upstream gene	reference	direct positive	direct negative	indirect positive	indirect negative	ambiguous	activator used	inhibitor used	stage analyzed	stage activated	miscellaneous remarks
SOX17b	Sinner et al 2004. Development 131:3069.	Hnfb1 Endodermin Foxa1 (Hnf3a) Foxa2 (Hnf3b) Sox17a	none identified	26D10 hydroxyl-acid oxidase	none indentified	because of effects of cycloheximide, Gata4, Gsc and Xnr4 are ambiguous targets Gata5, Gata6 levels were low in response to Sox17b, and so target relationship was ambiguous	dexamethasone (1mM)	cycloheximide (10mg/ml)	11	9/10?	Report that Sox3 and Lef1 activate Gsc and Gata6 (suppl. info). Report that cycloheximide alone induced expression of Xnr4, Gata4 and Gsc b-catenin enhanced Sox17b expression of Hnfb1, Endodermin, Foxa1, Foxa2 Sox17b did not induce expresssion of Mixer, Mix1.2, Bix1, Bix2, Bix3, Bix4, Xnr1, Xnr2, Cerberus, Xbra, Fzb1, Derriere or Hnf4a
SOX7	Zhang et al., 2005. Dev. Biol. 278:526 Zhang & Klymkowsky, unpublished.	Xnr4 Xnr5 Xnr6 Mixer			Ectodermin		dexamethasone (2 mM)	emetine (100 mg/ml)	stage11	stage 9	GR-SOX7-GFP construct
VegT	Tavener et al., 2005 Tada et al. 1998 Development 125: 3997	Bix1					Dexamethasone	cycloheximide
Otx2
AP2a (TFAP2a)	Luo et al., 2005. Dev.Growth Diff. 47:403.					desmoyokin, chitobiase, XK81, ZO-3 epithelial membrane protein 2 EF-hand domain containing Id2, calpain 8, fatty acid 2-hydroxylase tnx2, polo-like kinase FAST-1, BLIMP-1, GADPH, Slug PCNS, Myosin X, c-Myc, RTP801, Inca NIMA, MyoD, pinhead, nephrin-related	dexamethasone (10 mM)	not applicable	14	8/9	A member of a closely related family of proteins. Homo/heterodimers . Experiment carried out in animal caps co-injected with GR-AP2 0.6 ng/embryo), Wnt3a (0.3 ng/embryo) and chordin (5 ng/embryo) RNAs.
Xbra	Tada et al. 1997 Development 124:2225 Tada et al. 1998 Development 125: 3997	Bix1 (Brachyury-inducible homeobox)		Xbra		Xhox3 (+)	dexamethasone 1mM	cycloheximide 10mM	23	8-14	Xbra-GR construct appears more active at inducing muscle than does Xbra. Acctivation by Dex leads to protein destabilization Xbra induced Xbra expression requires FGF signaling Bix1 is present in vegetal regions, where Xbra is not. Bix1 promoter contains T-box binding site; also regulated by VegT
Vox
MyoD	Kolm & Sive 1995.
Bix1	Tada et al. 1998 Development 125: 3997					positive - XWnt8, Xvent1, aT4 globin, SOX17a, IFABP, endodermin, goosecoid, cerberus					Bix1 does not activate Xbra, eFGF, VegT, pintallavis, Xnot, chorin or saimois (data not shown) expressin in dorsal marginal zone explants reduces goosecoid and chordin expression (different from animal caps) and increases expression of Xwnt8, Xvent1, aT4-globin. and IFABP. Bix1 inhibits Xbra expression in disocciated marginal zonederived cells.
FAST-1 (FAST-VP16)	Watanabe & Whitman. 1999. Dev. 126:5621.	Mix.2		muscle Actin (analyzed at stge 28)		Xbra, Gsc, Xlim-1, Chordin, Xwnt8 endodermin, Sox17b (not 17a), Xlhbox8/Pdx1,IFABP repressed Xvent-1, epidermal keratin	dexamethasone	cycloheximide	10.5	9	full length protein is toxic ‘experiments carried out using Fast-1VP16-GR