmotic stress response
32	H-NS	hns	DNA curvature	FlhDC heterotetrameric complex	flhDC	protein-protein interactions	fliAZY	Coh-1	Flagella master regulator
33	MetJ	metJ	S-adenosyl-L-methionine	MetR	metR	homocysteine	metA	Coh-2	Methionine biosynthesis
34	OmpR	ompR-envZ	phosphorylation states of BarA and EnvZ	CsgD	csgDEFG	unknown, carnosine?	csgBA	Coh-1	Osmotic stress response
35	Rob	rob	dipyridyl, decanoate	MarA	marRAB	none likely/known	fumC	Coh-1	Drug response
36	Rob	rob	dipyridyl, decanoate	MarA	marRAB	none likely/known	nfo	Coh-1	Drug response
37	Rob	rob	dipyridyl, decanoate	MarA	marRAB	none likely/known	sodA	Coh-1	Drug response
38	Rob	rob	dipyridyl, decanoate	MarA	marRAB	none likely/known	zwf	Coh-1	Drug response
39	RpoN (a.k.a. &sigma54 and &sigmaN)	rpoN	ATPase-mediated hydrolysis of ATP	FhlA	fhlA hypABCDE-fhlA?	formate	fdhF	Coh-1	Formate hydrogen lyase system
40	RpoN (a.k.a. &sigma54 and &sigmaN)	rpoN	ATPase-mediated hydrolysis of ATP	FhlA	fhlA hypABCDE-fhlA?	formate	hycABCDEFGH	Coh-1	Formate hydrogen lyase system
41	RpoN (a.k.a. &sigma54 and &sigmaN)	rpoN	ATPase-mediated hydrolysis of ATP	GlnG [a.k.a. NtrC and NR(I)]	glnALG glnLG?	phosphorylation state of NR(I)	glnHPQ	Coh-1	Nitrogen utilization
42	RpoN (a.k.a. &sigma54 and &sigmaN)	rpoN	ATPase-mediated hydrolysis of ATP	GlnG [a.k.a. NtrC and NR(I)]	glnALG glnLG?	phosphorylation state of NR(I)	nac	Coh-1	Nitrogen utilization