Table 2. Genes regulated in the VTA of Clock mutant mice

AFFY #

Signal

log2 ratio Mut/Cont

P

value

Gene

Genes up-regulated in the VTA of Clock mutant mice vs littermate controls

103582_r_at

54.33333

1.1

0.003903

RIKEN cDNA 6130401J04 gene

101393_at

87.66667

1.1

0.002759

Annexin A3

100324_g_at

216.9

1.05

8.5E-06

---

92247_at

198

1

0.007882

Rho GTPase activating protein 5

98474_r_at

76.2

0.95

0.006026

TNFa -induced protein 6

101524_at

233.0333

0.9

0.021427

RIKEN cDNA 2610510D13 gene

99098_at

1402.733

0.9

0.003766

Farnesyl diphosphate synthetase

102703_s_at

728.1

0.9

0.006518

Aquaporin 4

94143_at

159.2667

0.8

0.002703

Glial fibrillary acidic protein

98770_at

184.3333

0.8

0.007123

Centromere autoantigen C

102885_at

140.2667

0.75

1.5E-06

Synaptobrevin like 1

94494_at

268.9667

0.75

0.01474

Phenylalanine-tRNA synthetase-like

96731_at

455.8333

0.7

0.000156

RIKEN cDNA 1110001P04 gene

92944_at

417.9

0.7

0.000333

Glutamate receptor, ionotropic, AMPA1 (a 1)

98762_f_at

59.9

0.65

0.004006

Zinc finger protein 97

103710_at

119.7667

0.65

0.000244

Sequence with weak similarity to protein pir:T14757 (Homo sapiens)

99121_at

97.2

0.65

0.00063

Fragile X mental retardation gene 1, autosomal homolog

102277_at

134.7

0.6

0.004991

Zinc finger protein 26

100690_at

2155.1

0.6

0.000001

Tyrosine hydroxylase

103569_at

191.7

0.6

0.008265

SH3-domain GRB2-like B1 (endophilin)

