Table 2

Down-regulated genes in rats fed with WPH diet*
Category and Gene Name
 Probe Set GB Accession No.
 Fold Change
 P value
Cell adhesion


     Embigin
 AJ009698
 -6.57
 0
     Cadherin 17
 L46874
 -4.8
 0.036
     Cadherin
 X78997
 -3.36
 0.004
     Protein tyrosine phosphatase
 M60103
 -2.64
 0.004
     Cytokeratin-8
 S76054
 -2.71
 0
     Trans-Golgi network integral membrane protein TGN38
 X53565
 -4.92
 0.012
     Tumor-associated calcium signal transducer 1
 AJ001044
 -9.37
 0.001
     Claudin-3
 AJ011656
 -7.55
 0.02
     Claudin-9
 AJ011811
 -5.12
 0
Cell cycle/growth control


     Mapk6
 M64301
 -2.61
 0.003
     Epithelial membrane protein 1
 Z54212
 -4.67
 0.015
     Glucagon
 K02813
 -7.73
 0.005
     Peptide tyrosine-tyrosine (YY)
 M17523
 -4.56
 0.001
     Src related tyrosine kinase
 U09583
 -3.31
 0.033
     FGF receptor activating protein
 U57715
 -4.25
 0.002
     Cyclin D1
 D14014
 -1.97
 0.001
     Neu oncogene
 X03362
 -2.61
 0.017
Defense/immunity protein


     Seminal vesicle secretion protein iv
 J00791
 -5.35
 0.001
     Putative cell surface antigen
 U89744
 -5.22
 0.008
     Decay accelerating factor GPI
 AF039583
 -6.12
 0
     Beta defensin-1
 AF093536
 -26.78
 0.001
Detoxification/antioxidation


     Glutathione S-transferase
 J02810
 -5.17
 0
     Glutathione S-transferase Yb
 X04229
 -9.33
 0

J03914
 -2.43
 0.002
     Glutathione S-transferase, alpha 1
 K01932
 -3.07
 0.002
     Glutathione transferase, subunit 8
 X62660
 -6.42
 0.001
     Glutathione S-transferase Yc1
 S72505
 -3.69
 0.004
     Glutathione S-transferase Yc2
 S72506
 -21.38
 0.008
     N-acetyltransferase 1
 U01348
 -4.64
 0.003
     Cytochrome P450CMF1b
 J02869
 -8.23
 0.001
     Cytochrome P450 4F4
 U39206
 -6.43
 0.004
     Cytochrome P450 monooxygenase
 U39943
 -2.82
 0.011
     Cytochrome P450 pseudogene
 U40004
 -2.87
 0
     Cytochrome P450 3A9
 U46118
 -6.91
 0
     Cytochrome P450IVF
 M94548
 -5.78
 0.002
     Cytochrome P450, subfamily 51
 U17697
 -2.07
 0.005
     Alcohol dehydrogenase
 M15327
 -2.06
 0.025
     Aldehyde dehydrogenase
 M23995
 -10.56
 0.035

AF001898
 -2.72
 0.004
     D-amino-acid oxidase
 AB003400
 -13.69
 0
     3-methylcholanthrene-inducible UDP-glucuronosyltransferase
 S56937
 -9
 0
     UDP-glucuronosyltransferase
 D38062
 -3.17
 0.005

D38065
 -3.29
 0.002
     UDP glycosyltransferase 1
 D83796
 -6.87
 0

J02612
 -6.58
 0

J05132
 -4.03
 0
Metabolism


     Meprin 1 alpha
 S43408
 -3.82
 0.014
     Brain serine protease bsp1
 AJ005641
 -4.42
 0.007
     Cystathionine gamma-lyase
 D17370
 -3.05
 0.002
     Cathepsin S
 L03201
 -2.62
 0
     Meprin beta-subunit
 M88601
 -5
 0.004
     Disintegrin and metalloprotease domain 7
 X66140
 -11.91
 0
     Fucosyltransferase 1
 AB006137
 -4.96
 0.001
     Fucosyltransferase 2
 AB006138
 -7.97
 0.017
     UDP-glucose:ceramide glycosyltransferase
 AF047707
 -2.86
 0.007
     Type II Hexokinase
 D26393
 -2.7
 0.001
     Hexokinase II
 S56464
 -4.45
 0.007
     CDP-diacylglycerol synthase
 AB009999
 -4.66
 0
     Carboxylesterase precursor
 AB010635
 -5.29
 0.002
     Fatty acid Coenzyme A ligase
 AB012933
 -2.5
 0.041
     3beta-HSD
 L17138
 -3.27
 0
     11-beta-hydroxylsteroid dehydrogenase type 2
 U22424
 -3
 0.001
     Peroxiredoxin 6
 AF014009
 -3.55
 0.01
     Platelet phospholipase A2
 X51529
 -3.25
 0.001
Ligand binding/carrier


