Table 1.
Gene expression signature in precancerous zinc-deficient rat esophagus
| Affymetrix id | Gene Symbol | Gene Title | Fold-Change ZD versus ZS |
Score | q-value (%) | Function |
|---|---|---|---|---|---|---|
| Sixty-one up-regulated genes associated with dietary ZD | ||||||
| 1368494_at | S100A8 | S100 calcium binding protein A8 (calgranulin A) | 57 | 8.7 | 0 | chemotaxis |
| 1384973_at | SERPINB3 | serins protease inhibitor B3 | 56 | 8.0 | 0 | serine-type endopeptidase inhibitor activity |
| 1379568_at | IFIT2 | interferon-induced protein with tetratricopeptide repeats 2 | 16 | 8.6 | 0 | binding |
| 1387620_a_at | TMPRSS11D | transmembrane protease, serine 11d | 16 | 8.9 | 0 | proteolysis |
| 1376908_at | IFIT3 | interferon-induced protein with tetratricopeptide repeats 3 | 15 | 3.9 | 0.6 | binding |
| 1376976_at | SECTM1 | secreted and transmembrane 1B | 13 | 7.9 | 0 | immune response |
| 1379747_at | PRSS35 | Protease, serine, 35 | 12 | 8.9 | 0 | proteolysis |
| 1367800_at | PLAT | plasminogen activator, tissue | 10 | 5.7 | 0.1 | protein modification process |
| 1367733_at | CA2 | carbonic anhydrase 2 | 9.5 | 7.4 | 0 | kidney development |
| 1369202_at | MX2 | myxovirus (influenza virus) resistance 2 | 8.7 | 3.0 | 2.0 | defense response |
| 1386889_at | SCD2 | stearoyl-Coenzyme A desaturase 2 | 8.4 | 3.6 | 0.9 | lipid metabolic process |
| 1369871_at | AREG | amphiregulin | 8.3 | 5.4 | 0.2 | epidermal growth factor receptor signaling pathway |
| 1367566_at | SCGB1A1 | secretoglobin, family 1A, member 1 (uteroglobin) | 8.2 | 4.9 | 0.3 | signal transduction |
| 1371100_at | ES2 | esterase 2 | 7.8 | 2.9 | 2.4 | carboxylesterase activity |
| 1370355_at | SCD1 | stearoyl-Coenzyme A desaturase 1 | 7.6 | 6.8 | 0 | lipid metabolic process |
| 1384960_at | CFTR | cystic fibrosis transmembrane conductance regulator homolog | 7.4 | 8.6 | 0 | transport |
| 1392678_a_at | DNMT3A | DNA methyltransferase 3A | 7.2 | 3.1 | 2.0 | DNA methylation |
| 1369640_at | GJA1 | gap junction membrane channel protein alpha 1 | 6.7 | 4.4 | 0.5 | in utero embryonic development |
| 1387391_at | CDKN1A | cyclin-dependent kinase inhibitor 1A | 6.6 | 5.3 | 0.2 | regulation of progression through cell cycle |
| 1380083_at | KLK10 | kallikrein 10 | 6.5 | 4.8 | 0.3 | proteolysis |
| 1381024_at | PPP2R1A | protein phosphatase 2 (formerly 2A) | 6.4 | 5.3 | 0.2 | protein phosphatase type 2A activity |
| 1395886_at | ACTR3 | ARP3 actin-related protein 3 homolog | 6.3 | 3.4 | 1.2 | structural constituent of cytoskeleton |
| 1391481_at | CAST | Calpastatin | 6.2 | 6.0 | 0.1 | myoblast fusion |
| 1380533_at | APP | amyloid beta (A4) precursor protein | 6.2 | 3.0 | 2.0 | G2 phase of mitotic cell cycle |
| 1369248_a_at | BIRC4 | baculoviral IAP repeat-containing 4 | 6.2 | 6.5 | 0 | apoptosis |
| 1368025_at | DDIT4 | DNA-damage-inducible transcript 4 | 6.2 | 9.4 | 0 | response to hypoxia |
| 1368325_at | EGF | epidermal growth factor | 6.1 | 5.7 | 0.1 | activation of MAPKK activity |
| 1397675_at | WBSCR1 | Williams-Beuren syndrome chromosome region 1 homolog | 5.8 | 4.7 | 0.4 | translation |
| 1370153_at | GDF15 | growth differentiation factor 15 | 5.6 | 3.5 | 1.1 | signal transduction |
| 1384784_at | CLCA2 | chloride channel calcium activated 2 | 5.5 | 4.2 | 0.5 | translation |
| 1369846_at | IVL | involucrin | 5.3 | 3.5 | 1.1 | keratinocyte differentiation |
| 1398143_at | PRKX | protein kinase, X-linked | 5.2 | 3.7 | 0.7 | protein amino acid phosphorylation |
| 1370627_at | RHOV | ras homolog gene family, member V | 5.1 | 6.6 | 0 | signal transduction |
| 1387982_at | TLR4 | toll-like receptor 4 | 5.1 | 3.8 | 0.7 | inflammatory response |
