Appendix 2.

RA-responsive genes with at least a 2-fold change in expression in F9 Wt cells relative to F9 RARγ−/− cells after RA treatment for 24 h. Fold change = F9 Wt +RA/F9 RARγ−/− +RA.

Affymetrix ID	Fold Changeab	Gene Symbol	Gene Title
1455498_at	122.6		Transcribed sequence with weak similarity to protein pir:A43932 (H. sapiens) A43932 mucin 2 precursor, intestinal – human
1423023_at	24.61	Sfrp5	secreted frizzled-related sequence protein 5
1448926_at	22.68	Hoxa5	Homeo box A5
1437347_at	21.85	Ednrb	endothelin receptor type B
1420603_s_at	14.36	Raet1a	retinoic acid early transcript alpha
1433428_x_at	12.67	Tgm2	transglutaminase 2, C polypeptide
1416855_at	12.61	Gas1	BB550400 RIKEN full-length enriched, 2 days pregnant adult female oviduct Mus musculus cDNA clone E230022A16 3′ similar to X65128 M.musculus gas1 mRNA, mRNA sequence.
1450624_at	10.81	Bhmt	betaine-homocysteine methyltransferase
1451191_at	9.949	Crabp2	cellular retinoic acid binding protein II
1436075_at	8.714	Sfrp5	secreted frizzled-related sequence protein 5
1437277_x_at	8.36	Tgm2	transglutaminase 2, C polypeptide
1453501_at	8.34	Hoxb1	Homeo box B1
1448470_at	7.705	Fbp1	fructose bisphosphatase 1
1421385_a_at	7.631	Myo7a	Myosin VIIa
1430425_at	6.958	5330435L01Rik	RIKEN cDNA 5330435L01 gene
1450839_at	6.684	D0H4S114	DNA segment, human D4S114
1420924_at	6.492	Timp2	tissue inhibitor of metalloproteinase 2
1428097_at	6.483	2510009E07Rik	RIKEN cDNA 2510009E07 gene, mRNA (cDNA clone IMAGE:6491720), partial cds
1438512_at	6.477	LOC210321	epididymal protein Av381126
1426785_s_at	6.38	Mgll	monoglyceride lipase
1439810_s_at	6.263	Pramel7	preferentially expressed antigen in melanoma like 7
1433662_s_at	5.664	Timp2	tissue inhibitor of metalloproteinase 2
1427433_s_at	5.661	5730446D14Rik	RIKEN cDNA 5730446D14 gene
1454677_at	5.545	Timp2	tissue inhibitor of metalloproteinase 2
1448494_at	5.482	Gas1	BB550400 RIKEN full-length enriched, 2 days pregnant adult female oviduct Mus musculus cDNA clone E230022A16 3′ similar to X65128 M.musculus gas1 mRNA, mRNA sequence.
1417500_a_at	5.389	Tgm2	transglutaminase 2, C polypeptide
1453836_a_at	5.373	Mgll	monoglyceride lipase
1423835_at	5.279	Zfp503	Zinc finger protein 503
1451481_s_at	5.22	D630035O19Rik	RIKEN cDNA D630035O19 gene
1448825_at	5.09	Pdk2	pyruvate dehydrogenase kinase, isoenzyme 2
1449397_at	5.047	Hoxb2	Homeo box B2
1450992_a_at	5.013	Meis1	myeloid ecotropic viral integration site 1
1433795_at	4.994	Tgfbr3	18-day embryo whole body cDNA, RIKEN full-length enriched library, clone:1110036H20 product:unknown EST, full insert sequence
1419430_at	4.84	Cyp26a1	cytochrome P450, family 26, subfamily a, polypeptide 1
1447845_s_at	4.806	Vnn1	Vanin 1
1453286_at	4.747	Plxna2	BB085537 RIKEN full-length enriched, adult male diencephalon Mus musculus cDNA clone 9330200E06 3′, mRNA sequence.