101966_s_at

1049.267

0.6

0.000145

Ring finger protein 13

93039_at

72.4

0.6

0.000215

RIKEN cDNA 1190003P12 gene

160266_r_at

205.6

0.6

0.00012

RIKEN cDNA 1110064N10 gene

93390_g_at

72.5

0.6

0.02839

Prominin 1

101590_at

464.8333

0.6

0.009483

Lysosomal membrane glycoprotein 2

100435_at

489.1667

0.6

3.65E-05

Endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 2

95093_at

85.93333

0.55

0.021511

RIKEN cDNA 2610511G16 gene

96885_at

89.83333

0.55

0.018079

RIKEN cDNA 2510015F01 gene

103321_at

120.8

0.55

0.007924

Hypothetical protein B230364F10

94144_g_at

603.6667

0.55

0.004874

Glial fibrillary acidic protein

103895_at

568.3333

0.55

0.014737

Expressed sequence AW549877

160678_at

126.3333

0.55

0.005337

EST AI426782

102704_at

1646.033

0.55

3.25E-05

Aquaporin4

93909_f_at

1776.433

0.55

0.003766

---

102872_f_at

49.5

0.5

0.01073

Zinc finger protein51

160392_at

228.2333

0.5

0.003148

RIKEN cDNA B430110G05 gene

160200_at

137.7667

0.5

0.0197

RIKEN cDNA 3230401D17 gene

97346_at

80.03333

0.5

0.003441

RIKEN cDNA 2610001J05 gene

96068_at

124.8333

0.5

0.004627

RIKEN cDNA 1500034J20 gene

96295_at

1711.767

0.5

0.024019

Phosphoserine aminotransferase1

94915_at

421.5

0.5

9.25E-05

Peptidylprolyl isomeraseB

97853_at

179.9667

0.5

0.021292

PC4 and SFRS1 interacting protein2

94459_at

183.6667

0.5

0.009662

Mus musculus cDNA clone MGC:36861 IMAGE:4460168, complete cds

94975_at

242.2

0.5

0.010096

Iron responsive element-binding protein2

97204_s_at

246.2333

0.5

0.000121

DnaJ (Hsp40) homolog, subfamily D, member 1

92257_at

204.7

0.5

0.000788

Circadian locomoter output cycles kaput

104135_at

803.4333

0.5

0.000784

ADP-ribosylation factor-like3

101781_f_at

138.2333

0.5

0.008955

---

101588_at

92.03333

0.45

0.000771

Solute carrier family 16 (monocarboxylic acid transporters), member 1

95502_at

1166.667

0.45

0.001427

Sirtuin 2 (silent mating type information regulation 2, homolog) 2 (S. cerevisiae)

95387_f_at

211.9333

0.45

0.025122

Semaphorin4B

101489_at

1285.333

0.45

0.007664

S

-adenosylmethionine decarboxylase1

97506_at

170.7

0.45

0.017044

Ring finger protein2

103257_at

395.0667

0.45

0.01065

RIKEN cDNA C730036B01 gene

95288_i_at

260.3667

0.45

0.00641

RIKEN cDNA C330012F17 gene

94895_at

175.2

0.45

0.000823

RIKEN cDNA 9430020E02 gene

102052_at

135.6

0.45

0.00279

RIKEN cDNA 1300003D03 gene

99445_at

92.46667

0.45

0.006568

RIKEN cDNA 1110028E10 gene

100711_at

1413.7

0.45

0.001477

Ribosomal protein L10A

92379_f_at

873.2333

0.45

0.000621

Protein tyrosine phosphatase, receptor type, Z polypeptide 1

93485_at

1217.3

0.45

0.001033

Protein tyrosine phosphatase, receptor type, D

97989_at

221.9

0.45

0.006547

Protein phosphatase 3, catalytic subunit, b isoform

103791_at

102.8333

0.45

0.00359

NMDA receptor-regulated gene1

92876_at

77.16667

0.45

0.017808

NADH dehydrogenase (ubiquinone) Fe-S protein 4

101946_at

230.3

0.45

0.000939

Lysophospholipase1

94214_at

327.4

0.45

0.022215

Fatty acid-binding protein 3, muscle and heart

93885_g_at

121.0333

0.45

0.025394

Endomucin

98025_at

992.1667

0.45

0.001676

Ecotropic viral integration site2

98132_at

541.5333

0.45

0.000759

Cytochrome c, somatic

93057_at

716.3

0.45

0.0197

Basic transcription factor3

104330_g_at

157.8

0.4

0.006429

SWI/SNF related, matrix associated, actin-dependent regulator of chromatin, subfamily f, member 1

101906_at

101.6667

0.4

0.02726

SMC4 structural maintenance of chromosomes 4-like 1 (yeast)