| 1368213_at | POR | P450 (cytochrome) oxidoreductase | 5.0 | 7.0 | 0 | electron transport |
| 1369517_at | PSCD1 | pleckstrin homology, Sec7 and coiled-coil domains 1 | 5.0 | 4.9 | 0.3 | Golgi to secretory vesicle transport |
| 1387125_at | S100A9 | S100 calcium binding protein A9 (calgranulin B) | 5.0 | 4.5 | 0.4 | inflammatory response |
| 1397674_at | EIF3S8 | eukaryotic translation initiation factor 3, subunit 8, 110kDa | 4.9 | 4.0 | 0.6 | translational initiation |
| 1368489_at | FOSL1 | fos-like antigen 1 | 4.9 | 6.3 | 0.1 | regulation of transcription, DNA-dependent |
| 1369568_at | STX6 | syntaxin 6 | 4.9 | 12 | 0 | transport |
| 1370255_at | SFTPC | surfactant associated protein C | 4.8 | 9.0 | 0 | respiratory gaseous exchange |
| 1370792_at | MAPRE1 | microtubule-associated protein, RP/EB family, member 1 | 4.7 | 3.4 | 1.2 | cell cycle |
| 1387605_at | CASP12 | caspase 12 | 4.6 | 4.0 | 0.6 | proteolysis |
| 1371108_a_at | ATP1A1 | ATPase, Na+/K+ transporting, alpha 1 polypeptide | 4.6 | 3.5 | 1.1 | ATP catabolic process |
| 1369406_at | ASAH2 | N-acylsphingosine amidohydrolase 2 | 4.6 | 3.1 | 1.7 | lipid metabolic process |
| 1387631_at | HPGD | hydroxyprostaglandin dehydrogenase 15 (NAD) | 4.4 | 3.1 | 1.7 | lipid metabolic process |
| 1371618_s_at | TUBB3 | tubulin, beta 3 | 4.3 | 5.5 | 0.2 | microtubule-based process |
| 1387788_at | JUNB | Jun-B oncogene | 4.3 | 9.8 | 0 | regulation of progression through cell cycle |
| 1370174_at | MYD116 | myeloid differentiation primary response gene 116 | 4.3 | 5.5 | 0.2 | myeloid differentiation primary response gene 116 |
| 1369587_at | VAPB | vesicle-associated membrane protein, associated protein B and C | 4.3 | 5.6 | 0.1 | protein complex assembly |
| 1370123_a_at | CTTN | cortactin | 4.3 | 5.5 | 0.2 | receptor-mediated endocytosis |
| 1396262_at | PBEF1 | pre-B-cell colony enhancing factor 1 | 4.3 | 4.5 | 0.4 | cell cycle |
| 1368024_at | QSCN6 | quiescin Q6 | 4.2 | 7.2 | 0 | regulation of progression through cell cycle |
| 1370477_at | OCM | oncomodulin | 4.2 | 3.5 | 1.1 | calcium ion binding |
| 1389123_at | CCL | chemokine (C-C motif) ligand 6 | 4.2 | 2.6 | 3.4 | apoptosis |
| 1384328_at | TOM1 | target of myb1 homolog (chicken) | 4.2 | 6.0 | 0.1 | intracellular protein transport |
| 1368947_at | GADD45A | growth arrest and DNA-damage-inducible 45 alpha | 4.2 | 3.9 | 0.6 | regulation of progression through cell cycle |
| 1387353_at | AKT2 | thymoma viral proto-oncogene 2 | 4.2 | 7.2 | 0 | protein amino acid phosphorylation |
| 1395614_at | U2AF2 | U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2 | 4.1 | 2.8 | 2.4 | nuclear mRNA splicing, via spliceosome |
| 1387870_at | ZFP36 | zinc finger protein 36 | 4.1 | 6.7 | 0 | mRNA catabolic process |
| 1368014_at |
PTGES |
prostaglandin E synthase |
4.1 |
4.2 |
0.5 |
prostaglandin biosynthetic process |
| Forty-two down-regulated genes associated with dietary ZD | ||||||
| 1387578_a_at | P2RX2 | purinergic receptor P2X, ligand-gated ion channel, 2 | 0.08 | -6.3 | 0.1 | transport |
| 1369381_a_at | SLC15A1 | solute carrier family 15 (oligopeptide transporter), member 1 | 0.09 | -3.8 | 0.5 | transport |
| 1388395_at | G0S2 | G0/G1 switch gene 2 | 0.11 | -3.4 | 0.7 | integral to membrane |
| 1370198_at | TRDN | triadin | 0.12 | -2.4 | 2.8 | calcium ion homeostasis |
| 1368252_at | KBTBD10 | kelch repeat and BTB (POZ) domain containing 10 | 0.13 | -2.8 | 1.7 | cell motility |
| 1372536_at | CABC1 | chaperone, ABC1 activity of bc1 complex like | 0.13 | -4.2 | 0.4 | protein folding |
| 1398243_at | CSRP3 | cysteine and glycine-rich protein 3 | 0.13 | -2.1 | 4.6 | blood vessel remodeling |
| 1371247_at | TNNT3 | troponin T3, skeletal, fast | 0.14 | -2.9 | 1.7 | muscle contraction |
