Table 2.
Genes differentially expressed in malignant vs benign thyroid tissue
| Gene Name | Gene Symbol | Adjusted p value | 1700 probe ID |
|---|---|---|---|
| Genes up-regulated in malignant vs benign | |||
| Active BCR-related gene | ABR | 0.014482 | 154399 |
| Adaptor-related protein complex 2, alpha 1 subunit | AP2A1 | 0.0312 | 115368 |
| Apoptosis, caspase activation inhibitor | AVEN | 0.030998 | 203738 |
| BCL2-associated X protein | BAX | 0.009782 | 146510 |
| BH3 interacting domain death agonist | BID | 0.021424 | 131216 |
| Brain abundant, membrane attached signal protein 1 | BASP1 | 0.024214 | 198318 |
| Brain acyl-CoA hydrolase | BACH | 0.014566 | 133876 |
| Bromodomain adjacent to zinc finger domain, 1A | BAZ1A | 0.03538 | 209809 |
| Calcium/calmodulin-dependent protein kinase I | CAMK1 | 0.041887 | 157712 |
| Cathepsin S | CTSS | 0.046544 | 105790 |
| CD44 antigen (homing function and Indian blood group system) | CD44 | 0.044181 | 133604 |
| Chemokine (C-X-C motif) ligand 16 | CXCL16 | 0.043234 | 199059 |
| Chromosome 1 open reading frame 38 | C1orf38 | 0.049072 | 202924 |
| CLIP-170-related protein | CLIPR-59 | 0.023629 | 102205 |
| Docking protein 1, 62 kDa (downstream of tyrosine kinase 1) | DOK1 | 0.041898 | 204989 |
| Epidermodysplasia verruciformis 1 | EVER1 | 0.003348 | 175569 |
| FXYD domain containing ion transport regulator 5 | FXYD5 | 0.01444 | 154607 |
| FXYD domain containing ion transport regulator 5 | FXYD5 | 0.023629 | 112771 |
| Galactose-4-epimerase, UDP | GALE | 0.047363 | 141143 |
| Genethonin 1 | GENX-3414 | 0.016836 | 124360 |
| Hypothetical gene BC008967 | BC008967 | 0.015683 | 108526 |
| Hypothetical protein FLJ10849 | FLJ10849 | 0.013822 | 224983 |
| Hypothetical protein FLJ22531 | FLJ22531 | 0.024391 | 145918 |
| Hypothetical protein MGC4607 | MGC4607 | 0.006507 | 211836 |
| Intercellular adhesion molecule 1 (CD54), human rhinovirus receptor | ICAM1 | 0.028746 | 109070 |
| Jun dimerization protein p21SNFT | SNFT | 0.043301 | 144215 |
| Lectin, galactoside-binding, soluble, 3 (galectin 3) | LGALS3 | 0.034491 | 179836 |
| Major vault protein | MVP | 0.0312 | 212354 |
| Matrix metalloproteinase 14 (membrane-inserted) | MMP14 | 0.038682 | 152076 |
| Milk fat globule-EGF factor 8 protein | MFGE8 | 0.02392 | 144588 |
| Mst3 and SOK1-related kinase | MST4 | 0.042028 | 112198 |
| neuronal cell adhesion molecule | NRCAM | 0.011178 | 106462 |
| Phospholipase D3 | PLD3 | 0.034491 | 143388 |
| Promyelocytic leukemia | PML | 0.016018 | 217558 |
| Protein inhibitor of activated STAT protein PIASy | PIASY | 0.00536 | 153434 |
| Protein tyrosine phosphatase, receptor type, E | PTPRE | 0.048653 | 221568 |
| Rho GDP dissociation inhibitor (GDI) beta | ARHGDIB | 0.043853 | 143589 |
| S100 calcium binding protein A11 (calgizzarin) | S100A11 | 0.019933 | 145550 |
| Similar to rat tricarboxylate carrier-like protein | BA108L7.2 | 0.025387 | 179870 |
| SP110 nuclear body protein | SP110 | 0.0312 | 113484 |
| Stimulated by retinoic acid gene 6 | FLJ12541 | 0.043234 | 193986 |