1438682_at	4.54	Pik3r1	Hypothetical protein C530050K14 (C530050K14), mRNA
1420831_at	4.52	Qscn6	quiescin Q6
1419602_at	4.455	Hoxa2	Homeo box A2
1417937_at	4.35	Dact1	dapper homolog 1, antagonist of beta-catenin (xenopus)
1449449_at	4.129	Ptges	prostaglandin E synthase
1448754_at	4.118	Rbp1	Retinol binding protein 1, cellular
1440143_at	4.067	F630022B06Rik	RIKEN cDNA F630022B06 gene
1418486_at	3.89	Vnn1	Vanin 1
1422674_s_at	3.854	Crygc	crystallin, gamma C
1435342_at	3.836	Kcnk6	potassium inwardly-rectifying channel, subfamily K, member 6
1451277_at	3.782	C530046K17Rik	RIKEN cDNA C530046K17 gene
1460287_at	3.777	Timp2	tissue inhibitor of metalloproteinase 2
1422597_at	3.726	Mmp15	Matrix metalloproteinase 15
1420565_at	3.686	Hoxa1	Homeo box A1
1454906_at	3.557	Rarb	retinoic acid receptor, beta
1415938_at	3.518	Spink3	serine protease inhibitor, Kazal type 3
1419309_at	3.429	Gp38	glycoprotein 38
1435184_at	3.393	B430320C24Rik	0 day neonate lung cDNA, RIKEN full-length enriched library, clone:E030020K21 product:weakly similar to HYPOTHETICAL 13.8 KDA PROTEIN [Homo sapiens], full insert sequence
1452302_at	3.393	Arhgef10	Ceroid-lipofuscinosis, neuronal 8
1422723_at	3.387	Stra6	Stimulated by retinoic acid gene 6
1420753_at	3.375	Tll	Tolloid-like
1420832_at	3.279	Qscn6	quiescin Q6
1456481_at	3.272	D9Ertd280e	hypothetical protein D930024E11
1419301_at	3.228	Fzd4	602109129F1 NCI_CGAP_Kid14 Mus musculus cDNA clone IMAGE:4237519 5′, mRNA sequence.
1418709_at	3.199	Cox7a1	cytochrome c oxidase, subunit VIIa 1
1424194_at	3.175	BC025872	cDNA sequence BC025872
1434069_at	3.041	BC067047	Adult male testis cDNA, RIKEN full-length enriched library, clone:4930413J11 product:mitochondria located 1 homolog (human), full insert sequence
1452303_at	2.966	Arhgef10	Ceroid-lipofuscinosis, neuronal 8
1424334_at	2.938	Fbxo23	F-box only protein 23
1449450_at	2.922	Ptges	prostaglandin E synthase
1420774_a_at	2.863	4930583H14Rik	RIKEN cDNA 4930583H14 gene
1455642_a_at	2.809	Fbxo23	F-box only protein 23
1419693_at	2.805	Colec12	collectin sub-family member 12
1434277_a_at	2.711	6430570G24	Adult male olfactory brain cDNA, RIKEN full-length enriched library, clone:6430570G24 product:unknown EST, full insert sequence
1452141_a_at	2.71	Sepp1	selenoprotein P, plasma, 1
1435693_at	2.62	BC012256	cDNA sequence BC012256
1448024_at	2.559	B430320C24Rik	0 day neonate lung cDNA, RIKEN full-length enriched library, clone:E030020K21 product:weakly similar to HYPOTHETICAL 13.8 KDA PROTEIN [Homo sapiens], full insert sequence
1419155_a_at	2.549	Sox4	SRY-box containing gene 4
1433575_at	2.506	Sox4	SRY-box containing gene 4
1460605_at	2.486	AA606869	Similar to Homeobox protein goosecoid-like (GSC-2) (LOC381848), mRNA
1418084_at	2.454	Nrp	Neuropilin
1419157_at	2.418	Sox4	SRY-box containing gene 4
1455796_x_at	2.418	Olfm1	olfactomedin 1
1443882_at	2.393		Transcribed sequence with weak similarity to protein ref:NP_081764.1 (M.musculus) RIKEN cDNA 5730493B19 [Mus musculus]
