Probe IDSymbolDescription and accession Fold ChangeP value A_23_P252306ID1 inhibitor of DNA binding 1, dominant negative helix-loop- helix protein [NM_002165] E-03 A_23_P114232PRDX4peroxiredoxin 4 [NM_006406] E-04 A_23_P216501TPM2tropomyosin 2 (beta) [NM_213674] E-03 A_23_P206724MT1Emetallothionein 1E [NM_175617] E-03 A_23_P334709FKBP9 FK506 binding protein 9, 63 kDa [NM_007270] E-02 A_23_P163782MT1Hmetallothionein 1H [NM_005951] E-02 A_24_P125096MT1Xmetallothionein 1X [NM_005952] E-02 A_23_P372874S100A13S100 calcium binding protein A13 [NM_005979] E-03 A_32_P94798ANXA2annexin A2 [NM_ ] E-02 A_23_P408095DSTN destrin (actin depolymerizing factor) [NM_ ] E-03 A_23_P14473CNIH cornichon homolog (Drosophila) [NM_005776] E-03 A_23_P145694ASNS asparagine synthetase (ASNS)[NM_001673] E-02 A_23_P68327CCDC104coiled-coil domain containing 104 [NM_080667] E-06 A_24_P800629TMED10P transmembrane emp24-like trafficking protein 10 (yeast) pseudogene [AJ004914] E-02 A_24_P361896MT2Ametallothionein 2A [NM_005953] E-02 A_32_P30926DYNC1I2 dynein, cytoplasmic, intermediate polypeptide 2 [NM_001378] E-03 A_32_P501400TCP1 t-complex 1 [NM_030752] E-02 A_32_P514599DCLK3doublecortin-like kinase 3 [NM_033403] E-02 A_32_P41292VDAC2voltage-dependent anion channel 2 [NM_003375] E-03 A_24_P391260PTTG1IP pituitary tumor-transforming 1 interacting protein [NM_004339] E-05 A_24_P67258EIF4B eukaryotic translation initiation factor 4B [NM_001417] E-02 A_23_P37983MT1B metallothionein 1B (functional) [NM_005947] E-02 A_32_P95397ITGB1 integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12) [NM_002211] E-03 A_32_P175098C8orf4 chromosome 8 open reading frame 4 (TC-1) [CR613736] E-03 A_23_P75056GATA3 GATA binding protein 3 [NM_ ] E-02 A_23_P60933MT1Gmetallothionein 1G [NM_005950] E-02 A_23_P142518NACC1 BTB (POZ) domain containing 14B [NM_052876] E-05 A_23_P99249SUCLG2 succinate-CoA ligase, GDP-forming, beta subunit [NM_003848] E-04 A_23_P427703MT1Lmetallothionein 1L (gene/pseudogene) [X97261] E-02 A_23_P152876RAB34 RAB34, member RAS oncogene family [NM_031934] E-03 A_23_P112634C4orf34chromosome 4 open reading frame 34 [NM_174921] E-04 A_24_P262355PHBprohibitin [NM_002634] E-03 A_23_P94911ZNF283zinc finger protein 283 [NM_181845] E-02 A_23_P368126AHCYL1 S-adenosylhomocysteine hydrolase-like 1 [NM_006621] E-02 A_23_P360983NDUFAF2 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor [NM_174889] E-02 A_23_P80068BTG3BTG family, member 3 [NM_006806] E-02 A_23_P434809S100A8 S100 calcium binding protein A8 (calgranulin A) [NM_002964] E-03 A_23_P37856HBA1 Homo sapiens hemoglobin, alpha 1 (HBA1), mRNA [NM_000558] E-10 A_23_P140384CTSGcathepsin G [NM_001911] E-02 A_23_P80867VWA5B2 von Willebrand factor A domain containing 5B2 [AL834499] E-02 A_23_P15055HBMhemoglobin mu chain [NM_ ] E-02 A_24_P831309FLJ45717Homo sapiens FLJ45717 protein [NM_207401] E-03 Supplementary Table 1 - Genes differentially expressed in osteosarcoma. List of 206 annotated genes that are significantly (P < 0.05) up- and down-regulated in osteosarcoma biopsies in comparison with non-malignant bone. The original list comprised 305 genes flagged as present in at least half

