Supplementary Figure S11: Regulation of an embryonic Wnt-interactive network by SYT-SSX2 and in human synovial sarcomas

Genes in black letters represent SYT-SSX2 transcriptional targets in the C2C12 myoblasts, in red letters and red underline are the SYT-SSX2 targets in human mesenchymal stem cells, genes in green letters and green asterisks were identified in the transcriptomes of two human synovial sarcoma arrays (Supplementary Tables S1-S3). Names in italics signify downregulated genes. The upper left columns list components of the Wnt pathway found in the four arrays. The lower left columns are mediators of the developmental pathways that interact with Wnt to drive embryogenesis. The right panel displays controllers of embryonic patterning and .

Supplementary Table S1: Differentially regulated Wnt components in mesenchymal precursor cells expressing SYT-SSX2 and in synovial sarcoma tumors Symbol Name Accession

C2C12 hMSCs SS tumors WNT 4 WNT 4 Wingless-related MMTV integration site 4 NM_030761 WNT 5a 1 Wingless-related MMTV integration site 5a NM_003392 WNT 6 1 Wingless-related MMTV integration site 6 NM_006522 WNT 7a Wingless-related MMTV integration site 7a NM_009527 WNT 7b WNT 7b Wingless-related MMTV integration site 7b NM_058238 WNT 11 WNT 11 Wingless-related MMTV integration site 11 NM_004626

WNT 2 1 Wingless-related MMTV integration site 2 NM_003391

FZD 1 FZD 1 1, 2 homolog 1 NM_021457

FZD 2 FZD 2 Frizzled homolog 2 NM_001466 FZD 3 FZD 3 Frizzled homolog 3 NM_017412 FZD 6 1, 2 Frizzled homolog 6 NM_003506 FZD 7 1, 2 Frizzled homolog 7 NM_003507 FZD 8 1, 2 Frizzled homolog 8 NM_031866 LRP 1 1, 2 Low density lipoprotein -related 1 NM_002332 LRP 4 Low density lipoprotein receptor-related protein 4 NM_172668 LRP 5 LRP 5 1 Low density lipoprotein receptor-related protein 5 NM_002335 LRP 8 1, 2 Low density lipoprotein receptor-related protein 8 NM_004631 LEF 1 LEF 1 1, 2 Lymphoid enhancer factor binding 1 NM_016269 TCF 7L2 1, 2 7-like 2 NM_030756 TCF 7L1 1, 2 Transcription factor 7-like 1 NM_003200 TCF 7 TCF 7 2 Transcription factor 7 NM_003202 CCDC88C DVL associating protein with a high frequency of leucine NM_001080414 AXIN 2 AXIN 2 AXIN 2 2 Axin 2 NM_004655 FRZB FRZB 1 Frizzled related protein NM_001463 SFRP 1 SFRP 1 2 Secreted frizzled-related protein 1 NM_003012 SFRP 4 1, 2 Secreted frizzled-related protein 4 NM_003014 DKK 3 DKK3 2 Dickkopf homolog 3 NM_015814 KREMEN 1 Kringle containing transmembrane protein 1 NM_001039570 DACT 1 DACT 1 Dapper homolog 1 NM_016651 ROR 2 ROR 2 1 Receptor tyrosine -like orphan receptor 2 NM_004560 RYK Receptor-like NM_013649 APCDD1 APCDD1 Adenomatous polyposis coli down-regulated 1 NM_153000 TLE 1 Transducin-like enhancer 1 NM_005077 TLE 2 TLE 2 1, 2 Transducin-like enhancer 2 NM_003260 TLE 3 TLE 3 TLE 3 2 Transducin-like enhancer 3 NM_005078 TLE4 TLE 4 1, 2 Transducin-like enhancer 4 NM_007005 RSPO 1 R-spondin homolog 1 NM_001038633 RSPO 2 R-spondin homolog 2 NM_178565 DAB 2 DAB 2 DAB 2 2 Disabled homolog 2 NM_001343 PPP2R2C PPP2R2C PPP2R2C 2 Protein phosphatase 2, regulatory subunit b, gamma NM_020416

Underlined genes are downregulated . A partial list was published in Garcia et al., 2012a.

