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Table 2 Down-regulated genes in rats fed with WPH diet*

From: Dietary exposure to soy or whey proteins alters colonic global gene expression profiles during rat colon tumorigenesis

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
  1. *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.