A_23_P403886GLYATglycine-N-acyltransferase NM_005838] E-03 A_23_P156708TNXBtenascin XB [NM_019105] E-03 A_23_P103932FGR Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog [NM_005248] E-02 A_23_P96072GRIN1 glutamate receptor, ionotropic, N-methyl D-aspartate 1 [NM_021569] E-02 A_23_P160849FCER1G Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide [NM_004106] E-02 A_23_P65370GLRX5glutaredoxin 5 [NM_016417] E-03 A_23_P27994TYROBP TYRO protein tyrosine kinase binding protein [NM_003332] E-02 A_23_P59798MKRN1makorin, ring finger protein, 1 [NM_013446] E-03 A_23_P502343ADAM33 a disintegrin and metalloproteinase domain 33 [NM_025220] E-03 A_23_P218770RAC2 ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2) [NM_002872] E-02 A_23_P63050URODuroporphyrinogen decarboxylase [NM_000374] E-02 A_23_P104689RELA v-rel reticuloendotheliosis viral oncogene homolog A (avian) (p65) [L19067] E-03 A_24_P384397RAVER1Homo sapiens RAVER1 [NM_133452] E-03 A_23_P137046NYXnyctalopin [NM_022567] E-04 A_23_P16089S1PR2sphingosine-1-phosphate receptor 2 [NM_004230] E-03 A_23_P79816EMILIN3elastin microfibril interfacer 3 [NM_052846] E-04 A_32_P27535C17orf72chromosome 17 open reading frame 72 [BC045676] E-02 A_24_P305784SPANXB2SPANX family, member B2 [NM_145664] E-03 A_23_P13382LSP1lymphocyte-specific protein 1 [NM_ ] E-03 A_23_P39386HCSThematopoietic cell signal transducer [NM_014266] E-03 A_23_P140675EPB42 erythrocyte membrane protein band 4.2 [NM_000119] E-03 A_24_P166407HIST1H4Bhistone 1, H4b [NM_003544] E-02 A_23_P109026KCNK15 potassium channel, subfamily K, member 15 [NM_022358] E-03 A_23_P9779IRX5iroquois homeobox protein 5 [NM_005853] E-03 A_23_P161324NUDT13 nudix (nucleoside diphosphate linked moiety X)-type motif 13 [NM_015901] E-02 A_23_P364619WDR21CWD repeat domain 21C [NM_152418] E-03 A_24_P242036RRP7B ribosomal RNA processing 7 homolog B (S. cerevisiae) [NR_002184] E-03 A_24_P40061LENG8 leukocyte receptor cluster (LRC) member 8 [NM_052925] E-03 A_24_P357037UBE2G2 ubiquitin-conjugating enzyme E2G 2 (UBC7 homolog, yeast) [NM_182688] E-03 A_23_P27353SLC14A2 solute carrier family 14 (urea transporter), member 2 [NM_007163] E-02 A_23_P158829ARRB2arrestin, beta 2 [NM_004313] E-03 A_23_P150162DRD4dopamine receptor D4 [NM_000797] E-02 A_23_P138706ADRA2Aadrenergic, alpha-2A-, receptor [NM_000681] E-02 A_23_P38795FPR1formyl peptide receptor 1 [NM_002029] E-02 Probe IDSymbolDescription and Accession Fold changeP value A_23_P153741AZU1 azurocidin 1 (cationic antimicrobial protein 37)[NM_001700] E-02 A_23_P22444PFCproperdin P factor, complement [NM_002621] E-02 A_23_P208866GMFGglia maturation factor, gamma [NM_004877] E-03 A_24_P207195IRX3iroquois homeobox protein 3 [NM_024336] E-03