Supplementary Table S2. Differentially regulated Wnt targets in mesenchymal precursor cells (4 pages) expressing SYT-SSX2 and in synovial sarcoma tumors

Symbol Name Accession C2C12 hMSCs SS tumors CCND 1 CCND 1 1, 2 Cyclin D1 NM_053056 CCND 2 CCND 2 CCND 2 1, 2 Cyclin D2 NM_001759 MYC MYC 1, 2 Myelocytomatosis oncogene NM_002467 WNT 11 WNT 11 Wingless-related MMTV integration site 11 NM_004626 AXIN 2 AXIN 2 AXIN 2 2 Axin 2 NM_004655 LGR 5 LGR 5 LGR 5 1 Leucine rich repeat coupled receptor 5 NM_003667 JUN 1, 2 JUN proto-oncogene NM_005354 MMP 2 Matrix metallopeptidase 2 NM_008610 MMP 9 Matrix metallopeptidase 9 NM_013599 MMP 10 MMP 10 MMP 10 2 Matrix metallopeptidase 10 NM_002425 MMP 11 Matrix metallopeptidase 11 NM_008606 MMP 13 Matrix metallopeptidase 13 NM_008607 MMP 14 Matrix metallopeptidase 14 NM_008608 MMP 15 MMP 15 MMP 15 1, 2 Matrix metallopeptidase 15 NM_002428 MMP 16 Matrix metallopeptidase 16 NM_019724 MMP 19 MMP19 MMP19 2 Matrix metallopeptidase 19 NM_002429 EPH A2 Eph receptor A2 NM_010139 EPH A3 Eph receptor A3 NM_005233 EPH A4 EPH A4 EPH A4 2 Eph receptor A4 NM_004438 EPH A8 Eph receptor A8 NM_007939 EPH B1 EPH B1 EPH B1 1 Eph receptor B1 NM_004441 EPH B2 EPH B2 2 Eph receptor B2 NM_004442 EPH B3 EPH B3 EPH B3 1 Eph receptor B3 NM_004443 EPH B4 EPH B4 2 Eph receptor B4 NM_004444 EPH B6 EPH B6 EPH B6 2 Eph receptor B6 NM_004446 EFN A1 EFN A1 1, 2 A1 NM_004428 EFN A3 EFN A3 NM_004952 EFN A4 EFN A4 2 NM_005227 EFN A5 Ephrin A5 NM_001962 EFN B1 EFN B1 NM_004429 EFN B2 1 NM_004093 LIF Leukemia inhibitory factor NM_008501 LBH LBH Limb bud heart NM_030915 ID 1 Inhibitor of DNA binding 1 NM_181353 ID 2 ID 2 1, 2 Inhibitor of DNA binding 2 NM_002166 ID 3 ID 3 1 Inhibitor of DNA binding 3 NM_002167 ID 4 ID 4 1, 2 Inhibitor of DNA binding 4 NM_001546 IGF2 IGF2 IGF2 1, 2 -like 2 NM_000612 IGFBP2 IGFBP2 IGFBP2 1, 2 Insulin-like growth factor binding protein 2 NM_000597 SHH SHH homolog NM_000193 GLI 2 GLI 2 1 Glioma-associated oncogene family 2 NM_005270 DLL 1 DLL 1 DLL 1 1, 2 Delta-like 1 NM_005618 JAG 1 JAG 1 2 Jagged 1 NM_000214 JAG 2 JAG 2 1 Jagged 2 NM_002226 NOTCH 1 NOTCH 1 2 NOTCH (Drosophila) homolog 1 NM_017617 HES 1 HES 1 Hairy and enhancer of split 1 NM_005524 FGF2 FGF 2 1, 2 2 NM_002006 FGF7 FGF 7 1, 2 Fibroblast growth factor 7 NM_002009 FGF 9 FGF 9 Fibroblast growth factor 9 NM_002010 FGF 18 FGF 18 1, 2 Fibroblast growth factor 18 NM_003862 FGF 19 Fibroblast growth factor 19 NM_005117 TGFB 3 Transforming growth factor beta 3 NM_009368 NOG Noggin NM_005450 RET RET RET proto-oncogene NM_020975 GDNF 1 Glial cell-derived neurotrophic factor NM_010275 MITF 1, 2 Microphthalmia-associated transcription factor NM_198159 SOX 9 SOX 9 1, 2 SRY-related HMG-box 9 NM_000346 SOX 4 1 SRY-related HMG-box 4 NM_003107 SOX 3 1 SRY-related HMG-box 3 NM_005634 SOX 17 SRY-related HMG-box 17 NM_022454 PROX 1 PROX 1 Prospero 1 NM_002763 RUNX2 1 Runt-related transcription factor 2 NM_001024630 DLX 3 DLX 3 Distal-less homeobox 3 NM_005220 DLX 4 1 Distal-less homeobox 4 NM_138281 DLX 5 DLX 5 1 Distal-less homeobox 5 NM_005221 MSX 1 Msh homeobox 1 NM_010835 MSX 2 1, 2 NM_002449 FOX C2 Forkhead box protein C2 NM_013519 FOX C1 FOX C1 1, 2 Forkhead box protein C1 NM_001453 FOX D1 FOX D1 2 Forkhead box protein D1 NM_008242 FOX G1B 1 Forkhead box protein G1B NM_005249 FOX M1 Forkhead box protein M1 NM_202002 HOX B6 HOX B6 Homeobox B6 NM_018952 HOX B8 Homeobox B8 NM_010461 HOX B9 HOX B9 Homeobox B9 NM_024017 PAX 9 Paired box 9 NM_011041 BMP 4 BMP 4 1, 2 Bone morphogenetic protein 4 NM_001202 RARG RARG 1, 2 gamma NM_000966 RSPO 1 R-spondin homolog 1 NM_001038633 RSPO 2 R-spondin homolog 2 NM_178565 HMGA 1 High mobility group AT-hook 1 NM_001025427 HMGA2 HMGA 1 2 High mobility group AT-hook 2 NM_010441 GBX2 brain homeobox 2 NM_001485 NEUROD1 Neurogenic differentiation 1 NM_002500

