EASE Categories Significantly Enriched in vs MG vs vs MGC4-2 Pt1-C vs C4-2 Pt1-C UP-Regulated Genes MG System Gene Category EASE Global MGRWV Pt1-N RWV Pt1-N Score FDR GO Molecular Extracellular matrix cellular construction 0.0008 0 110 genes up- Function Interpro EGF-like domain 0.0009 0 regulated GO Molecular Oxidoreductase activity\ acting on single dono 0.0015 0 Function GO Molecular Calcium ion binding 0.0018 0 Function Interpro Laminin-G domain 0.0025 0 GO Biological Process Cell Adhesion 0.0045 0 Interpro Collagen Triple helix repeat 0.0047 0 KEGG pathway Complement and coagulation cascades 0.0053 0 KEGG pathway Immune System – Homo sapiens 0.0053 0 Interpro Fibrillar collagen C-terminal domain 0.0062 0 Interpro Calcium-binding EGF-like domain 0.0077 0 GO Molecular Cell adhesion molecule activity 0.0105 0 Function EASE Categories Significantly Enriched in Down-Regulated Genes System Gene Category EASE Global Score FDR GO Biological Process Copper ion homeostasis 2.5E-09 0 Interpro Metallothionein 6.1E-08 0 Interpro Vertebrate metallothionein, Family 1 6.1E-08 0 GO Biological Process Transition metal ion homeostasis 8.5E-08 0 GO Biological Process Heavy metal sensitivity/resistance 1.9E-07 0 GO Biological Process Di-, tri-valent inorganic cation homeostasis 6.3E-07 0 GO Biological Process Metal ion homeostasis 6.3E-07 0 GO Biological Process Cation homeostasis 2.1E-06 0 GO Biological Process Cell ion homeostasis 2.1E-06 0 GO Biological Process Ion homeostasis 2.1E-06 0 GO Molecular Helicase activity 2.3E-06 0 Function GO Biological Process Cell homeostasis 4.6E-06 0 GO Biological Process Homeostasis 5.5E-06 0 GO Molecular Cadmium ion binding 0.0002 0 Function GO Molecular Copper/cadmium binding 0.0002 0 Function GO Molecular Zinc ion binding 0.0004 0 Function GO Biological Process DNA replication initiation 0.0008 0 GenMAPP pathway Hs_Cell cycle 0.0008 0 GO Biological Process Cell growth and/or maintenance 0.0009 0 KEGG pathway Cell cycle – Homo sapiens 0.0011 0 GO Biological Process DNA replication 0.0018 0 GO Biological Process Mitotic cell cycle 0.0018 0 GO Biological Process S phase of mitotic cell cycle 0.0020 0 KEGG pathway Cell growth and Death – Homo Sapiens 0.0031 0 GO Molecular Binding 0.0043 0 Function GO Biological Process Obsolete biological process 0.0049 0 54 genes down- GO Molecular Catalytic activity 0.0129 0 Function regulated GO Biological Process Cell cycle 0.0139 0 GO Biological Process Regulation of cell cycle 0.0190 0 GO Biological Process Cell proliferation 0.0198 0 4985 unique 164 common GO Molecular Purine nucleotide binding 0.0226 0 Function genes genes GO Molecular Nucleotide binding 0.0237 0 TABLE 1.Genes Up-Regulated in Both MGC4-2 and PTC with 1-Sample T-Test q-value <10% ENTREZ AVE FOLD ENTREZ AVE FOLD HUGO NAME GENBANK GENE ¨ HUGO NAME GENBANK GENE ¨ DNA SYNTHESIS / TRANSCRIPTION REGULATION / DNA REPAIR SIGNAL TRANSDUCTION RFX5 Regulatory factor X 5 (influences HLA class II expression) AA418045 5993 1.8 DKK1 Dickkopf homolog 1 (Xenopus laevis) AA253464 22943 3.4 FLJ11196 La ribonucleoprotein domain family member 6 AA130193 55323 1.6 DUSP6 Dual specificity phosphatase 6 AA630374 1848 1.8 CYLN2 Cytoplasmic