92579_at

282

0.4

0.000837

Sjogren syndrome antigenB

99185_at

352.4333

0.4

0.005913

RIKEN cDNA 2810443J12 gene

96688_at

127.1

0.4

0.000385

RIKEN cDNA 2610318G18 gene

98491_at

503.4333

0.4

0.025206

RIKEN cDNA 2610313E07 gene

96672_at

577.3333

0.4

0.000193

RIKEN cDNA 2300002F06 gene

97874_at

520.8667

0.4

0.000331

RIKEN cDNA 1500032D16 gene

104386_f_at

1440.9

0.4

0.00623

RIKEN cDNA 1110004F14 gene

94913_at

627.1

0.4

2.05E-05

Ras-GTPase-activating protein (GAP<120>) SH3-domain-binding protein 2

102395_at

567.4333

0.4

0.001519

Peripheral myelin protein

96082_at

550.6333

0.4

0.001034

Mitochondrial ribosomal protein L30

93078_at

682.5667

0.4

0.001898

Lymphocyte antigen 6 complex, locus A

95359_at

6454.5

0.4

0.001108

Heat-shock protein 1, b

98026_g_at

1335.167

0.4

0.001191

Ecotropic viral integration site2

99128_at

1791.5

0.4

0.002592

ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit

104602_at

177.4

0.35

0.01441

Wiskott-Aldrich syndrome protein interacting protein

103328_at

212.8333

0.35

0.010525

TRAF family member-associated Nf-k B activator

103074_f_at

366.7667

0.35

0.008492

TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor

93471_at

515.7

0.35

0.001094

Solute carrier family 4, sodium bicarbonate cotransporter, member 7

99179_at

408

0.35

0.008499

RIKEN cDNA 3010002G01 gene

95743_at

1290.2

0.35

0.007723

RIKEN cDNA 2310050K10 gene

103567_at

485.5333

0.35

0.022124

RIKEN cDNA 2010313D22 gene

93580_at

1174.767

0.35

0.009042

Pumilio 2 (Drosophila)

101992_at

841.8333

0.35

0.020526

Proteasome (prosome, macropain) subunit b type 6

93623_at

88.86667

0.35

0.01303

Dystrophin, muscular dystrophy

96059_at

299.5667

0.35

0.002777

DNA segment, Chr 4, ERATO Doi 786, expressed

160655_at

206.0667

0.35

0.009076

CarboxypeptidaseD

92575_at

544.2333

0.35

0.019418

Aryl-hydrocarbon receptor-interacting protein

103745_at

224.2

0.3

0.015185

Sorting nexin13

104709_at

1290.333

0.3

0.005919

SEC23A (S. cerevisiae)

97315_at

286.8333

0.3

0.016868

RIKEN cDNA 2610028L19 gene

98039_at

412.4333

0.3

0.012747

RIKEN cDNA 2410015M20 gene

98397_at

112.3667

0.3

0.025333

RIKEN cDNA 1700030G05 gene

98089_at

95.36667

0.3

0.02404

RIKEN cDNA 1190005P17 gene

104725_at

702.6667

0.3

0.022716

Ras homolog gene family, member Q

96632_at

2964.9

0.3

0.00811

Mortality factor 4 like2

95003_at

422.2667

0.3

0.02054

Metallothionein-I activator

92816_r_at

284.0333

0.3

0.022873

Eukaryotic translation initiation factor 4A1

94766_at

8905.767

0.3

0.002975

Eukaryotic translation elongation factor 1 a 1

97248_at

1545.5

0.3

0.004408

Diazepam-binding inhibitor

160326_at

231.3

0.3

0.026864

Carnitine deficiency-associated gene expressed in ventricle 3

98079_at

565.1

0.3

0.002753

Carbonic anhydrase14

98254_f_at

6327.333

0.3

0.006856

---

Genes down-regulated in the VTA of Clock mutant mice vs littermate controls

92501_s_at

69.83333

-1.4

0.97294

Pleiomorphic adenoma gene-like 1

160841_at

173.4667

-1.2

0.999696

D site albumin promoter-binding protein

92925_at

119.4667

-1

0.999957

CCAAT/enhancer binding protein (C/EBP), b

160878_at

190.9333

-0.75

0.999464

Block of proliferation 1

101007_at

169.6667

-0.75

0.980898

MAP kinase-interacting serine/threonine kinase 2

99390_at

65.56667

-0.75

0.99751

Wingless-related MMTV integration site 5A

93619_at

71.06667

-0.7

0.96911

Period homolog 1 (Drosophila)

96055_at

1593.867

-0.65

0.999982

Cholecystokinin

104685_g_at

132.8

-0.65

0.9971

Glutamate receptor, ionotropic, NMDA1 (z 1)

98008_at

1678.2

-0.6

1

chemokine (C-X3-C motif) ligand 1

160965_at

143.3333

-0.6

0.996315

EST AA793972

92749_at

983.2667

-0.6

0.999965

GABA-A receptor, subunit b 1

102313_at

152

-0.6

0.999829

GTP cyclohydrolase 1

92180_at

373.6333

-0.6

0.997895

H1 histone family, member X

97336_at

606.6333

-0.55

0.99989

Cathepsin F

94811_s_at

2635.733

-0.55

0.999625

General transcription factor II H, polypeptide 1

104409_at

268.7

-0.55

0.999761

Glutamate receptor, ionotropic, kainate 5 (g 2)