Probe IDSymbolDescription and Accession Fold valueP value A_23_P23996MAT1A methionine adenosyltransferase I, alpha [NM_000429] E-02 A_32_P460973HLA-E major histocompatibility complex, class I, E [NM_005516] E-03 A_24_P231546FAM178B family with sequence similarity 178, member B [NM_016490] E-03 A_24_P321093SPOCK2 sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 2 [NM_014767] E-02 A_24_P359859HDAC4histone deacetylase 4 [NM_006037] E-03 A_24_P190190CACNB1 calcium channel, voltage-dependent, beta 1 subunit [NM_000723] E-02 A_23_P391926LPHN1latrophilin 1 [NM_ ] E-06 A_24_P178011MYC v-myc myelocytomatosis viral oncogene homolog (avian) [M13929] E-16 A_23_P hypothetical gene supported by BC [BC042812] E-03 A_23_P126089SPRR2Csmall proline-rich protein 2C (pseudogene) [M21539] E-04 A_24_P264154SHPC065Homo sapiens HSPC065 protein [NM_014157] E-03 A_24_P259819FAM128B family with sequence similarity 128, member B [AK024408] E-02 A_32_P356316HLA-DOA major histocompatibility complex, class II, DO alpha [NM_002119] E-02 A_24_P318457E2F4 E2F transcription factor 4, p107/p130-binding [NM_001950] E-03 A_23_P1962RARRES3 retinoic acid receptor responder (tazarotene induced) 3 NM_004585] E-03 A_24_P315862LOC similar to Ig heavy chain V-II region ARH-77 precursor [BX248300] E-02 A_23_P57227SNTA1 syntrophin, alpha 1 (dystrophin-associated protein A1, 59kDa, acidic component) [NM_003098] E-03 A_32_P110372SLC8A1 solute carrier family 8 (sodium/calcium exchanger), member 1 [NM_021097] E-03 A_32_P185229ATP8B2ATPase, Class I, type 8B, member 2 [NM_020452] E-04 A_23_P123018WBSCR23 Williams-Beuren syndrome chromosome region 23 [NM_025042] E-02 A_24_P267619PTPNS1 protein tyrosine phosphatase, non-receptor type substrate 1 [NM_080792] E-02 A_24_P383277KIAA1715Homo sapiens KIAA1715 [NM_030650] E-02 A_23_P355447ZDHHC22 zinc finger, DHHC domain containing 22 [NM_174976] E-02 A_24_P361816IGLV6-57immunoglobulin lambda variable 6-57 [AF267874] E-03 A_24_P379693DNPEPaspartyl aminopeptidase. [AK023005] E-02 A_24_P279704MAGmyelin associated glycoprotein [NM_080600] E-10 A_23_P142075ACP5acid phosphatase 5, tartrate resistant [NM_001611] E-03 A_32_P75902C16orf73 chromosome 16 open reading frame 73 [NM_152764] E-02 A_23_P130653RTBDNretbindin [NM_031429] E-03 A_23_P109201C20orf3chromosome 20 open reading frame 3 [NM_020531] E-03 A_23_P253982HOXA4homeo box A4 [NM_002141] E-02 A_23_P117082HEBP1heme binding protein 1 [NM_015987] E-03 A_23_P30913HLA-DPA1 major histocompatibility complex, class II, DP alpha 1 [NM_033554] E-03 A_23_P379630SLC38A10solute carrier family 38, member 10 [NM_138570] E-02 A_32_P134657KIAA0240 Homo sapiens KIAA0240 (KIAA0240), mRNA [NM_015349] E-02

Probe IDSymbolDescription and accession Fold changeP value A_23_P206371NOL3 nucleolar protein 3 (apoptosis repressor with CARD domain) [NM_003946] E-04 A_23_P158596AGTRAP angiotensin II receptor-associated protein [NM_020350] E-02 A_23_P144627PCDHB13protocadherin beta 13 NM_018933] E-03 A_23_P141699PARD6G par-6 partitioning defective 6 homolog gamma (C. elegans) [NM_032510] E-03 A_23_P421935ATXN7L3ataxin 7-like 3 [AL390158] E-03 A_24_P37887GPR150 G protein-coupled receptor 150 [NM_199243] E-04 A_23_P40025DAZAP2DAZ associated protein 2 [NM_014764] E-02 A_23_P24135TACR2 