NEUROG3 Neurogenin 3 NM_020999 NKX2-2 NK2 homeobox 2 NM_002509 SIX 1 SIX 1 Sine oculis-related homeobox 1 NM_009189 ZCCHC12 ZCCHC12 Zinc finger CCHC domain containing 12 NM_173798 ODZ3 Odz odd Oz/ten-m homolog 3 NM_011857 ETS2 Erythroblastosis virus E26 oncogen homolog 2e NM_005239 PBX 3 1, 2 Pre-B- cell leukemia homeobox 3 NM_006195 ZEB 1 Zinc finger E-box binding homeobox 1 NM_011546 SNAI 2 SNAI 2 1, 2 Snail homolog 2 NM_011415 THBS 1 THBS 1 1, 2 Thrombospondin 1 NM_003246 THBS 2 THBS 2 1, 2 Thrombospondin 2 NM_003247 THBS 3 THBS 3 2 Thrombospondin 3 NM_007112 THBS 4 1 Thrombospondin 4 NM_003248 BIRC 5 BIRC 5 2 Survivin NM_001168 ENPP1 ENPP 1 ENPP1 1, 2 Ectonucleotide pyrophosphatase/phosphodiesterase 1 NM_006208 ENPP 2 ENPP2 2 Ectonucleotide pyrophosphatase/phosphodiesterase 2 NM_006209 ENPP 3 Ectonucleotide pyrophosphatase/phosphodiesterase 3 NM_134005 EGFR EGFR 1 Epidermal NM_005228 MET MET 2 receptor NM_001127500 VDR Vitamin D (1,25- dihydroxyvitamin D3) receptor NM_009504 NRP 1 Neuropilin 1 NM_008737 NRP 2 NRP 2 1, 2 Neuropilin 2 NM_201266 MAPT MAPT 1 Microtubule associated protein Tau NM_016835 STRA 6 STRA 6 Stimulated by retinoic acid gene 6 NM_022369 VEGFC VEGFC 2 Vascular endothelial growth factor C NM_005429 PLAU PLAU 1, 2 Plasminogen activator urokinase NM_002658 PLAUR PLAUR 1, 2 Plasminogen activator urokinase receptor NM_002659 TNC Tenascin C NM_002160 FST NM_006350 POSTN POSTN POSTN 2 Periostin NM_006475 PTN PTN 1 NM_002825 PTTG 1 PTTG 1 2 Pituitary tumor-transforming 1 NM_004219 CLU CLU CLU 2 Clusterin NM_001831 CALML 4 Calmodulin-like 4 NM_138304 VCAN VCAN 2 Versican NM_001081249 ANGPTL 4 -like 4 NM_020581 UNC 5B UNC 5B 2 Unc-5 homolog b (C.elegans) NM_170744 SEMA 3A SEMA 3A SEMA 3A 2 3A NM_006080 LAMC 2 1 Laminin gamma 2 NM_005562 FN 1 FN 1 1 NM_212482 C3 C3 Complement component 3 NM_000064 IL8 8 NM_000584 IL6 1 NM_000600 NRCAM NRCAM NRCAM 1 Neuronal cell adhesion molecule NM_001037132 L1CAM L1CAM L1 cell adhesion molecule NM_000425