| 1383875_at | UPK1B | uroplakin 1B | 0.14 | -3.5 | 0.7 | epithelial cell differentiation |
| 1387181_at | MYF6 | myogenic factor 6 | 0.14 | -2.6 | 2.4 | somitogenesis |
| 1374248_at | MYBPC1 | myosin binding protein C, slow type | 0.14 | -2.9 | 1.5 | muscle contraction |
| 1367572_at | MYL3 | myosin, light polypeptide 3 | 0.14 | -2.9 | 1.5 | muscle contraction |
| 1371053_at | MYH8 | myosin, heavy polypeptide 8, skeletal muscle, perinatal | 0.14 | -3.8 | 0.6 | striated muscle contraction |
| 1374391_at | SLN | sarcolipin | 0.14 | -3.2 | 1.1 | transport |
| 1370165_at | SMPX | small muscle protein, X-linked | 0.15 | -2.7 | 2.0 | striated muscle contraction |
| 1368108_at | ATP2A1 | ATPase, Ca++ transporting, cardiac muscle, fast twitch 1 | 0.16 | -2.7 | 2.0 | ATP catabolic process |
| 1368145_at | PCP4 | Purkinje cell protein 4 | 0.16 | -4.9 | 0.3 | central nervous system development |
| 1370026_at | CRYAB | crystallin, alpha B | 0.16 | -3.6 | 0.6 | glucose metabolic process |
| 1372639_at | TRIM54 | tripartite motif-containing 54 | 0.16 | -3.8 | 0.6 | negative regulation of microtubule |
| 1370982_at | PYGM | muscle glycogen phosphorylase | 0.16 | -3.4 | 0.7 | response to hypoxia |
| 1391429_at | HFE2 | hemochromatosis type 2 (juvenile) homolog (human) | 0.16 | -2.9 | 1.5 | GPI anchor binding |
| 1367782_at | COX6A2 | cytochrome c oxidase, subunit Vla, polypeptide 2 | 0.17 | -2.9 | 1.5 | electron transport |
| 1378430_at | MOXD1 | monooxygenase, DBH-like 1 | 0.17 | -8.2 | 0 | catecholamine metabolic process |
| 1367626_at | CKM | creatine kinase, muscle | 0.17 | -2.3 | 4.0 | phosphocreatine metabolic process |
| 1387082_at | FETUB | fetuin beta | 0.17 | -5.9 | 0.1 | cysteine protease inhibitor activity |
| 1390355_at | RYR1 | ryanodine receptor 1, skeletal muscle | 0.17 | -3.7 | 0.6 | transport |
| 1387122_at | PLAGL1 | pleiomorphic adenoma gene-like 1 | 0.17 | -8.3 | 0 | induction of apoptosis |
| 1367962_at | ACTN3 | actinin alpha 3 | 0.18 | -4.2 | 0.4 | muscle contraction |
| 1372383_at | GPSM1 | G-prolein signalling modulator 1 | 0.18 | -6.2 | 0.1 | signal transduction |
| 1372190_at | AQP4 | Aquaporin 4 | 0.18 | -4.8 | 0.3 | transport |
| 1367964_at | TNNI2 | troponin I type 2 (skeletal, fast) | 0.18 | -2.8 | 1.7 | hydrogen transport |
| 1368724_a_at | TPM1 | tropomyosin 1, alpha | 0.18 | -3.1 | 1.2 | cell motility |
| 1386907_at | ENO3 | enolase 3, beta | 0.18 | -2.8 | 1.7 | glycolysis |
| 1387092_at | FXYD4 | FXYD domain-containing ion transport regulator 4 | 0.19 | -2.6 | 2.4 | transport |
| 1377499_a_at | HRC | histidine rich calcium binding protein | 0.19 | -3.8 | 0.6 | structural molecule activity |
| 1369067_at | NR4A3 | nuclear receptor subfamily 4, group A, member 3 | 0.20 | -2.3 | 4.0 | mesoderm formation |
| 1367951_at | PGAM2 | phosphoglycerate mutase 2 | 0.20 | -2.4 | 2.8 | glycolysis |
| 1370033_at | MLC3 | myosin, light polypeptide 1 | 0.21 | -3.1 | 1.2 | cardiac muscle contraction |
| 1378698_at | MYH13 | myosin, heavy polypeplide 8, skeletal muscle, perinatal | 0.21 | -2.3 | 4.0 | striated muscle contraction |
| 1368966_at | MYBPH | myosin binding protein H | 0.21 | -2.2 | 4.6 | striated muscle contraction |
| 1367739_at | COX8H | Cytochrome c oxidase subunit Vlll-H (heart/muscle) | 0.22 | -2.5 | 2.8 | electron transport |
| 1390822_at | CDH16 | cadherin 16 | 0.22 | -2.5 | 2.8 | tRNA aminoacylation for protein translation |
A group of 103 differentially expressed genes were identified, using a cutpoint of q value <5% and fold-change ≥4.0. Score is the T-statistic value; q-value is the lowest False Discovery Rate at which the gene is considered significant. ZD = zinc-deficient; ZS = zinc-sufficient.