linker 2 H15662 7461 1.6 SSB1 SplA/ryanodine receptor domain and SOCS box containing 1 T97925 80176 1.6 HIST1H2AC Histone 1 H2ac N50797 8334 1.5 FZD8 Frizzled homolog 8 (Drosophila) AA457138 8325 1.5 SSX2IP Synovial sarcoma X breakpoint 2 interacting protein H20847 117178 1.5 PSD3 Pleckstrin and Sec7 domain containing 3 AA460826 23362 1.5 JMY Junction-mediating and regulatory protein AA608739 133746 1.5 FURIN Furin (paired basic amino acid cleaving enzyme) AA856874 5045 1.5 TUSC3 Tumor suppressor candidate 3 N66008 7991 1.4 SOCS5 Suppressor of cytokine signaling 5 N90775 9655 1.4 CALR Calreticulin H99170 811 1.4 MAPK1 Mitogen-activated protein kinase 1 AA683077 5594 1.4 U2AF2 U2 (RNU2) small nuclear RNA auxiliary factor 2 AA405748 11338 1.4 ADAM10 ADAM metallopeptidase domain 10 AA043347 102 1.4 JUNB Jun B proto-oncogene T99236 3726 1.4 TRIO Triple functional domain (PTPRF interacting) AA487480 7204 1.4 LMO4 LIM domain only 4 H27986 8543 1.4 EPS8 Epidermal growth factor receptor pathway substrate 8 H13623 2059 1.3 HIS1 Hexamethylene bis-acetamide inducible 1 W68585 10614 1.4 STRUCTURAL / ADHESION / MOTILITY ETV5 Ets variant gene 5 (ets-related molecule) AA460265 2119 1.4 CDH6 Cadherin 6 type 2 K-cadherin (fetal kidney) AA421819 1004 3.6 SNAI2 Snail homolog 2 (Drosophila) H57310 6591 1.3 KRTHA4 Keratin hair acidic 4 W49755 | AA28 3885 2.6 CTDSP2 CTD (carboxy-terminal domain RNA polymerase II polypeptide A) small phos AA404264 10106 1.3 TNC Tenascin C (hexabrachion) R39239 3371 2.2 PRRG2 Proline rich Gla (G-carboxyglutamic acid) 2 AA430552 5639 1.3 COL5A2 Collagen type V alpha 2 AA461456 1290 2.0 GROWTH / DIFFERENTIATION / APOPTOSIS COL12A1 Collagen type XII alpha 1 AA478481 1303 1.9 ANXA4 Annexin A4 AA419015 307 1.8 FBLN2 Fibulin 2 AA452840 2199 1.9 STK38L Serine/threonine kinase 38 like AA148542 23012 1.7 ALCAM Activated leukocyte cell adhesion molecule R39862 214 1.9 TM4SF10 Transmembrane protein 47 N52772 83604 1.7 COL5A1 Collagen type V alpha 1 R75635 1289 1.8 MAP3K8 Mitogen-activated protein kinase kinase kinase 8 W56266 1326 1.6 TIMP3 TIMP metallopeptidase inhibitor 3 (Sorsby fundus dystrophy pseudoinflammaAA099153 7078 1.7 RARRES3 Retinoic acid receptor responder (tazarotene induced) 3 W47350 5920 1.6 AGRN Agrin AA458878 375790 1.7 BNIP3L BCL2/adenovirus E1B 19kDa interacting protein 3-like AA025112 665 1.6 COL3A1 Collagen type III alpha 1 (Ehlers-Danlos syndrome type IV autosomal dominaT98612 1281 1.6 PLK2 Polo-like kinase 2 (Drosophila) AA460152 10769 1.4 CKB Creatine kinase brain AA894557 1152 1.6 VMP1 Transmembrane protein 49 AA485373 81671 1.4 CNN3 Calponin 3 acidic AA043228 1266 1.6 FHL1 Four and a half LIM domains 1 AA455925 2273 1.4 DCBLD2 Discoidin CUB and LCCL domain containing 2 AA431438 131566 1.5 PINK1 PTEN induced putative kinase 1 AA412184 65018 1.3 CDC42EP3 CDC42 effector protein (Rho GTPase binding) 3 AA115248 10602 1.5 RAF1 V-raf-1 murine leukemia viral oncogene homolog 1 N25425 5894 1.3 C9orf13 Sushi von Willebrand factor type A EGF and pentraxin domain containing 1 AA424560 79987 1.5 GSPT1 G1 to S phase transition 1 R93719 2935 1.3 CLDN11 Claudin 11 (oligodendrocyte transmembrane protein) AA443966 5010 1.5 IMMUNE / INFAMMATORY / STRESS RESPONSE SPARC Secreted protein acidic cysteine-rich (osteonectin) H95960 6678 1.4 DAF Decay accelerating factor for complement (CD55 Cromer blood group systemR09561 1604 1.7 SDC4 Syndecan 4 (amphiglycan ryudocan) AA148737 6385 1.4 G1P3 Interferon alpha-inducible protein (clone IFI-6-16) AA448478 2537 1.6 KAL1 Kallmann syndrome 1 sequence H17883 3730 1.4 B7H3 CD276 antigen N54338 80381 1.5 HSPG2 Heparan sulfate proteoglycan 2 (perlecan) AA427561 3339 1.4 THY1 Thy-1 cell surface antigen AA496283 7070 1.5 THBS2 Thrombospondin 2 H38240 7058 1.4 CD81 CD81 antigen (target of antiproliferative antibody 1) AA486556 975 1.4 CSPG2 Chondroitin sulfate proteoglycan 2 (versican) AA101875 1462 1.4 PROS1 Protein S (alpha) T74192 5627 1.4 PTPRS Protein tyrosine phosphatase receptor type S AA137072 5802 1.4 MCP Membrane cofactor protein (CD46 trophoblast-lymphocyte cross-reactive ant AA463497 4179 1.3 TRANSLATION - PROTEIN SYNTHESIS CD59 CD59 antigen p18-20 (antigen identified by monoclonal antibodies 163A5 EJ H60549 966 1.3 EIF2B3 Eukaryotic translation initiation factor 2B subunit 3 gamma 58kDa W58368 8891 2.5 METABOLISM - CARBOHYDRATE PLOD2 Procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 H99816 5352 1.6 XYLT1 Hypothetical protein LOC283824 R56916 64131 1.6 PLOD1 Procollagen-lysine 1 2-oxoglutarate 5-dioxygenase 1 AA476241 5351 1.5 KIAA0746 KIAA0746 protein AA456569 23231 1.6 PDIR Protein disulfide isomerase family A member 5 AA404387 10954 1.5 TKT Transketolase (Wernicke-Korsakoff syndrome) AA070358 7086 1.4 GOLPH2 Golgi phosphoprotein 2 AA454597 51280 1.4 MGAT3 Mannosyl (beta-14-)-glycoprotein beta-14-N-acetylglucosaminyltransferase AA421473 4248 1.3 EIF1AY Eukaryotic translation initiation factor 1A Y-linked AA047039 9086 1.3 GAA Glucosidase alpha acid (Pompe disease glycogen storage disease type II) AA444009 2548 1.3 CPEB2 Cytoplasmic polyadenylation element binding protein 2 N36923 132864 1.3 METABOLISM - LIPID/STEROL PTGFRN Prostaglandin F2 receptor negative regulator AA427887 5738 1.3 PTGS2 Prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cycR80217 5743 2.3 PPIB Peptidylprolyl isomerase B (cyclophilin B) N45313 5479 1.2 ALDH3B2 Aldehyde dehydrogenase 3 family member B2 AA443630 222 1.8 TRANSPORT/TRAFFICKING ALOX5 Arachidonate 5-lipoxygenase H51574 240 1.7 FABP5 Fatty acid binding protein 5 (psoriasis-associated) N47717 2171 1.9 SCD Stearoyl-CoA desaturase (delta-9-desaturase) AA457700 6319 1.7 CRABP2 Cellular retinoic acid binding protein 2 AA598508 1382 1.9 HMGCS1 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble) T56013 3157 1.6 KCNK1 Potassium channel subfamily K member 1 N62620 3775 1.6 METABOLISM - PROTEIN SEC24D SEC24 related gene family member D (S cerevisiae) AA449107 9871 1.5 ASS Argininosuccinate synthetase AA676466 445 1.4 SNX1 Sorting nexin 1 AA410893 6642 1.4 P4HA1 Procollagen-proline 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase) alpAA457671 5033 1.3 KIAA0515 KIAA0515 AA481143 84726 1.4 METABOLISM - OTHER SLC16A1 AKR7 family pseudogene AA043133 6566 1.3 RDH10 Retinol dehydrogenase 10 (all-trans) AA449821 157506 2.2 SEC13L1 SEC13-like 1 (S cerevisiae) AA496784 6396 1.2 EDEM1 ER degradation