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.