tachykinin receptor 2 [NM_001057] E-03 A_23_P7636PTTG1pituitary tumor-transforming 1 [NM_004219] E-02 A_23_P64058RASGRP2 RAS guanyl releasing protein 2 (calcium and DAG- regulated) [NM_005825] E-02 A_23_P46017KAT3kynurenine aminotransferase III [NM_ ] E-03 A_23_P208132BCL2B-cell CLL/lymphoma 2 [NM_000657] E-03 A_24_P160104TUBA8 tubulin, alpha 8 [NM_018943] E-02 A_23_P419764CCDC149coiled-coil domain containing 149 [NM_173463] E-02 A_23_P169358STX17 syntaxin 17 [NM_017919] E-02 A_24_P366566OR5H1 olfactory receptor, family 5, subfamily H, member 1 [NM_ ] E-03 A_23_P107735CD79A CD79A antigen (immunoglobulin-associated alpha) [NM_001783] E-02 A_23_P103511C1orf226 chromosome 1 open reading frame 226 [NM_ ] E-03 A_24_P76911RNF167ring finger protein 167 [NM_015528] E-02 A_24_P478495TMEM191Btransmembrane protein 191B [XM_ ] E-03 A_24_P75324TTBK1tau tubulin kinase 1 [AK131217] E-02 A_23_P66540PIK3R5 phosphoinositide-3-kinase, regulatory subunit 5, p101 [NM_014308] E-02 A_24_P151582TEFthyrotrophic embryonic factor [NM_003216] E-02 A_23_P44919ACSM5 acyl-CoA synthetase medium-chain family member 5 [BC068516] E-02 A_23_P113716HLA-Cmajor histocompatibility complex, class I, C [M21963] E-02 A_23_P141335ARHGAP27Rho GTPase activating protein 27 [NM_199282] E-03 A_32_P123255ANKRD58ankyrin repeat domain 58 [CR593492] E-02 A_23_P107661PPP2R1A protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform [NM_014225] E-03 A_23_P120883HMOX1heme oxygenase (decycling) 1 [NM_002133] E-03 A_23_P48868RASL12RAS-like, family 12 [NM_016563] E-02 A_23_P388900SLC22A15 solute carrier family 22 (organic cation transporter), member 15 [NM_018420] E-03 A_23_P61633TNK2tyrosine kinase, non-receptor, 2 [NM_005781] E-05 A_23_P159927ARHGAP4Rho GTPase activating protein 4 [NM_001666] E-03 A_23_P78808SYMPK symplekin [NM_004819] E-03 A_23_P109864GHSR growth hormone secretagogue receptor [NM_004122] E-03 A_24_P166443HLA-DPB1 major histocompatibility complex, class II, DP beta 1 [NM_002121] E-02 A_23_P117852KIAA0101 KIAA0101 [NM_014736] E-02 A_23_P107369KIF1Ckinesin family member 1C [NM_006612] E-03 A_24_P38895H2AFXH2A histone family, member X [NM_002105] E-02 A_24_P102895WDTC1WD and tetratricopeptide repeats 1 [NM_015023] E-03

Probe IDSymbolDescription and accession Fold changeP value A_23_P9823MLXIPMLX interacting protein [AB020674] E-02 A_23_P78405LIPGlipase, endothelial [NM_006033] E-02 A_24_P322229RASL10BRAS-like, family 10, member B NM_033315] E-02 A_24_P914134H.sapiens mRNA for prion protein. [X82545] E-02 A_23_P99980HMGB1 high-mobility group box 1 [NM_002128] E-02 A_24_P401990ERCC2 excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D) [NM_000400] E-02 A_23_P219060GPSM3 G-protein signalling modulator 3 (AGS3-like, C. elegans) [NM_022107] E-02 A_24_P112803SOX1SRY (sex determining region Y)-box 1 [NM_005986] E-02 A_23_P54636ATP6V0D1 ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d isoform 1 [NM_004691] E-02 A_24_P384990LOC642852hypothetical LOC [BC022830] E-02 A_32_P187327TUBB2tubulin, beta, 2 [NM_006088] E-03 