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.