     Carnitine transporter
 AB017260
 -3.95
 0.005
     Chloride channel (ClC-2)
 AF005720
 -5.69
 0.002
     Putative potassium channel
 AF022819
 -4.84
 0
     Mitochondrial dicarboxylate carrier
 AJ223355
 -3.55
 0.009
     Aquaporin 3
 D17695
 -7.83
 0
     Na_H_Exchanger
 L11236
 -9.81
 0.003
     Angiotensin/vasopressin receptor (AII/AVP)
 M85183
 -3.3
 0.002
     H+, K+-ATPase
 M90398
 -13.87
 0
     Intestinal fatty acid binding protein
 K01180
 -7.29
 0.001
     Apolipoprotein A-I precursor
 M00001
 -3.45
 0.023
     Apolipoprotein A-I
 J02597
 -2.47
 0.003
     Sodium-hydrogen exchange protein-isoform 3
 M85300
 -7.36
 0.004
     Liver fatty acid binding protein
 V01235
 -2.62
 0
     Sodium transporter
 X59677
 -3.8
 0
     Cation transporter
 X78855
 -3.62
 0.003
     ATP-binding cassette
 AB010467
 -3.89
 0.004
     Methionine adenosyltransferase II, alpha
 J05571
 -2.91
 0.007
     Phenylalanine hydroxylase
 M12337
 -7.43
 0
     Carbonic anhydrase IV
 S68245
 -4.28
 0.011
Signal transduction


     B7 antigen
 X76697
 -170.95
 0.002
     CD24 antigen
 U49062
 -3.08
 0
     Chemokine CX3C
 AF030358
 -5.04
 0.011
     Itmap1
 AF022147
 -7.5
 0.001
     HCNP
 E05646
 -2.5
 0.001
     Brain glucose-transporter protein
 M13979
 -2.97
 0.019
     Protein kinase C delta
 M18330
 -2.48
 0.002
     Guanylate cyclase 2C
 M55636
 -4.58
 0.003
     A2b-adenosine receptor
 M91466
 -2.8
 0.04
     Guanylate cyclase activator 2A
 M95493
 -4.18
 0.005
     Phospholipase C beta-3
 M99567
 -2.57
 0.018
     Tm4sf3
 Y13275
 -3.33
 0
     Phospholipase D
 AB000778
 -2.71
 0.009
     BEM-2
 D45413
 -6.41
 0.015
     Sgk
 L01624
 -3.93
 0
Stress response/apoptosis


     Prostaglandin D synthetase
 J04488
 -43.11
 0.009
     GTP cyclohydrolase I
 M58364
 -3.26
 0.014
Structure proteins


     Chromogranin B (Chgb)
 AF019974
 -2.56
 0.005
     Intestinal mucin
 M76740
 -5.09
 0.002
     Muc3
 U76551
 -11.07
 0.006
     Mucin-like protein
 M81920
 -11.97
 0.001
     Myosin 5B
 U60416
 -3.94
 0
     Keratin 18
 X81448
 -3.23
 0.004
     Keratin 19
 X81449
 -2.69
 0.001
     ZG-16p protein
 Z30584
 -4.43
 0.002
     Plasmolipin
 Z49858
 -7.2
 0
     Cytokeratin 21
 M63665
 -4.96
 0
     Syndecan
 S61865
 -3.3
 0.006
     Claudin 3
 M74067
 -6.68
 0.01
Transcription factor/regulator


     Hepatocyte nuclear factor 3 gamma
 AB017044
 -6.96
 0
     Apolipoprotein B mRNA editing protein
 L07114
 -2.34
 0
     DNA-binding inhibitor
 L23148
 -4.1
 0.01
     Kruppel-like factor 4 (gut)
 L26292
 -3.08
 0.017
Others


     Prolactin receptor
 M74152
 -3.26
 0.014
     LOC286964
 U89280
 -2.96
 0.003
     Ckmt1
 X59737mRNA
 -2.65
 0.025
     Arginase II
 U90887
 -23.69
 0
     Deleted in malignant brain tumors 1
 U32681
 -3.47
 0.002
     3' end GAA-triplet repeat
 L13025
 -2.73
 0.001
     Polymeric immunoglobulin receptor
 L13235
 -2.93
 0.004

*Changes in gene expression were determined by t-test (DMT), comparative analysis (MAS 5.0), and SAM (Stanford). Gene expression profiles from CAS animals were used as control. P value and fold change are based on DMT analysis; whereas final genes listed met all of the analytical criteria as described in Methods.

Xiao et al. Molecular Cancer 2005 4:1   doi:10.1186/1476-4598-4-1