Supplementary Table 1b for Miller, Chang, Galecki, Al-Regaiey, Kopchick, and Bartke, "Gene Expression Patterns in Calorically Restricted Mice: Partial Overlap With Long-Lived Mutant Mice," Molecular Endocrinology, in press

Supplementary Table 1b (for web site posting): Genes Decreased by CR Diet

GenBank

Description

p(t)

Mean in CR

Mean in AL

Ratio: CR/AL

S65036

3-hydroxy-3-methylglutaryl-Coenzyme A lyase

0.0001

36

130

0.28

L12059

5` nucleotidase

0.0319

30

56

0.55

D43921

5-azacytidine induced gene 1

0.0328

30

53

0.56

U41765

a disintegrin and metalloproteinase domain 9 (meltrin gamma)

0.0038

29

68

0.42

U37222

adipocyte complement related protein of 30 kDa

0.0000

32

85

0.37

M61704

alkaline phosphatase 5

0.0098

28

57

0.50

X68680

alpha 1 microglobulin/bikunin

0.0016

2921

5628

0.52

L04538

amyloid beta (A4) precursor-like protein 1

0.0009

16

34

0.48

U41736

ancient ubiquitous protein

0.0005

157

356

0.44

AF048838

Bcl2-interacting killer-like

0.0105

19

34

0.54

U36475

breast cancer 1

0.0035

16

31

0.51

AF028071

calbindin-D9K

0.0154

12

19

0.64

Y12582

calpain 6

0.0082

12

19

0.62

AJ012475

calpain 7

0.0004

22

44

0.49

X62519

calpastatin

0.0010

14

31

0.47

U16741

capping protein alpha 2

0.0035

22

45

0.49

M32452

carbonic anhydrase 1

0.0230

18

27

0.66

AF050105

carbonic anhydrase 11

0.0305

21

38

0.55

M27796

carbonic anhydrase 3

0.0614

840

1860

0.45

X51971

carbonic anhydrase 5, mitochondrial

0.0518

155

289

0.54

U19522

caspase 3, apoptosis related cysteine protease

0.0273

32

62

0.51

Y13087

caspase 6

0.0274

80

132

0.61

AF067834

caspase 8

0.0241

37

73

0.50

AF033564

CDC-like kinase 2

0.0012

36

87

0.41

AF033565

CDC-like kinase 3

0.0040

17

38

0.44

AF081536

cell division cycle 45 homolog (S. cerevisiae)-like

0.0008

14

34

0.42

AA123049

clone IMAGE: 539666

0.0112

38

109

0.34

AA472776

clone IMAGE:873597

0.0091

20

36

0.54

AJ001101

complement component 1, q subcomponent binding protein

0.0123

43

90

0.48

AF032995

crystallin, gamma S

0.0035

17

32

0.53

AF031825

cystatin F (leukocystatin)

0.0154

22

40

0.56

U43384

cytochrome b-245, beta polypeptide

0.0304

17

27

0.61

U00689

cytotoxic granule-associated RNA-binding protein 1

0.0094

17

30

0.55

AJ005669

dachshund 1 (Drosophila)

0.0022

21

39

0.53

Z38117

DEAD (aspartate-glutamate-alanine-aspartate) box polypeptide 3

0.0215

31

72

0.44

D14859

DEAD (aspartate-glutamate-alanine-aspartate) box polypeptide 4

0.0171

13

23

0.57

D50494

DEAD (aspartate-glutamate-alanine-aspartate) box polypeptide 6

0.0000

59

212

0.28

AF017153

DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 15

0.0343

18

30

0.61

X61431

diazepam binding inhibitor

0.0009

627

1515

0.41

X14805

DNA methyltransferase (cytosine-5) 1

0.0122

14

27

0.52

AF068625

DNA methyltransferase 3A

0.0017

21

42

0.49

AF068626

DNA methyltransferase 3B

0.0005

19

46

0.43

D13546

DNA polymerase alpha 2, 68 kDa

0.0056

303

770

0.39

D13544

DNA primase, p49 subunit

0.0099

20

39

0.51

D13545

DNA primase, p58 subunit

0.0041

13

22

0.58

D50000

double C2, alpha

0.0065

14

24

0.57

AB011678

Doublecortin

0.0051

92

183

0.50

U58884

drebrin-like

0.0189

38

72

0.54

AF042811

ectonucleoside triphosphate diphosphohydrolase 2

0.0141

16

32

0.49

M73329

endoplasmic reticulum protein

0.0025

36

88

0.41

X17373

eukaryotic translation initiation factor 3

0.0472

55

98

0.56

U76112

eukaryotic translation initiation factor 4, gamma 2

0.0264

137

292

0.47

X03039

eukaryotic translation initiation factor 4A1

0.0272

186

354

0.52

M61731

eukaryotic translation initiation factor 4E

0.0053

17

37

0.46

U75530

eukaryotic translation initiation factor 4E binding protein 2

0.0119

45

101

0.45

U43184

Fas-associating protein with death domain

0.0006

23

60

0.38

D49920

ferredoxin reductase

0.0340

27

45

0.60

U42384

fibroblast growth factor inducible 15

0.0015

21

41

0.51

L07063

FK506 binding protein 6 (65 kDa)