| Syndecan 3 (N-syndecan) | SDC3 | 0.048804 | 143980 |
| Tax interaction protein 1 | TIP-1 | 0.006673 | 119665 |
| TBC1 domain family, member 2 | TBC1D2 | 0.029907 | 205982 |
| Tenascin C (hexabrachion) | TNC | 0.032355 | 143831 |
| Thymosin, beta 4, Y chromosome | TMSB4Y | 0.040937 | 193911 |
| Tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor) | TIMP1 | 0.032306 | 134692 |
| Topoisomerase (DNA) II alpha 170 kDa | TOP2A | 0.040937 | 135302 |
| Transforming growth factor, beta 1 | TGFB1 | 0.016836 | 170749 |
| Transgelin 2 | TAGLN2 | 0.031971 | 172296 |
| Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide | YWHAH | 0.039009 | 188379 |
| v-yes-1 Yamaguchi sarcoma viral related oncogene homolog | LYN | 0.016175 | 194134 |
| Genes down-regulated in malignant vs benign | |||
| Aldehyde oxidase 1 | AOX1 | 0.003227 | 106573 |
| Ankyrin 2, neuronal | ANK2 | 0.035357 | 155780 |
| Aspartate beta-hydroxylase | ASPH | 0.002064 | 221656 |
| Aspartate beta-hydroxylase | ASPH | 0.019666 | 114180 |
| ATPase, Cu++ transporting, beta polypeptide | ATP7B | 0.044511 | 198852 |
| Brain-specific protein p25 alpha | p25 | 0.023629 | 120622 |
| Casein kinase | LOC149420 | 0.022382 | 149347 |
| Cellular retinoic acid binding protein 1 | CRABP1 | 0.008315 | 100295 |
| Centromere protein J | CENPJ | 0.0312 | 164563 |
| Ceroid-lipofuscinosis, neuronal 5 | CLN5 | 0.011021 | 205999 |
| Chloride channel Kb | CLCNKB | 0.040418 | 176266 |
| Chondroitin beta1,4 N-acetylgalactosaminyltransferase | ChGn | 0.013148 | 101140 |
| Chromosome 11 open reading frame 8 | C11orf8 | 0.001977 | 174025 |
| Chromosome 11 open reading frame 8 | C11orf8 | 0.004148 | 108279 |
| Chromosome 21 open reading frame 4 | C21orf4 | 0.0042 | 156895 |
| Clusterin-like 1 (retinal) | CLUL1 | 0.019631 | 186062 |
| Component of oligomeric golgi complex 3 | COG3 | 0.003664 | 129212 |
| Coxsackie virus and adenovirus receptor | CXADR | 0.004648 | 108284 |
| Crystallin, alpha B | CRYAB | 0.030418 | 190274 |
| Cytosolic sialic acid 9-O-acetylesterase homolog | CSE-C | 0.040993 | 213856 |
| Dicarbonyl/l-xylulose reductase | DCXR | 0.001977 | 103350 |
| DnaJ (Hsp40) homolog, subfamily B, member 4 | DNAJB4 | 0.043853 | 103618 |
| ERO1-like beta (S. cerevisiae) | ERO1LB | 0.013962 | 207998 |
| Extracellular link domain containing 1 | XLKD1 | 0.039738 | 195865 |
| Family with sequence similarity 13, member A1 | FAM13A1 | 0.019631 | 116936 |
| Fatty acid binding protein 4, adipocyte | FABP4 | 0.014832 | 150137 |
| Fc fragment of IgG binding protein | FCGBP | 0.001965 | 118361 |
| Fibroblast growth factor receptor 2 | FGFR2 | 0.0042 | 110548 |
| FLJ35740 protein | FLJ35740 | 0.020224 | 101102 |
| Friedreich ataxia region gene X123 | X123 | 0.032602 | 133505 |
| Glutamate-ammonia ligase (glutamine synthase) | GLUL | 0.014649 | 175147 |
| Glycine amidinotransferase (l-arginine/glycine amidinotransferase) | GATM | 0.013962 | 111904 |
| Glycoprotein M6A | GPM6A | 0.011739 | 215326 |
| Growth hormone receptor | GHR | 0.017721 | 190306 |
| HLA complex group 4 | HCG4 | 0.025807 | 191199 |