RHOU RHOU Ras homolog gene family member U NM_021205 Immunoglobulin superfamily containing leucine rich ISLR repeats NM_012043 EDN1 1 1 NM_001955 CD44 1, 2 CD44 molecule NM_000610 EMP 1 Epithelial 1 NM_001423 EMP 2 EMP 2 1, 2 Epithelial membrane protein 2 NM_001424 EMP 3 1, 2 Epithelial membrane protein 3 NM_001425 ENC 1 ENC 1 1, 2 Ectodermel-neural cortex NM_003633 MEG 3 MEG 3 1, 2 Maternally expressed 3 NM_003530 CLDN 1 CLDN 1 Claudin 1 NM_021101 PPAP2B Phosphatidic acid phosphatase type 2b NM_080555 LPL LPL 1, 2 Lipoprotein lipase NM_000237 CYP26B1 CYP26B1 Cytochrome p450, family 26, subfamily b polypeptide 1 NM_019885 KRT 17 KRT 17 KRT 17 1 Keratin 17 NM_000422 CXCL1 Chemokine 1 NM_008176 CXCR 4 CXCR 4 Chemokine receptor 4 NM_001008540 CXCL16 1 Chemokine ligand 16 NM_022059 PLA2G 2A PLA2G 2A 1 Phospholipase A2, group IIA NM_000300

Underlined genes are downregulated. 1 indicates SS tumor microarray by Nielsen et al., 2002; 8 human SS tumors. 2 indicates SS tumor microarray by Francis et al., 2007; 32 human SS tumors.

Supplementary Table S3 (Part 1). The embryonic Wnt interactive network in mesenchymal precursor cells (3 pages) expressing SYTSSX2 and in synovial sarcoma tumors

Symbol Name Accession C2C12 hMSCs SS tumors NOTCH NOTCH 1 NOTCH 1 2 NOTCH (Drosophila) homolog 1 NM_017617 DLL 1 DLL 1 DLL 1 1, 2 Delta-like 1 NM_005618 JAG 1 JAG 1 2 Jagged 1 NM_000214 JAG 2 JAG 2 1 Jagged 2 NM_002226 LFNG Lunatic fringe homolog NM_001040167 HES 1 HES 1 Hairy and enhancer of split 1 NM_005524 HEY L Hairy/enhancer-of-split related with YRPW motif-like NM_014571 HEY 1 1 Hairy/enhancer-of-split related with YRPW motif 1 NM_012258 HEY 2 HEY 2 1 Hairy/enhancer-of-split related with YRPW motif 2 NM_012259 FGF FGFR 1 1, 2 Fibroblast growth factor receptor 1 NM_023110 FGFR 2 FGFR 2 FGFR 2 1 Fibroblast growth factor receptor 2 NM_000141 FGFR 3 FGFR 3 FGFR 3 1,2 Fibroblast growth factor receptor 3 NM_000142 FGFR 4 2 Fibroblast growth factor receptor 4 NM_213647 FRAG 1 2 FGF receptor activating protein 1 NM_001256235 FGF 1 Fibroblast growth factor 1 NM_000800 FGF 2 FGF2 1, 2 Fibroblast growth factor 2 NM_002006 FGF3 Fibroblast growth factor 3 NM_005247 FGF5 Fibroblast growth factor 5 NM_004464 FGF 7 FGF7 1, 2 Fibroblast growth factor 7 NM_002009 FGF 9 FGF 9 Fibroblast growth factor 9 NM_002010 FGF 11 Fibroblast growth factor 11 NM_004112 FGF 18 FGF 18 1, 2 Fibroblast growth factor 18 NM_003862 FGF 19 Fibroblast growth factor 19 NM_005117 SPRY 1 Sprouty homolog 1 NM_005841 SPRY 2 SPRY 2 1 Sprouty homolog 2 NM_005842 SPRY 4 SPRY 4 1 Sprouty homolog 4 NM_030964 Sonic Hedgehog SHH SHH Sonic hedgehog homolog NM_000193 GLI 2 GLI 2 1 GLI-Kruppel family member GLI2 NM_005270 PTCHD 1 Patched domain containing 1 NM_173495 PTCHD 2 Patched domain containing 2 NM_020780 PTCH 1 PTCH1 PTCH 1 2 Patched homolog 1 NM_001083603 HHAT HHAT 2 Hedgehog acyltransferase NM_144881 DISP DISP 2 2 Dispatched homolog 1 NM_032890 TGFβ / BMP TGFBR 1 TGFBR 1 2 Transforming growth factor, beta receptor I NM_004612