0.0091

68

162

0.42

AF045766

G protein-coupled receptor 33

0.0055

25

49

0.51

K01347

glial fibrillary acidic protein

0.0050

20

37

0.55

J02623

glutamate oxaloacetate transaminase 1, soluble

0.0002

147

451

0.32

J02655

glycerol phosphate dehydrogenase 1, cytoplasmic adult

0.0003

250

438

0.57

M20567

heat shock protein, 70 kDa 2

0.0360

26

49

0.53

D85734

heat shock protein, 70 kDa 3

0.0073

22

52

0.42

M18186

heat shock protein, 84 kDa 1

0.0022

104

280

0.37

M36830

heat shock protein, 86 kDa 1

0.0096

69

189

0.37

X58426

hepatic lipase

0.0638

20

52

0.38

D86728

heterogeneous nuclear ribonucleoprotein A1

0.0432

39

75

0.52

L31961

heterogeneous nuclear ribonucleoprotein K

0.0318

43

95

0.45

D88315

hippocampus abundant gene transcript 1

0.0048

41

95

0.43

U39473

histidyl tRNA synthetase

0.0015

27

68

0.40

AF076845

Hus1 homolog (S. pombe)

0.0069

34

70

0.49

X95685

hydroxysteroid 17-beta dehydrogenase 2

0.0024

85

264

0.32

AF022371

interferon activated gene 203

0.0078

68

159

0.43

U43084

interferon-induced protein with tetratricopeptide repeats 1

0.0000

15

40

0.37

U43085

interferon-induced protein with tetratricopeptide repeats 2

0.0092

13

25

0.53

L32974

interferon-induced protein with tetratricopeptide repeats 3

0.0020

21

45

0.48

S48315

keratin complex 1 gene 5

0.0180

13

22

0.59

AF053235

keratin complex 1, acidic, gene 16

0.0192

57

113

0.50

S48295

keratin complex 2 gene 16

0.0154

22

36

0.60

M10937

keratin complex 2, basic, gene 1

0.0031

15

35

0.43

M92088

keratin complex 2, basic, gene 10

0.0068

17

32

0.52

X12789

keratin complex 2, basic, gene 8

0.0000

129

351

0.37

X74784

keratin complex 2, gene 17

0.0030

15

27

0.54

M22810

kidney androgen regulated protein

0.0033

14

26

0.52

U13371

kidney cell line derived transcript 1

0.0160

20

39

0.52

D12646

kinesin heavy chain member 4

0.0333

38

67

0.56

D49733

lamin A

0.0013

44

103

0.43

D13455

lamin B2

0.0006

22

46

0.48

Y11550

LanC (bacterial lantibiotic synthetase component C)-like

0.0192

33

53

0.62

U41805

lymphocyte antigen 84 ligand

0.0030

18

37

0.49

M17015

lymphotoxin A

0.0183

17

27

0.64

M65142

lysyl oxidase

0.0218

22

39

0.57

AF053368

lysyl oxidase-like 2

0.0065

15

28

0.55

M16355

major urinary protein 1

0.0124

2224

5465

0.41

X76537

matrix metalloproteinase 10

0.0184

12

21

0.59

Z12604

matrix metalloproteinase 11

0.0003

16

34

0.47

D86332

matrix metalloproteinase 15

0.0068

13

21

0.60

Y15197

microtubule-associated protein 7

0.0003

77

166

0.46

M36411

Mpv17 transgene, kidney disease mutant

0.0050

15

32

0.47

M20772

myosin light chain, alkali, cardiac atria

0.0069

31

75

0.41

U04443

myosin light chain, alkali, nonmuscle

0.0209

202

391

0.52

Z31012

Neurofilament, heavy polypeptide

0.0044

16

26

0.61

AB004048

Neuronatin

0.0002

18

48

0.37

X53257

Neurotrophin 3

0.0235

12

19

0.65

M81385

nuclear receptor subfamily 5, group A, member 2

0.0020

110

218

0.51

M27009

Orosomucoid 2

0.0141

34

79

0.43

AF091846

otoconin 90

0.0035

12

20

0.59

X96606

ovary testis transcribed

0.0062

17

33

0.53

U69172

palate, lung, and nasal epithelium expressed transcript

0.0020

17

34

0.51

U97149

pale ear

0.0009

21

46

0.46

M60456

Peptidylprolyl isomerase B

0.0208

219

378

0.58

W66916

Peroxisomal farnesylated protein

0.0075

31

74

0.43

L27842

Peroxisomal membrane protein 3, 35 kDa

0.0187

23

41

0.55

X95346

Phospholipase C, gamma 1

0.0372

23

39

0.60

U87868

Phospholipase D1

0.0198

16

27

0.60

D50460

pigment epithelium-derived factor

0.0007

1287

2563

0.50

J03520

Plasminogen activator, tissue

0.0361

24

40

0.60

X75947

poly(rC) binding protein 2

0.0036

63

158