A_32_P197489KLF13 Homo sapiens Kruppel-like factor 13 (KLF13), mRNA [NM_015995] E-03 A_24_P368943EVX1 even-skipped homeo box homolog 1 (Drosophila)[NM_001989] E-03 A_23_P151791LTB4R leukotriene B4 receptor [NM_181657] E-06 A_23_P21644DHRS8 dehydrogenase/reductase (SDR family) member 8 [NM_016245] E-03 A_23_P27381SDCCAG33 serologically defined colon cancer antigen 33 [NM_005786] E-02 A_23_P103812FAM5C family with sequence similarity 5, member C [NM_199051] E-03 A_23_P388150PLA2G12Bphospholipase A2, group XIIB [NM_032562] E-02 A_23_P129829ORMDL3 ORM1-like 3 (S. cerevisiae) [NM_139280] E-02 A_24_P285158FCRL2Fc receptor like 2 [NM_152378] E-02 A_24_P3005SCN9A sodium channel, voltage-gated, type IX, alpha[NM_002977] E-03 A_32_P83997RTN3reticulon 3 (RTN3), transcript variant 4 [NM_201430] E-05 A_24_P348885CYB561D1cytochrome b-561 domain containing 1 [NM_182580] E-03 A_23_P39453RKHD1 ring finger and KH domain containing 1 [NM_203304] E-02 A_23_P15798KRTAP4-12keratin associated protein 4-12 [NM_031854] E-02 A_23_P4662BCL3B-cell CLL/lymphoma 3 [NM_005178] E-02 A_24_P243528HLA-DPA1 major histocompatibility complex, class II, DP alpha 1 [NM_033554] E-02 A_23_P55076SKIP skeletal muscle and kidney enriched inositol phosphatase [NM_130766] E-02 A_23_P363196TCL6T-cell leukemia/lymphoma 6 [NM_014418] E-03 A_24_P21715RAD9ARAD9 homolog A (S. pombe) [NM_004584] E-03 A_24_P355609MRGPRFMAS-related GPR, member F [NM_145015] E-02 A_23_P422922TAF3 TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa [BC073884] E-02 A_23_P371794CACNB3 calcium channel, voltage-dependent, beta 3 subunit [NM_000725] E-02 A_23_P255884GSNgelsolin (amyloidosis, Finnish type) [NM_198252] E-02 A_32_P207124CT47cancer/testis CT47 family, member 11 [NM_173571] E-02 A_23_P60324UBADC1 ubiquitin associated domain containing 1 [NM_016172] E-02 A_23_P207842RARAretinoic acid receptor, alpha [NM_000964] E-03

Probe IDSymbolDescription and accession Fold changeP value A_23_P128503IL26interleukin 26[NM_018402] E-03 A_23_P120513C20orf141 chromosome 20 open reading frame 141 [NM_080739] E-03 A_23_P53018HRASLS5 HRAS-like suppressor family, member 5 [NM_054108] E-03 A_23_P105442GRASP GRP1 (general receptor for phosphoinositides 1)- associated scaffold protein [NM_181711] E-03 A_23_P5679CFC1cripto, FRL-1, cryptic family 1 [NM_032545] E-05 A_24_P392201TBC1D10CTBC1 domain family, member 10C [NM_198517] E-03 A_32_P40547MEG3 maternally expressed 3 (non-protein coding) [BX161432] E-04 A_23_P33141UTF1 undifferentiated embryonic cell transcription factor 1 [NM_003577] E-03 A_23_P168788PLOD3 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 [NM_001084] E-02 A_23_P152873NEK8 NIMA (never in mitosis gene a)- related kinase 8 [NM_178170] E-02 A_24_P728604TMEM114transmembrane protein 114 [XM_208930] E-02 A_23_P48455AMNamnionless homolog (mouse) [NM_030943] E-03 A_23_P133474GPX3glutathione peroxidase 3 (plasma) [NM_002084] E-02 A_24_P932293KIAA0913 full-length cDNA clone CS0DI059YG13 of Placenta Cot 25-normalized of Homo sapiens (human). [CR610954] E-03