| Hypothetical protein BC009561 | LOC119710 | 0.003227 | 211319 |
| Hypothetical protein BC019238 | LOC120379 | 0.013438 | 201200 |
| Hypothetical protein FLJ13204 | FLJ13204 | 0.003227 | 145066 |
| Hypothetical protein FLJ13842 | FLJ13842 | 0.016448 | 208504 |
| Hypothetical protein FLJ14054 | FLJ14054 | 0.049072 | 202017 |
| Hypothetical protein FLJ20154 | FLJ20154 | 0.014428 | 143310 |
| Hypothetical protein FLJ20513 | FLJ20513 | 0.019493 | 154130 |
| Hypothetical protein FLJ32110 | FLJ32110 | 0.015507 | 229492 |
| Hypothetical protein FLJ32343 | FLJ32343 | 0.012208 | 116902 |
| Hypothetical protein FLJ33516 | FLJ33516 | 0.03965 | 224600 |
| Hypothetical protein FLJ37549 | FLJ37549 | 0.001956 | 218577 |
| Hypothetical protein FLJ39378 | FLJ39378 | 0.005853 | 163223 |
| Hypothetical protein FLJ40021 | FLJ40021 | 0.023629 | 174198 |
| Hypothetical protein LOC134285 | LOC134285 | 0.018694 | 163671 |
| Hypothetical protein MGC10946 | MGC10946 | 0.022382 | 195982 |
| Hypothetical protein MGC14425 | MGC14425 | 0.015445 | 161569 |
| Hypothetical protein MGC17299 | MGC17299 | 0.026062 | 168452 |
| Hypothetical protein MGC17943 | MGC17943 | 0.0042 | 147296 |
| Hypothetical protein MGC23980 | MGC23980 | 0.018694 | 224619 |
| Hypothetical protein MGC24047 | MGC24047 | 0.001956 | 138122 |
| Hypothetical protein MGC33607 | MGC33607 | 0.033547 | 100645 |
| Ionized calcium binding adapter molecule 2 | IBA2 | 0.0042 | 179489 |
| KIAA0390 gene product | KIAA0390 | 0.014832 | 119936 |
| KIAA0703 gene product | KIAA0703 | 0.032602 | 146652 |
| Lectin, mannose-binding, 1 | LMAN1 | 0.031092 | 179632 |
| Leiomodin 1 (smooth muscle) | LMOD1 | 0.022352 | 120404 |
| Likely ortholog of rat SNF1/AMP-activated protein kinase | SNARK | 0.044605 | 157942 |
| LIM domain kinase 2 | LIMK2 | 0.002409 | 151439 |
| Low density lipoprotein-related protein 1B (deleted in tumors) | LRP1B | 0.00536 | 209464 |
| Low density lipoprotein-related protein 2 | LRP2 | 0.040937 | 114919 |
| Matrilin 2 | MATN2 | 0.0042 | 167316 |
| Metallothionein 1A (functional) | MT1A | 0.013822 | 204773 |
| Metallothionein 1A (functional)|metallothionein 1E (functional)|metallothionein 1K| metallothionein 2A | MT1A|MT2A|MT1E|MT1K | 0.027037 | 146368 |
| Metallothionein 1A (functional)|metallothionein 1E (functional)|metallothionein 2A| metallothionein 1K | MT1A|MT2A|MT1K|MT1E | 0.043841 | 182305 |
| Metallothionein 1A (functional)|metallothionein 2A|metallothionein 1K| metallothionein 1E (functional) | MT1A|MT1K|MT1E|MT2A | 0.011739 | 223856 |
| Metallothionein 1B (functional) | MT1B | 0.019631 | 174119 |
| Metallothionein 1F (functional) | MT1F | 0.024726 | 144569 |
| Metallothionein 1G | MT1G | 0.0192 | 164525 |
| Metallothionein 1G | MT1G | 0.03965 | 171539 |
| Metallothionein 1J | MT1J | 0.008315 | 227956 |
| Metallothionein 1X | MT1X | 0.008335 | 119685 |
| Metallothionein 1X | MT1X | 0.010748 | 173072 |
| Metallothionein IV | MT4 | 0.007447 | 223241 |
| Methionine adenosyltransferase II, alpha | MAT2A | 0.014428 | 158350 |
| Mitogen-activated protein kinase 4 | MAPK4 | 0.042306 | 131252 |