0.40

X52101

Polypyrimidine tract binding protein

0.0002

130

448

0.29

U06944

praja1

0.0001

129

314

0.41

D86344

Programmed cell death 4

0.0274

21

43

0.48

D01093

Proprotein convertase subtilisin/kexin type 4

0.0333

34

54

0.62

M14342

protein tyrosine phosphatase, receptor type, C

0.0342

23

39

0.58

L09192

pyruvate decarboxylase

0.0534

106

198

0.53

U25995

receptor (TNFRSF)-interacting serine-threonine kinase 1

0.0040

11

24

0.48

Z27088

Relaxin

0.0081

12

20

0.60

X16642

renin 1 structural

0.0197

14

24

0.57

AF061743

retinal short-chain dehydrogenase/reductase 1

0.0007

102

265

0.38

X99273

Retinaldehyde dehydrogenase 2

0.0296

13

32

0.40

AF048993

Ribonuclease H1

0.0001

21

59

0.36

L10382

Ribonuclease L (2`, 5`-oligoisoadenylate synthetase-dependent)

0.0237

17

28

0.61

X81987

Ribosomal protein L6

0.0022

754

1531

0.49

AF031568

RNA binding motif protein, X chromosome retrogene

0.0038

26

58

0.45

S77493

Sepiapterin reductase

0.0228

108

192

0.56

M74012

seryl-aminoacyl-tRNA synthetase

0.0243

54

111

0.49

L27990

Sjogren syndrome antigen A1

0.0148

18

41

0.45

U95114

sperm specific antigen 1

0.0001

93

248

0.37

L10244

Spermidine/spermine N1-acetyl transferase

0.0338

63

112

0.56

AF036894

Sphingosine phosphate lyase 1

0.0000

32

120

0.26

U75680

stem-loop binding protein

0.0030

16

30

0.53

S85260

steroid-11-beta-hydroxylase

0.0513

12

25

0.50

L36061

Steroidogenic acute regulatory protein

0.0238

32

55

0.58

D50646

stromal cell derived factor 2

0.0030

99

224

0.44

X52128

t-complex protein 11

0.0098

16

29

0.55

AF081947

tektin 1

0.0031

22

45

0.50

AF069519

thymine DNA glycosylase

0.0195

33

65

0.50

Y09688

thymine glycol DNA glycosylase/AP lyase

0.0002

26

72

0.37

U55861

Tial1 cytotoxic granule-associated RNA-binding protein-like 1

0.0354

36

65

0.56

D50586

tissue factor pathway inhibitor 2

0.0001

18

54

0.32

AB013603

Topoisomerase (DNA) III beta

0.0156

39

77

0.51

M55154

Transglutaminase 2, C polypeptide

0.0000

75

342

0.22

S76831

Tropomodulin 1

0.0281

36

65

0.55

M29793

troponin C, cardiac/slow skeletal

0.0347

22

38

0.58

U09181

troponin I, cardiac

0.0114

13

21

0.60

L47549

troponin T2, cardiac

0.0006

16

34

0.47

X69657

Tryptophanyl-tRNA synthetase

0.0028

12

34

0.35

M13443

tubulin alpha 7

0.0132

27

50

0.54

U05333

tubulin cofactor a

0.0158

30

59

0.50

AF061346

tumor necrosis factor, alpha-induced protein 1 (endothelial)

0.0002

25

67

0.37

L24118

tumor necrosis factor, alpha-induced protein 2

0.0002

20

57

0.36

U19463

tumor necrosis factor, alpha-induced protein 3

0.0008

19

47

0.40

X03687

tyrosinase related protein

0.0267

23

40

0.57

M29395

uridine monophosphate synthetase

0.0295

18

33

0.56

M26251

Vimentin

0.0004

44

108

0.41

AF075261

X transporter protein 3

0.0187

18

33

0.55

Note for Supplementary Table 1a and 1b: The mean values are given in "background-subtracted pixel volumes." As explained in the text, each raw value was adjusted by (a) subtraction of local background level computed from an annulus adjacent to the scanned spot image; (b) logarithmic transformation; (c) adjustment by linear regression against a standard vector consisting of median levels across the set of 28 32 samples; (d) calculation of mean values; and (e) antilog transformation to express as an equivalent to the original pixel volumes. The raw data values were, on average, 15% above background for the 206 genes with a mean transformed expression level of less than 60 pixel volume units, 32% above background for the 62 genes with a mean transformed expression level between 60 and 100 units, and 83% above background for the 84 genes with a mean transformed expression level above 100 units.