Upregulated Genes in Pleomorphic Adenoma

7 Supplementary Table 1a: Upregulated genes in pleomorphic adenoma compared to normal salivary glands

1. Growth factors

J03242 Insulin-like growth factor II

Insulin-like growth factor II

AF059293 Cytokine-like factor-1

M37435 Macrophage colony stimulating factor-1

M60314 Bone morphogenetic protein 5

M22489 Bone morphogenetic protein 2

L42379 Bone-derived growth factor

Hs.112432 Muellerian inhibiting factor

U78110 Neurturin

M31682 Inhibin beta B chain

U43030 Cardiotrophin-1

2. Growth factor receptors

M64347 Fibroblast growth factor receptor 3 [Precursor]

X66945 Basic fibroblast growth factor receptor 1 [Precursor]

M34641 Basic fibroblast growth factor receptor 1 [Precursor]

X75958 BDNF/NT-3 growth factors receptor [Precursor]

3. Growth factor binding proteins

M34057 Latent transforming growth factor beta binding protein 1L[Precursor]

Z37976 Latent transforming growth factor beta binding protein 2

U20982 Insulin-like growth factor binding protein 4 [Precursor]

M62403 Insulin-like growth factor binding protein 4 [Precursor]

4. Growth regulation proteins

M25667 Neuromodulin

U35139 Necdin

L13698 Growth-arrest-specific protein 1

L13720 Growth-arrest-specific protein

5. Cell division and cell-cycle-related proteins

S78187 M-phase inducer phosphatase 2

M92287 G1/S-specific cyclin D3

U73379 Ubiquitin-conjugating enzyme E2 C

AF035811 Septin 4

U29725 Mitogen-activated protein kinase 7

X57348 14-3-3 protein sigma

6. Apoptosis-related proteins

X98172 Caspase-8 [Precursor]

Y09392 Tumor necrosis factor receptor superfamily member 12 [Precursor]

7. Proto-oncogenes

U65002 Zinc finger protein PLAG1

X12949 Proto-oncogene tyrosine-protein kinase receptor ret

U16954 Protein AF1Q

M14333 Proto-oncogene tyrosine-protein kinase FYN

D43969 Runt-related transcription factor 1

M73554 G1/S-specific cyclin D1

M13995 Apoptosis regulator Bcl-2

X61118 Rhombotin-2

8. Tumor suppressor genes

U81992 Zinc finger protein PLAGL1

M22898 Cellular tumor antigen p53

D64137 Cyclin-dependent kinase inhibitor 1C

9. Transcriptional regulators

M97815 Retinoic acid-binding protein II, cellular

X77956 DNA-binding protein inhibitor ID-1

AL022726 DNA-binding protein inhibitor ID-4

Hs.76884 DNA-binding protein inhibitor ID-3

AC004774 Homeobox protein DLX-5

L07919 Homeobox protein DLX-2

X61755 Homeobox protein Hox-C5

AB002305 Aryl hydrocarbon receptor nuclear translocator 2

AB018303 Smad-and Olf-interacting zinc finger protein [Fragment]

L07592 Peroxisome proliferator activated receptor delta

D13969 DNA-binding protein Mel-18

J03258 Vitamin D3 receptor

AF041210 Midline 1 protein

X96381 Ets-related protein ERM

U15655 ETS-domain transcription factor ERF

AF055376 Short form transcription factor C-MAF

X70683 Transcription factor SOX-4

L31881 Nuclear factor 1 X-type

X53390 Nucleolar transcription factor 1

AB006909 Microphthalmia-associated transcription factor

AF035528 Mothers against decapentaplegic homolog 6

AF010193 Mothers against decapentaplegic homolog 7

X70991 NGFI-A binding protein 2

U49857 Transcriptional activator

U66619 SWI/SNF complex 60 kDa subunit

10. Proteins involved in signalling

Kinases

X74764 Discoidin domain receptor 2 [Precursor]

M97675 Tyrosine-protein kinase transmembrane receptor ROR1

AB011109 Probable serine/threonine-protein kinase KIAA0537

D10495 Protein kinase C, delta type

AB023182 KIAA0965 protein [Fragment]

