Table 2. SSTF Genes (1691 genes; 3574 probe sets) Activated by Lbx1 in the Neural Tube (4.1%).

Classa	#b	SSTFc	NTd	UCRe	Heterof (n = 3)	Mutantf (n = 3)	Fold Δg
							(Highest)	Average Signal of PS				(Lowest)
1. Basic (177 genes; 362 probe set) 5% activated
bZIP	1	Mafa	+		487± 115	48± 12	−10.2
	2	Mafb	da		271± 33	64± 8	−4.2	−2.6
	3	Jun	+		255± 52	129± 13	−2.0	−2.1
	4	Jundm2	ns	75	442± 12	313± 23	−1.4
bHLH	5	Neurog3	vz		25±4	12±5	−2.1	−1.1*†
	6	Id4	d	+	7606±306	3816±930	−2.0	−1.9	−1.9	−2.5
	7	Id3	d		324±42	191±58	−1.7
	8	Hes5	vz		369±62	289±47	−1.3*	−1.5*
2. Zinc-coordinated (749 genes; 1627 probe sets) 3% activated
C4	9	Nr2f2	+	81/+	833±23	412±66	−2.0	−2.4	−2.0	−2.4
	10	Trps1	d, vz	+	158±32	113±19	−1.4*	−1.2*	−1.2*	−1.8
	11	Sall3	da,vz	28	777±184	77±16	−10.1	−4.9
	12	Sall4	+	76	95±28	26±8	−3.7	−1.5*†
	13	Zic5	da	63	477±113	63±12	−7.6	−4.5	−1.8
	14	Zic4	da	62/+	414±157	105±18	−3.9	−3.4
	15	Zic3	da	95	1625±212	601±34	−2.7	−3.2
	16	Zic2	da	63/+	327±71	110±7	−3.0
	17	Zic1	da	62	14774±804	6851±417	−2.2	−3.8
	18	Wt1	+		35±18	10±3	−3.5*†
	19	Zfp804a	nd		584±72	195±19	−3.0	−1.6*†
	20	Klf5	ns		33±6	12±2	−2.9	−1.8†	−1.5*†
	21	Zfpm2	pm	21/+	199±54	97±16	−2.1	−1.4
	22	Ikzf4	+		197± 12	142± 16	−1.4	−2.2	−1.1*†
	23	Bcl11a	pm	13/+	5272±514	2881±141	−1.8	−1.9	−2.1
	24	Zcchc11	nd		1899±34	1838±86	−1.0*	−1.2*	−1.8*	−1.1*
	25	Hivep2	vz		153±20	95±5	−1.6	−1.8
	26	Rest	da		187±9	108±13	−1.7	−1.4*	−1.1*†	−1.0*†
	27	Zfp704	nd		361±52	226±15	−1.6	−1.2*†
	28	Zfp467	ns		227±21	138±9	−1.6	−1.7	−1.3*
	29	Zfp775	nd		208±29	142±11	−1.5
	30	B930008K04Rik	nd		62±5	43±6	−1.4
	31	Zfp784	nd		54±5	38±2	−1.4
CCHC	32	Zcchc12	pm		337±71	151±36	−2.2
CXXC	33	Cxxc5	nd		3114±127	1975±7	−1.6	−1.4
	34	Cxxc4	nd		1398±118	1105±129	−1.3	−1.4	1.1*†
3. Helix-turn-helix (512 genes; 1026 probe sets) 5% activated
HD	35	Gbx1	da		1422± 288	67± 29	−21.2
	36	Gbx2	da	86	3027±237	1216±169	−2.5
	37	Lbx1	da		3374±137	331±7	−10.2	−7.6
	38	Tshz2	d,pm	76	1372±238	209±24	−6.6	−8.1	−5.3
	39	Lhx2	d,pm	104	240±179	34±3	−7.0*
	40	Lhx1	pm	50/+	5763±271	2575±1214	−2.2	−2.4
	41	Pknox2	d, pm		1865±198	437±43	−4.3	−2.5
	42	Satb2	+	+	216±28	70±12	−3.1	−1.0*
	43	Lmx1b	da	+	601± 135	286± 50	−2.1	−1.1*†
	44	Nkx6-1	vz,svz	31	81±27	47±12	−1.7*
	45	Hoxa4	pm	56	149±15	99±4	−1.7*	−1.5
	46	Hoxb2	d,pm	82	2517±160	1526±130	−1.6
	47	Hoxb8	d,pm	82	4850±249	3297±476	−1.5
	48	Msx1	d,vz		77±14	46±7	−1.7	1.1*
	49	Msx2	d,vz		14±1	10±2	−1.5
	50	Zfhx1b	d,svz	2/+	853±100	519±90	−1.6	−1.8	−1.7*	−1.2*†
	51	Pax6	vz,da	83/+	72±11	51±5	−1.4	1.0*	−1.1*
	52	Prrxl1	da	101/+
PD	53	Pax8	pm		861±224	84±24	−10.2
	54	Pax5	+	90	350±45	209± 24	−1.7	1.2*†	1.0*†
FH	55	E2F8	nd		53±11	33±7	−1.6	1.0*†
TC	56	Ets2	d		346±90	140±22	−2.5
	57	Elk3	+		103±29	48±14	−2.1	1.1*	−1.3*
	58	Etv5	d		46±5	23±4	−2.0	1.4*	1.0*†
WH	59	Depdc1a	nd		31±3	16±3	−2.0
	60	Cdc6	nd		36±9	20±4	−1.8
	61	Rfx4	d		524±50	323±86	−1.6	1.1*†
	62	Myst4	d		1420±39	992±80	−1.4	−1.1*†
	63	Rfxdc2	d		2433±54	2177±121	−1.1	−1.1*†	−1.6*†	1.0*†
4. ß-scaffold (116 genes; 281 probe sets) 2% activated
STAT	64	Stat1	ns		76±6	53±10	−1.4	−1.5*	−1.3*
HMG	65	Sox13	pm		127±28	66±7	−1.9
5. Other (138 genes; 279 probe sets) 4% activated
	66	Dmrt3	pm	148	63±31	12±1	−5.5
	67	Lbxcor1	pm	+	25659+ 1614	6284± 653	−4.1
	68	Dmrtb1	nd		357±63	169±11	−2.1
	69	Notch3	vz		282±82	143±23	−2.0	−1.3*
	70	Notch2	vz		266±32	158±33	−1.7	1.0*†
	71	Obfc2a	nd		186±41	104±15	−1.8	−1.3*	−1.5*	−1.3*†	1.0*†	1.0*†

^a–gAs in Table 1.