| Myc-induced nuclear antigen, 53 kDa | MINA53 | 0.011959 | 130284 |
| NIMA (never in mitosis gene a)- related kinase 11 | NEK11 | 0.001965 | 194628 |
| Otospiralin | LOC150677 | 0.018694 | 182360 |
| PDZ/coiled-coil domain binding partner for the rho-family GTPase TC10 | PIST | 0.013822 | 103651 |
| Phospholipase A2 receptor 1, 180 kDa | PLA2R1 | 0.004029 | 134379 |
| Phospholipase C-like 1 | PLCL1 | 0.022657 | 206894 |
| Phosphotidylinositol transfer protein, beta | PITPNB | 0.014428 | 122698 |
| Polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 | PKHD1L1 | 0.0042 | 199896 |
| Polymerase (DNA directed) iota | POLI | 0.003227 | 167492 |
| Potassium channel, subfamily K, member 9 | KCNK9 | 0.000849 | 108648 |
| Potassium channel-interacting protein 4 | KCNIP4 | 0.011447 | 147058 |
| Potassium inwardly-rectifying channel, subfamily J, member 13 | KCNJ13 | 0.008972 | 124187 |
| pp21 Homolog | LOC51186 | 0.004326 | 127636 |
| Pre-B cell leukemia transcription factor 4 | PBX4 | 0.030311 | 199118 |
| Protein kinase, cAMP-dependent, catalytic, beta | PRKACB | 0.023863 | 198878 |
| Protein phosphatase 4, regulatory subunit 2|hypothetical protein LOC151987 | PPP4R2|LOC151987 | 0.011338 | 200919 |
| RAB23, member RAS oncogene family | RAB23 | 0.000659 | 122394 |
| Ras association (RalGDS/AF-6) domain family 6 | RASSF6 | 0.048804 | 119072 |
| Sarcoglycan, delta (35 kDa dystrophin-associated glycoprotein) | SGCD | 0.011178 | 120415 |
| Serum deprivation response (phosphatidylserine binding protein) | SDPR | 0.011021 | 156433 |
| SH3 and multiple ankyrin repeat domains 2 | SHANK2 | 0.043996 | 193906 |
| Solute carrier family 26, member 7 | SLC26A7 | 0.0042 | 225067 |
| Solute carrier family 26, member 7 | SLC26A7 | 0.005853 | 213530 |
| Solute carrier family 5 (iodide transporter), member 8 | SLC5A8 | 0.031284 | 231731 |
| SPARC related modular calcium binding 2 | SMOC2 | 0.021505 | 135930 |
| Syndecan 2 (heparan sulfate proteoglycan 1, cell surface-associated, fibroglycan) | SDC2 | 0.001258 | 209676 |
| Syntaxin 12 | STX12 | 0.01117 | 199949 |
| T-box 22 | TBX22 | 0.024297 | 177517 |
| Thioredoxin-like, 32 kDa | TXNL | 0.001102 | 192552 |
| Thyroid stimulating hormone receptor | TSHR | 0.02176 | 108606 |
| Tissue inhibitor of metalloproteinase 4 | TIMP4 | 0.023629 | 184795 |
| Trefoil factor 3 (intestinal) | TFF3 | 0.004648 | 114445 |
| Trefoil factor 3 (intestinal) | TFF3 | 0.014428 | 100949 |
| UDP-N-acetyl-alpha-d-galactosamine/polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9) | GALNT9 | 0.031284 | 161042 |
| WEE1 homolog (S. pombe) | WEE1 | 0.024101 | 123533 |
| WW domain containing oxidoreductase | WWOX | 0.012208 | 224298 |
| WW domain containing oxidoreductase | WWOX | 0.024101 | 135080 |
| Zinc finger protein 258 | ZNF258 | 0.013962 | 225961 |
| Zinc finger protein 36, C3H type-like 2 | ZFP36L2 | 0.018837 | 210469 |
Two-tail ANOVA with p value correction yielded 173 probes (52 up-, 121 down-regulated in PTC) significantly different (p < 0.05) between the malignant and benign thyroid tissues.