Table 3. Differentially expressed genes in rat and mouse bone associated with embryological development and body patterning.

Skull∶Limb ratio	GENE	RAT	MOUSE		RAT	MOUSE
	Hoxa3		2.33	Skull only	Hoxa2	Phox2a
	Hoxa5	0.05	0.12		Hoxd3	Tbx18
	Hoxa7	0.19	0.17		Irx1	Tbx19
	Hoxa10	0.06	0.14		Irx2
	Hoxa11		0.15		Irx4
	Hoxa11s		0.04		Twist2
	Hoxb7	0.41			Msx2
	Hoxb8	0.25			Tbx1
	Hoxc5	0.30			Tbx3
	Hoxc6		0.30		Runx1
	Hoxd8		0.27	Limb only	Hoxc9	Tcfe3
	Cart1	10.76	4.55/3.65		Tcfe3
	Dlx1		2.21/0.31
	Dlx3	2.16	2.38
	Dlx5	2.22	2.60
	Msx1		3.19/0.44
	Msx2		2.96
	Phox2a	0.31
	Shox2	0.08/0.14	0.06/0.18
	Tbx2	2.36/2.4	2.75
	Tbx3		0.32
	Tbx5	0.07
	Tbx14		0.06
	Tbx15	0.44	0.36
	Tcf3	2.04	2.07
	Tcf4		0.20
	Tcf7	3.51
	Tcfcp212		2.91
	Twist1	2.31/2.70	11.49
	Twist2		0.34
	Zic1	4.26	25.80
	Zic2		12.53
	Zic3	8.66	24/4.79
	Zic4	8.13	5.20/4.34
	Zic5		9.32/6.65

Some genes are represented with more than one probe set on the array, therefore some genes have two values.