1427195_at	2.36		Transcribed sequence with weak similarity to protein ref:NP_081764.1 (M.musculus) RIKEN cDNA 5730493B19 [Mus musculus]
1424951_at	2.347	1300006M19Rik	RIKEN cDNA 1300006M19 gene
1417133_at	2.329	Pmp22	peripheral myelin protein
1448727_at	2.293	Tle6	Transducin-like enhancer of split 6, homolog of Drosophila E(spl)
1439341_at	2.261		Transcribed sequences
1435743_at	2.244	C130068N17Rik	RIKEN cDNA C130068N17 gene
1416674_at	2.235	Ptpru	Protein tyrosine phosphatase, receptor type, U
1418415_at	2.225	Hoxb5	Homeo box B5
1417605_s_at	2.209	Camk1	calcium/calmodulin-dependent protein kinase I
1456329_at	2.081	A230098A12Rik	RIKEN cDNA A230098A12 gene
1417956_at	2.055	Cidea	cell death-inducing DNA fragmentation factor, alpha subunit-like effector A
1418445_at	2.006	Slc16a2	solute carrier family 16 (monocarboxylic acid transporters), member 2
1457829_at	2.004	Clgn	Calmegin
1422912_at	0.497	Bmp4	Bone morphogenetic protein 4
1424643_at	0.483	Tcof1	Treacher Collins Franceschetti syndrome 1, homolog
1438824_at	0.466	Slc20a1	solute carrier family 20, member 1
1460204_at	0.465	Tec	cytoplasmic tyrosine kinase, Dscr28C related (Drosophila)
1444390_at	0.444		Transcribed sequences
1426041_a_at	0.426	Fgd4	FYVE, RhoGEF and PH domain containing 4
1435436_at	0.405		Transcribed sequences
1430433_at	0.405	4933406J08Rik	RIKEN cDNA 4933406J08 gene
1428283_at	0.401	Cyp2s1	cytochrome P450, family 2, subfamily s, polypeptide 1
1424310_at	0.399	Mocs2	molybdenum cofactor synthesis 2
1433733_a_at	0.396	Cry1	cryptochrome 1 (photolyase-like)
1430780_a_at	0.394	Pmm1	Phosphomannomutase 1
1424942_a_at	0.391	Myc	Myelocytomatosis oncogene
1437588_at	0.391	Pou4f2	POU domain, class 4, transcription factor 2
1419735_at	0.39	Csnk	Casein kappa
1429937_at	0.379	D530033C11Rik	RIKEN cDNA D530033C11 gene
1416967_at	0.374	Sox2	SRY-box containing gene 2
1419930_at	0.372	D15Ertd55e	Transcribed sequences
1422887_a_at	0.364	Ctbp2
1438861_at	0.357	Bnc2	RIKEN cDNA 5031434M05 gene
1431425_a_at	0.354	4930535B03Rik	RIKEN cDNA 4930535B03 gene
1451527_at	0.345	Pcolce2	procollagen C-endopeptidase enhancer 2
1454197_a_at	0.341	D19Ertd678e	unnamed protein product; hypothetical protein (evidence: rsCDS,ProCrest,decoder,NCBI CDS Predictor, Longest-ORF) putative; Mus musculus adult male testis cDNA, RIKEN full-length enriched library, clone:4933411H20 product:hypothetical protein, full insert sequence.
1436865_at	0.335	F630021I08Rik	RIKEN cDNA F630021I08 gene
1449455_at	0.333	Hck	hemopoietic cell kinase
1423259_at	0.332	Idb4	inhibitor of DNA binding 4
1416899_at	0.329	Utf1	undifferentiated embryonic cell transcription factor 1
1434705_at	0.329	D7Wsu87e	TRAF-binding protein
1416505_at	0.321	Nr4a1	nuclear receptor subfamily 4, group A, member 1
1421317_x_at	0.314	Myb	myeloblastosis oncogene
1443786_at	0.313	Utf1	BB000218 RIKEN full-length enriched, ES cells XhoI/SstI Mus musculus cDNA clone 2410014O14 3′ similar to NM_009482 Mus musculus undifferentiated embryonic cell transcription factor 1 (Utf1), mRNA sequence.
