Table 2.

Regionally significant genes (FDR < 0.10)

Symbol	Gene description	iP vs. iNP fold change
Accumbens
Ahi1	Abelson helper integration site 1	-1.54
Gsta4	glutathione S-transferase, alpha 4	-1.52
Lin7c	lin-7 homolog C (C. elegans)	-1.51
Rps2	ribosomal protein S2	-1.48
RT1-Aw2^a	RT1 class Ib, locus Aw2	-1.37
Sephs2	selenophosphate synthetase 2	-1.61
Stk38	serine/threonine kinase 38	-1.37
Scn3a	sodium channel, voltage-gated, type III, alpha polypeptide	-1.38
Slc5a3	solute carrier family 5 (inositol transporters), member 3	-1.40
Akap11	A kinase (PRKA) anchor protein 11	1.50
Ampd3	adenosine monophosphate deaminase 3	1.37
Cat	Catalase	1.42
Lyz	Lysozyme	2.11
Pgk1	Phosphoglycerate kinase 1	2.05
Psma5	proteasome (prosome, macropain) subunit, alpha type 5	1.44
RT1-Bb	RT1 class II, locus Bb	1.46
Amygdala
Hmgcr	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	-1.28
Phgdh^a	3-phosphoglycerate dehydrogenase	-1.36
Ahi1	Abelson helper integration site 1	-1.35
Csnk1d	casein kinase 1, delta	-1.18
Casp3	caspase 3, apoptosis related cysteine protease	-1.21
Ddr2	discoidin domain receptor family, member 2	-1.18
Fgfr1	Fibroblast growth factor receptor 1	-1.21
Fn1^a	fibronectin 1	-1.32
Gsta4^a	glutathione S-transferase, alpha 4	-1.78
Nyw1	ischemia related factor NYW-1	-1.38
Kdr	kinase insert domain protein receptor	-1.50
Lin7c	lin-7 homolog C (C. elegans)	-1.27
Lox	lysyl oxidase	-1.22
Pak2	p21 (CDKN1A)-activated kinase 2	-1.20
Rps2^a	ribosomal protein S2	-1.63
RT1-Aw2^a	RT1 class Ib, locus Aw2	-1.41
Sephs2	selenophosphate synthetase 2	-1.39
Scn3a^a	sodium channel, voltage-gated, type III, alpha polypeptide	-1.44
Slc28a2	solute carrier family 28 (sodium-coupled nucleoside transporter), member 2	-1.25
Slc5a3	solute carrier family 5 (inositol transporters), member 3	-1.77
Shc3	src homology 2 domain-containing transforming protein C3	-1.29
Tagln	Transgelin	-1.22
Atic	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	1.32
Acsl1	acyl-CoA synthetase long-chain family member 1	1.27
Amigo	amphoretin-induced gene and ORF	1.22
Argbp2^a	Arg/Abl-interacting protein ArgBP2	1.22
Asns	asparagine synthetase	1.25
Atrn	Attractin	1.33
Btg2	B-cell translocation gene 2, antiproliferative	1.19
Celsr2	cadherin EGF LAG seven-pass G-type receptor 2	1.25
Cd24^a	CD24 antigen	1.32
Chgb	chromogranin B	1.25
Eif2b1^a	eukaryotic translation initiation factor 2B, subunit 1 alpha	1.29
Fth1	ferritin, heavy polypeptide 1	1.29
Gfm	G elongation factor	1.30
Irak2	interleukin-1 receptor-associated kinase 2	1.22
Ldhb	lactate dehydrogenase B	1.23
Lcp2	lymphocyte cytosolic protein 2	1.18
Lyz	Lysozyme	1.81
Nrn1	Neuritin	1.19
Nptx1	neuronal pentraxin 1	1.32
Pdlim3	PDZ and LIM domain 3	1.28
Pmpcb	peptidase (mitochondrial processing) beta	1.26
Pcm1	pericentriolar material 1	1.52
Pgk1	phosphoglycerate kinase 1	2.08
Prps1	phosphoribosyl pyrophosphate synthetase 1	1.19
Pbef1	pre-B-cell colony enhancing factor 1	1.25
Psma5	proteasome (prosome, macropain) subunit, alpha type 5	1.57
RT1-N3	RT1 class Ib gene, H2-TL-like, grc region (N3)	1.26