104686_at

192.4

-0.55

0.999902

Glutamate receptor, ionotropic, NMDA1 (z 1)

93694_at

21.06667

-0.55

0.999992

Period 2

104269_at

487.3333

-0.55

0.985713

Synaptotagmin 5

96637_at

164.4

-0.55

0.98255

TBC1 domain family, member 1

96069_at

538.6667

-0.5

0.99538

Aldo-keto reductase family 7, member A5 (aflatoxin aldehyde reductase)

100439_i_at

1239.333

-0.5

0.999979

Ankyrin 1, erythroid

97925_at

393.0333

-0.5

0.999994

Casein kinase 1, e

102196_at

213.2

-0.5

0.999884

Guanine nucleotide binding protein, a 11

96911_at

1542.3

-0.5

0.999921

Guanine nucleotide binding protein, b 2

93019_at

525.3333

-0.5

0.999781

H2A histone family, member X

92908_at

291.7

-0.5

0.999921

Human immunodeficiency virus type I enhancer-binding protein 1

99109_at

100.1667

-0.5

0.983275

Immediate early response 2

101947_at

349.5667

-0.5

0.999873

Neighbor of A-kinase anchoring protein 95

94932_at

711.8333

-0.5

0.999993

Platelet derived growth factor, a

93347_at

1243.533

-0.5

0.998228

RAB24, member RAS oncogene family

161243_f_at

598.6

-0.5

0.999764

RIKEN cDNA 0910001L24 gene

99514_at

1031.5

-0.45

0.999879

Brain expressed myelocytomatosis oncogene

104589_at

367.8333

-0.45

0.998384

Expressed sequence C80913

99872_s_at

1897.567

-0.45

0.999993

Ferritin light chain1

95489_at

385.7

-0.45

0.990941

Flightless I homolog (Drosophila)

160335_at

290

-0.45

0.979469

Glutamate-cysteine ligase, modifier subunit

96656_at

356.4333

-0.45

0.99846

Golgi reassembly stacking protein 1

97227_at

243.4333

-0.45

0.99992

Guanine nucleotide-binding protein, a 12

161214_r_at

1172.333

-0.45

0.99913

Hypothetical protein MGC47434

160820_at

1006.4

-0.45

0.997023

Immunoglobulin superfamily, member8

160417_at

1143.633

-0.45

0.992719

Kinesin family member5B

93642_at

457.3667

-0.45

0.999648

Longevity assurance homolog 1 (S. cerevisiae)

104554_at

327

-0.45

0.996066

Nuclear receptor subfamily 2, group F, member 6

160412_at

91.03333

-0.45

0.991294

Programmed cell death2

103501_at

1507.467

-0.45

0.999674

Purine rich element-binding protein A

97104_g_at

836.1333

-0.45

0.999993

RIKEN cDNA 0610038L10 gene

94958_at

133.5667

-0.45

0.992878

RIKEN cDNA 1110013L07 gene

94925_at

193.5667

-0.45

0.994772

RIKEN cDNA 1810055D05 gene

97722_at

254.5333

-0.45

0.976877

Signal sequence receptor, a

103910_at

382.2

-0.4

0.997959

---

97263_s_at

946.5

-0.4

0.980606

Casein kinase 1, d

95619_at

114.8667

-0.4

0.999132

Chaperonin subunit 7 (h )