1423748_at	0.312	D530020C15Rik	RIKEN cDNA D530020C15 gene
1428775_at	0.311	1110008L16Rik	RIKEN cDNA 1110008L16 gene
1449231_at	0.31	Zfp296	Zinc finger protein 296
1455692_x_at	0.308	1700097N02Rik	Adult male testis cDNA, RIKEN full-length enriched library, clone:1700122G02 product:unknown EST, full insert sequence
1418649_at	0.302	Egln3	EGL nine homolog 3 (C. elegans)
1438160_x_at	0.301	Slco4a1	AV348121 RIKEN full-length enriched, adult male olfactory bulb Mus musculus cDNA clone 6430631M08 3′, mRNA sequence.
1452609_at	0.298	1190005I06Rik	RIKEN cDNA 1190005I06 gene
1416605_at	0.292	Nola2	nucleolar protein family A, member 2
1434239_at	0.288	AA408556	expressed sequence AA408556
1442379_at	0.287		Transcribed sequences
1432018_at	0.281	Ascl2	achaete-scute complex homolog-like 2 (Drosophila)
1420086_x_at	0.279	Fgf4	fibroblast growth factor 4
1450282_at	0.277	Fgf4	fibroblast growth factor 4
1449484_at	0.276	Stc2	stanniocalcin 2
1416316_at	0.272	Slc27a2	solute carrier family 27 (fatty acid transporter), member 2
1444292_at	0.27	D7Ertd143e	NACHT, LRR and PYD containing protein 12
1440563_at	0.269		15 days embryo head cDNA, RIKEN full-length enriched library, clone:D930010N06 product:unknown EST, full insert sequence
1451026_at	0.267	Ftsj3	FtsJ homolog 3 (E. coli)
1453345_at	0.26	3830408G10Rik	RIKEN cDNA 3830408G10 gene
1452004_at	0.259	Calca	calcitonin/calcitonin-related polypeptide, alpha
1426431_at	0.252	Jag2	AV264681 RIKEN full-length enriched, adult male testis (DH10B) Mus musculus cDNA clone 4930502C11 3′ similar to Y14331 Mus musculus partial mRNA for jagged2 protein, clone MB16, mRNA sequence.
1438084_at	0.221		Transcribed sequences
1418744_s_at	0.215	Tesc	Tescalcin
1417745_at	0.21	Cpn1	carboxypeptidase N, polypeptide 1
1420085_at	0.208	Fgf4	fibroblast growth factor 4
1453072_at	0.208	Gpr160	G protein-coupled receptor 160
1449146_at	0.199	Notch4	Notch gene homolog 4 (Drosophila)
1424531_a_at	0.191	Tcea3	transcription elongation factor A (SII), 3
1436657_at	0.187		LOC380738 (LOC380738), mRNA
1452384_at	0.187	Enpp3	Ectonucleotide pyrophosphatase/phosphodiesterase 3
1426808_at	0.181	Lgals3	Lectin, galactose binding, soluble 3
1450989_at	0.18	Tdgf1	teratocarcinoma-derived growth factor
1439746_at	0.126	C130085G02Rik	RIKEN cDNA C130085G02 gene
1423378_at	0.115	Adam23	a disintegrin and metalloprotease domain 23
1425926_a_at	0.0799	Otx2	orthodenticle homolog 2 (Drosophila)
1450177_at	0.0773	Ngfr	Nerve growth factor receptor (TNFR superfamily, member 16)
1431711_a_at	0.07	9030409G11Rik	RIKEN cDNA 9030409G11 gene

^aAverage from three experiments.

^bSome genes have multiple distinct probes on the GeneChip® resulting in different fold-changes from different probes.