M65066 cAMP-dependent protein kinase type I-beta regulatory chain

X80907 Phosphatidylinositol 3-kinase regulatory beta subunit

Kinase binding proteins

D83018 Protein kinase C-binding protein NELL2 [Precursor]

Phosphatases

M93426 Protein-tyrosine phosphatase zeta [Precursor]

U12128 Protein tyrosine phosphatase, non-receptor type 13

L11329 Dual specificity protein phosphatase 2

Adenylate cyclases

AB011083 Adenylate cyclase type III

Receptors and ligands

Hs.91622 Neuronal pentraxin receptor

X57830 5-hydroxytryptamine 2A receptor

L22214 Adenosine A1 receptor

X77777 Vasoactive intestinal polypeptide receptor 1 [Precursor]

AF062006 Orphan G protein-coupled receptor HG38

AB017365 Frizzled 7 [Precursor]

L37882 Frizzled 2 [Precursor]

U91903 Frizzled-related protein [Precursor]

AJ225028 Gamma-aminobutyric acid type B receptor, subunit 1 [Precursor]

U95367 Gamma-aminobutyric-acid receptor pi subunit [Precursor]

L20814 Glutamate receptor 2 [Precursor]

L19058 Glutamate receptor, ionotropic kainate 1 [Precursor]

M59911 Integrin alpha-3 [Precursor]

X13916 Low-density lipoprotein receptor-related protein 1 [Precursor]

M33210 Colony stimulating factor receptor [Fragment]

U32324 INTERLEUKIN-11 RECEPTOR

U23850 Inositol 1,4,5-trisphosphate receptor type 1

D37965 PDGF receptor beta-like tumor suppressor

S62539 Insulin receptor substrate-1

U09303 Ephrin-B1 [Precursor]

Signal transduction inhibitors

U27655 Regulator of G-protein signaling 3

GTP-binding proteins

L07807 Dynamin-1

D90150 Guanine nucleotide-binding protein G(z), alpha subunit

X04828 Guanine nucleotide-binding protein G(i), alpha-2 subunit

K03460 Alpha-tubulin isotype H2-alpha [Fragment]

X00734 Tubulin beta-5 chain

AB023061 Ras-related protein Rab-36

U10550 GTP-binding protein GEM

ATP-binding proteins

AF070598 ATP-binding cassette, sub-family B, member 6, mitochondrial

AF020267 Myosin IXb

AF104942 Multidrug resistance-associated protein 5

D87119 GS3955

GTPase activation

Z83844 SH3-domain binding protein 1

X78817 Rho-GTPase-activating protein 4

11. Metabolism-related proteins

Polymerases and general transcription

X63564 DNA-directed RNA polymerase II largest subunit

U52427 DNA-directed RNA polymerase II 19 kDa polypeptide

U02619 TFIIIC BOX B-BINDING SUBUNIT

U44755 snRNA activating protein complex 45 kDa subunit

L25444 Transcription initiation factor TFIID 70 kDa subunit

AL049650 Small nuclear ribonucleoprotein associated proteins B and B'

Hydrolases

J05070 92 kDa type IV collagenase [Precursor]

U06088 N-acetylgalactosamine-6-sulfatase [Precursor]

X63422 ATP synthase delta chain, mitochondrial [Precursor]

L15702 Complement factor B [Precursor]

U47927 Ubiquitin carboxyl-terminal hydrolase 5

M91029 AMP deaminase 2

D78586 CAD protein

D63391 Platelet-activating factor acetylhydrolase IB gamma subunit

M22430 Phospholipase A2, membrane associated [Precursor]

AF038440 Phospholipase D2

U76421 Double-stranded RNA-specific editase 1

AF093774 Iodithyronine deiodinase

M22324 Aminopeptidase N

Ligases

M91670 Ubiquitin-conjugating enzyme E2-24 kDa

AF032456 biquitin-conjugating enzyme E2 G2

AL096725 Tubulin tyrosine ligase-like protein HOTTL

Oxidoreductases

AF046889 Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 [Precursor]

J02947 Extracellular superoxide dismutase [Cu-Zn] [Precursor]

U08997 Glutamate dehydrogenase 2, mitochondrial [Precursor]

J02871 Cytochrome P450 4B1

Protease inhibitors

AJ228139 Serine protease inhibitor Kazal-type 5 [Precursor]