92223_at

541.2667

-0.4

0.999346

Complement component 1, q subcomponent, g polypeptide

162469_r_at

2395.533

-0.4

0.997532

Cytochromec-1

101367_at

1364.367

-0.4

0.99007

Dynactin1

104109_at

699.9

-0.4

0.999932

F-box only protein21

95095_at

848.3333

-0.4

0.977229

Flotillin1

94295_at

1331.533

-0.4

0.999062

General transcription factor II I

95566_at

412.1667

-0.4

0.98559

Glycosylphosphatidylinositol specific phospholipase D1

98511_at

121.1

-0.4

0.978722

HnRNP-associated with lethal yellow

96741_at

161.2

-0.4

0.9716

Mus musculus mRNA for mKIAA1523 protein

97520_s_at

1922.267

-0.4

0.999896

Neuronatin

99599_s_at

2116.233

-0.4

0.999572

Prostate tumor overexpressed gene 1

96313_at

1281.267

-0.4

0.999853

RAS protein-specific guanine nucleotide-releasing factor 1

97514_at

188.5333

-0.4

0.996121

RIKEN cDNA 1810063B05 gene

104320_at

1228.233

-0.4

0.992107

RIKEN cDNA 2310036D04 gene

100633_at

520.8333

-0.4

0.995761

RIKEN cDNA 2810484M10 gene

160204_at

172.5

-0.4

0.987205

RIKEN cDNA 3110013H01 gene

103220_at

227.7

-0.4

0.999898

RIKEN cDNA 5730494G16 gene

160196_at

492.5667

-0.4

0.979481

Stromal membrane-associated protein1

94457_at

462.2

-0.4

0.998709

Ubiquitin conjugating enzyme 7 interacting protein 3

97724_at

214.7333

-0.35

0.982532

Cryptochrome 2 (photolyase-like)

101975_at

890

-0.35

0.999594

Delta-like 1 homolog (Drosophila)

99150_at

192.1667

-0.35

0.994637

Immature colon carcinoma transcript 1

94516_f_at

1535.1

-0.35

0.992157

Preproenkephalin1

92545_f_at

2208.4

-0.35

0.997533

Prostaglandin D2 synthase (brain)

160393_at

1307.767

-0.35

0.970397

RIKEN cDNA 4930555L11 gene

92757_at

614.2333

-0.35

0.999822

Seizure-related gene6

101446_at

153.8333

-0.35

0.99675

Tumor protein D52-like1

98617_at

885.9

-0.35

0.970653

WW domain-binding protein 11

102835_at

295.6

-0.3

0.968314

Adaptor protein complex AP-2, a 2 subunit

95000_g_at

81.96667

-0.3

0.986379

Mus musculus mRNA for hypothetical protein

99449_at

1003.033

-0.3

0.990248

Potassium voltage-gated channel, subfamily Q, member 2

104422_at

1343.4

-0.3

0.997804

Protein tyrosine phosphatase, receptor type, N

160240_at

1132.467

-0.3

0.999811

RIKEN cDNA 1110003E01 gene

96320_at

1477.1

-0.3

0.95387

RIKEN cDNA 2310044H10 gene

104375_at

3760.567

-0.3

0.980251

Sparc/osteonectin, cwcv and kazal-like domains proteoglycan 2

Cell growth or death.

SH3-domain GRB2-likeB1, peripheral myelin protein, ecotropic viral integration site2, mortality factor 4 like 2, block of proliferation 1, brain expressed myelocytomatosis oncogene, programmed cell death 2, platelet-derived growth factor a , pleiomorphic adenoma gene-like 1.

Regulation of transcription.

Metallothionein-1 activator; matrix associated actin-dependent regulator of chromatin f1; basic transcription factor 3; ring finger protein 2; Circadian locomotor output cycles kaput; sirtuin 2; aryl-hydrocarbon receptor-interacting protein; zinc finger proteins 26, 51, and 97; centromere autoantigen C; TAF9 RNA polymerase II; H1 histone X; H2A histone X; HIV 1 enhancer-binding protein 1; ankyrin1; CCAAT/enhancer-binding protein b ; D site albumin promoter-binding protein; general transcription factor 2H1; general transcription factor 2I; nuclear receptor 2F6; purine rich element-binding protein A; period 1; period 2; cryptochrome 2.