RT1-Bb	RT1 class II, locus Bb	1.39
Sh3gl3	SH3 domain protein 2 C1	1.18
Spats1	spermatogenesis associated, serine-rich 1	1.29
Scp2	sterol carrier protein 2	1.25
Thrsp	thyroid hormone responsive protein	1.30
Frontal cortex
Phgdh	3-phosphoglycerate dehydrogenase	-1.42
Gsta4	glutathione S-transferase, alpha 4	-1.75
Rps2	ribosomal protein S2	-1.76
Scn3a	sodium channel, voltage-gated, type III, alpha polypeptide	-1.39
Slc5a3	solute carrier family 5 (inositol transporters), member 3	-1.44
Gfap	glial fibrillary acidic protein	1.44
Pgk1	phosphoglycerate kinase 1	2.08
Psma5	proteasome (prosome, macropain) subunit, alpha type 5	1.78
Hippocampus
Phgdh^a,^b	3-phosphoglycerate dehydrogenase	-1.39
Azi2	5-azacytidine induced gene 2	-1.28
Ahi1	Abelson helper integration site 1	-1.48
B2m	beta-2 microglobulin	-1.31
Fn1	fibronectin 1	-1.55
Gsta4^a	glutathione S-transferase, alpha 4	-2.07
Lxn	Latexin	-1.34
Rab5a^b	RAB5A, member RAS oncogene family	-1.29
Rps2	ribosomal protein S2	-1.53
RT1-Aw2^b	RT1 class Ib, locus Aw2	-1.41
Sephs2^b	selenophosphate synthetase 2	-1.47
Stk38	serine/threonine kinase 38	-1.21
Slc5a3	solute carrier family 5 (inositol transporters), member 3	-1.47
Tagln	Transgelin	-1.23
Akap11^b	A kinase (PRKA) anchor protein 11	1.32
Dcn^b	Decorin	1.29
Grb1^b4	growth factor receptor bound protein 14	1.32
Iag2^b	implantation-associated protein	1.31
Pgk1^b	phosphoglycerate kinase 1	2.28
RT1-N3	RT1 class Ib gene, H2-TL-like, grc region (N3)	1.35
Slit1	slit homolog 1 (Drosophila)	1.32
Caudate-putamen
Phgdh^a	3-phosphoglycerate dehydrogenase	-1.33
Ahi1	Abelson helper integration site 1	-1.46
Apobec1	apolipoprotein B editing complex 1	-1.23
Fn1	fibronectin 1	-1.35
Gsta4^a	glutathione S-transferase, alpha 4	-2.00
Lin7c	lin-7 homolog C (C. elegans)	-1.31
Prkag1	protein kinase, AMP-activated, gamma 1 noncatalytic subunit	-1.19
Rpl6	ribosomal protein L6	-1.21
Rps2	ribosomal protein S2	-1.64
RT1-Aw2^a	RT1 class Ib, locus Aw2	-1.39
Sephs2	selenophosphate synthetase 2	-1.45
Scn3a	sodium channel, voltage-gated, type III, alpha polypeptide	-1.46
Slc5a3	solute carrier family 5 (inositol transporters), member 3	-1.41
Shc3	src homology 2 domain-containing transforming protein C3	-1.39
Akap5	A kinase (PRKA) anchor protein 5	1.39
Akr1b4	aldo-keto reductase family 1, member B4 (aldose reductase)	1.21
Agt	Angiotensinogen	1.30
Asns	asparagine synthetase	1.20
Cryab	crystallin, alpha B	1.35
Hspa2	heat shock protein 2	1.24
Nefh	neurofilament, heavy polypeptide	1.44
Pgk1	phosphoglycerate kinase 1	2.24
Psma5	proteasome (prosome, macropain) subunit, alpha type 5	1.63
Znf386	zinc finger protein 386 (Kruppel-like)	1.22

FDR = false discovery rate; iP = inbred alcohol-preferring rat; iNP = inbred alcoholenon-preferring rat.

Genes represented by significant differential expression (FDR < 0.10) of more than one probe set. The largest absolute fold change for the gene among significant probe sets is listed. In all cases, the significant probe sets expressed differential expression in the same direction.

Gene also significant in Edenberg et al. (2005)