M97252 Anosmin 1 [Precursor]

L10343 Elafin [Precursor]

L02870 Collagen alpha 1(VII) chain [Precursor]

U14394 Metalloproteinase inhibitor 3 [Precursor]

Transferases

U67191 Exostosin-like 1

AB017915 CHONDROITIN 6-SULFOTRANSFERASE

Y18643 METHYLTRANSFERASE-LIKE PROTEIN 1

Y10805 Protein arginine N-methyltransferase 1

Other enzymes

AF046798 Glycogen phosphorylase, liver form

AF053944 AORTIC CARBOXYPEPTIDASE-LIKE PROTEIN ACLP

Z84718 D-dopachrome tautomerase

AJ130733 Alpha-methylacyl-CoA racemase

12. Extracellular matrix / cell adhesion proteins

M95610 Collagen alpha 2(IX) chain [Precursor]

J03464 Collagen alpha 2(I) chain [Precursor]

V00503 Collagen alpha 2(I) chain [Precursor]

AL031228 Collagen alpha 2(XI) chain [Precursor]

J04177 Collagen alpha 1(XI) chain [Precursor]

M92642 Collagen alpha 1(XVI) chain [Precursor]

L10347 Alpha-1 type II collagen

L41162 Collagen alpha 3(IX) chain [Precursor]

U19718 Microfibril-associated glycoprotein [Precursor]

L38486 Microfibril-associated glycoprotein 4

X63556 Fibrillin 1 [Precursor]

X15998 Versican core protein [Precursor]

D32039 Versican core protein [Precursor]

X78565 Tenascin [Precursor]

D13666 OSTEOBLAST SPECIFIC FACTOR 2 [Precursor]

J03040 SPARC [Precursor]

X82494 Fibulin-2 [Precursor]

J04599 Bone/cartilage proteoglycan I [Precursor]

L32137 Cartilage oligomeric matrix protein [Precursor]

M10905 Fibronectin [Precursor]

X02761 Fibronectin [Precursor]

L12350 Thrombospondin 2 [Precursor]

Y12642 Lymphocyte antigen Ly-6D [Precursor]

U59632 Platelet glycoprotein IB beta chain [Precursor]

AB029037 Trophinin

AB001466 Embryonal Fyn-associated substrate

D21255 OB-cadherin-2

D21254 Cadherin-11 [Precursor]

AB023138 Neurexin 2-alpha [Precursor]

M55172 Aggrecan core protein [Precursor]

X17406 Aggrecan core protein [Precursor]

X96753 Melanoma-associated chondroitin sulfate proteoglycan

Z48199 Syndecan-1 [Precursor]

X54232 Glypican-1 [Precursor]

13. Miscellaneous

Salivary gland

X07704 Salivary proline-rich protein PO [Fragment]

K03207 Salivary proline-rich protein PO [Precursor]

Actin-binding

U03057 Fascin

AF059611 Ectoderm-neural cortex-1 protein

M94345 Macrophage capping protein

SH3 domain

AF036271 SH3-containing GRB2-like protein 3

AL008637 Neutrophil cytosol factor 4

AB007884 KIAA0424 protein

AB007925 KIAA0456 protein [Fragment]

AB029035 KIAA1112 protein [Fragment]

M92303 Dihydropyridine-sensitive L-type, calcium channel beta-1 subunit

Intermediate Filament - keratin

AF061812 KERATIN 16

L42611 Keratin, type II cytoskeletal 6E

M28439 Keratin, type I cytoskeletal 17 [Version 2]

X07696 Keratin, type I cytoskeletal 15

X81420 KERATIN

AB002351 Desmuslin

M13452 Lamin A/C

Vitamin A - Transport

S74445 Retinoic acid-binding protein I, cellular

Interferon-induction

J04164 Interferon-induced transmembrane protein 1

X57351 Interferon-induced transmembrane protein 2

Pentraxin-related proteins

U29195 Neuronal pentraxin II [Precursor]

M31166 Pentaxin-related protein PTX3 [Precursor]

Transmembrane glycoproteins involved in signalling

U23070 Putative transmembrane protein NMA [Precursor]

X76534 Putative transmembrane protein NMB [Precursor]