Signal transduction, second messengers.

Protein phosphatase 3 catalytic b , RAS-GTPase-activating protein, RAS homolog Q, r GTPase activating protein 5, ADP-ribosylation factor-like3, TRAF family member-Nfk B activator, protein tyrosine phosphatase receptor D, protein tyrosine phosphatase receptor Z1, endothelial differentiation G-protein coupled receptor 2, G-proteins a 11, a 12, b 2, casein kinase 1 d , casein kinase 1 e , MAP kinase-interacting serine/threonine kinase 2, RAB24, RAS protein specific guanine nucleotide-releasing factor 1, wingless-related MMTV integration site 5A, protein tyrosine phosphatase receptor N.

RNA binding, translational control, protein synthesis.

Eukaryotic translation initiation factor 4A1, fragil X mental retardation gene 1 homolog, pumilio 2, Sjogren syndrome antigen B, lysosomal membrane glycoprotein 2, phenylalanine-tRNA synthetase-like, eukaryotic translation elongation factor 1 a 1, mitochondrial ribosomal protein L30, ribosomal protein L10A, iron responsive element-binding protein 2, hnRNP-associated with lethal yellow, immature colon carcinoma transcript 1.

Cell structure, motility, adhesion.

Dystrophin, glial fibrillary acidic protein, TNFa -induced protein 6, Wiskott-Aldrich syndrome protein interacting protein, structural maintenance of chromosomes 4-like 1, adaptor protein complex AP-2 a 2, d -like 1 homolog, dynactin 1, flightless 1 homolog, kinesin family 5B, chemokine ligand 1.

Protein folding, degredation, proteolysis.

Peptidylprolyly isomerase B, carboxypeptidase D, ring finger protein 13, heat-shock protein 1 b , proteasome subunit b 6, DNAJ (Hsp40) homolog D1, cathepsin F,chaperonin 7 h ubiquitin conjugating enzyme 7 interacting protein 3.

Synaptic transmission, neurotransmitter synthesis, release and receptors.

Tyrosine hydroxylase, synaptobrevin like 1, NMDA receptor-regulated gene 1, GluR1, cholecystokinin, GABAA receptor b 1, glutamate receptor ionotropic kainate 5 g 2, glutamate receptor NMDA z 1, synaptotagmin 5, preproenkephalin 1, potassium channel Q2.

Transport activity.

Aquaporin 4, monocarboxylic acid transporter 1, SEC23A, diazepam-binding inhibitor, fatty acid-binding protein 3, ATP synthase H+ transporting F1 O, sodium bicarbonate cotransporter 7, ferritin light chain 1.

Cell metabolism, enzymes.

S-adenosylmethionine decarboxylase 1, farnesyl diphosphate synthetase, carbonic anhydrase 14, phosphoserine aminotransferase 1, cytochrome C somatic, PC4 and SFRS1 interacting protein 2, NADH dehydrogenase Fe-S protein 4, lysophospholipase 1, annexin A3, aldo-keto reductase 7A5, cytochrome C-1, glutamate-cysteine ligase modifier, glycosylphosphatidylinositol specific phospholipase D1, GTP cyclohydrolase 1, prostaglandin D2 synthase, sparc/osteonectin cwcv and kazal-like domains proteoglycan 2.

Others.

Carnitine deficiency-associated gene expressed in ventricle 3, endomucin, sorting nexin 13, lymphocyte antigen 6 complex locus A, semaphorin 4B, prominin 1, and 35 ESTs , complement component 1Q g , F-box only protein 21, flotillin 1, Golgi reassembly stacking protein 1, immediate early response 2, Ig 8, longevity assurance homolog, neighbor of A-kinase anchoring protein 95, neuronatin, prostate tumor overexpressed gene 1, seizure related gene 6, stromal membrane-associated protein 1, WW domain-binding protein 11, tumor protein D52-like 1, TBC1 domain family 1, signal sequence receptor a , and 19 ESTs.