DNA repair proteins

L40399 DNA mismatch repair protein Mlh3

Other

X57985 Histone H2A.q [Fragment]

K02054 Gastrin-releasing peptide [Precursor]

Y16270 Paralemmin

U24578 Complement C4 [Precursor]

AB023204 Band 4.1-like protein 3

U60060 Fasciculation and elongation protein zeta 1

AJ002962 Fatty acid-binding protein, brain

U49184 Occludin

D21267 Synaptosomal-associated protein 25

M59488 S-100 protein, beta chain

AF043472 Shab-related delayed-rectifier K+ channel alpha subunit

AB014551 GEF-H1 protein

Z98046 Melanoma-associated antigen D2

AB003184 ISLR [Precursor]

U18467 Pregnancy-specific beta-1-glycoprotein 7 [Precursor]

M73628 Kappa casein [Precursor]

U58516 Lactadherin [Precursor]

M15036 Vitamin K-dependent protein S [Precursor]

AC003107 COMP_HUMAN

M12529 Apolipoprotein E [Precursor]

U04313 Maspin [Precursor]

Y08374 Chitinase-3 like protein 1 [Precursor]

U33147 Mammaglobin A [Precursor]

U81375 Equilibrative nucleoside transporter 1

Z71460 Vacuolar proton translocating ATPase 116 kDa subunit A isoform1

AF016004 Neuronal membrane glycoprotein M6-b

AF022813 Transmembrane 4 superfamily, member 7

M83664 HLA-DPB1 [Precursor]

X92841 MHC class I chain-related protein A

U87947 Epithelial membrane protein-3

U51240 Lysosomal-associated multitransmembrane protein

U42360 N33 protein

U17077 BENE protein

AB018279 KIAA0736 protein

AF030428 MEMBRANE GLYCOPROTEIN GP36 [Precursor]

AJ224677 Scrapie-responsive protein 1 [Precursor]

AF054506 Erythroid K:Cl cotransporter splicing isoform 2

AJ012737 Filamin, muscle isoform

U63825 Delta-interacting protein A

AF006084 ARP2/3 complex 41 kDa subunit

AB014520 KIAA0620 protein [Fragment]

U76702 FOLLISTATIN-RELATED PROTEIN FLRG

D78014 Dihydropyrimidinase related protein-3

U97105 Dihydropyrimidinase related protein-2

U78556 Cisplatin resistance associated alpha protein

AB022660 SET-binding protein

AL049946 Hypothetical 63.9 kDa protein [Fragment]

14. Unknown function

L35594 Autotaxin

M91669 Autoantigen [Fragment]

AJ000388 Calpain 6

AL049653 CDT6

L36720 Bystin

X99688 TYL protein

AF068197 BCE-1 protein

U66306 ORF-2

AB002304 Capicua protein

AB011539 MEGF6 [Fragment]

Y09160 Sub1.5 protein

AF097021 GW112 protein

AB020647 KIAA0840 PROTEIN [Fragment]

AB020628 KIAA0821 protein

AF027734 IB3089A

D38548 Hypothetical protein KIAA0076

D87458 KIAA0282 protein [Fragment]

AL050118 Hypothetical 37.1 kDa protein [Fragment]

AB018339 KIAA0796 protein [Fragment]

AB029016 KIAA1093 protein [Fragment]

U79259 Hypothetical 26.4 kDa protein

AF070572 Hypothetical 63.6 kDa protein [Fragment]

AB029012 KIAA1089 protein [Fragment]

AL050138 Hypothetical 104.2 kDa protein [Fragment]

AB002331 KIAA0333 protein [Fragment]

AB029028 KIAA1105 protein [Fragment]

D31891 KIAA0067 protein

AB014585 KIAA0685 protein

AL049953 Hypothetical 27.7 kDa protein [Fragment]

D87463 Hypothetical protein KIAA0273

AB014577 KIAA0677 PROTEIN

AB018345 KIAA0802 protein [Fragment]

D87468 KIAA0278 protein [Fragment]

AB028959 KIAA1036 PROTEIN

AB002354 KIAA0356 protein [Fragment]

AB020704 KIAA0897 protein [Fragment]

AL031781 DJ51J12.1 [Fragment]