TGFBR 2 TGFBR 2 TGFBR 2 1, 2 Transforming growth factor, beta receptor II NM_001024847 TGFBR 3 1 Transforming growth factor, beta receptor III NM_003243 TGFB 1 2 Transforming growth factor, beta 1 NM_000660 TGFB 2 TGFB 2 1,2 Transforming growth factor, beta 2 NM_003238 TGFB 3 Transforming growth factor, beta 3 NM_009368 TGFB1I1 Transforming growth factor beta1induced transcript1 NM_009365 TGFBI 1 Transforming growth factor, beta-induced NM_000358 TIEG 1 TGFB- induced early growth response NM_005655 TINP 1 2 TGFB inducible nuclear protein 1 NM_001252390 SMAD 6 SMAD 6 SMAD 6 2 SMAD family member 6 NM_005585 GDF6 Growth differentiation factor 6 NM_001001557 BMP 1 BMP 1 2 Bone morphogenetic protein 1 NM_009755 BMP 2 BMP 2 1 Bone morphogenetic protein 2 NM_001200 BMP 3 Bone morphogenetic protein 3 NM_001201 BMP 4 BMP 4 1, 2 Bone morphogenetic protein 4 NM_001202 BMP 5 1, 2 Bone morphogenetic protein 5 NM_021073 BMP 6 BMP 6 1 Bone morphogenetic protein 6 NM_001718 BMP 7 BMP 7 1, 2 Bone morphogenetic protein 7 NM_001719 BAMBI BMP and activin membrane-bound inhibitor NM_012342 Bone/Cartilage specification PTHR 1 PTHR 1 1, 2 Parathyroid 1 NM_000316 ROR 2 ROR 2 1 -like orphan receptor 2 NM_004560 SOX 9 SOX 9 1, 2 SRY-related HMG-box 9 NM_000346 RUNX 2 1 Runt-related transcription factor 2 NM_001024630 DLX 5 DLX 5 1 Distal-less homeobox 5 NM_005221 MSX 1 Msh homeobox 1 NM_010835 MSX 2 1, 2 Msh homeobox 2 NM_002449 JUN 1, 2 JUN proto-oncogene NM_005354 FOS 1, 2 v-fos FBJ osteosarcoma viral oncogene homolog NM_005252 FOX C1 FOX C1 1, 2 Forkhead box protein C1 NM_001453 FOX C2 Forkhead box protein C2 NM_013519 PADI 4 Peptidyl arginine deiminase, type IV NM_012387 PADI 2 PADI 2 Peptidyl arginine deiminase, type II NM_007365 OSR 2 Odd-skipped related 2 NM_053001 PAX 9 Paired box 9 NM_011041 LPL LPL 1, 2 Lipoprotein lipase NM_000237 ACAN Aggrecan NM_013227 FN1 FN 1, 2 Fibronectin 1 NM_212482 MMP 9 Matrix metallopeptidase 9 NM_013599 MMP 13 Matrix metallopeptidase 13 NM_008607 CDH2 N-cadherin NM_001792 TGFBR 1 TGFBR 1 2 Transforming growth factor, beta receptor I NM_004612 TGFBR 2 TGFBR 2 TGFBR 2 1, 2 Transforming growth factor, beta receptor II NM_001024847 TGFBR 3 1 Transforming growth factor, beta receptor III NM_003243 TGFB 2 TGFB 2 1, 2 Transforming growth factor, beta 2 NM_003238 TGFB 3 Transforming growth factor, beta 3 NM_009368 TGFB1I1 Transforming growth factor beta1induced transcript1 NM_009365 TGFBI 1 Transforming growth factor, beta-induced NM_000358 TIEG 1 TGFB- induced early growth response NM_005655 SMAD 6 SMAD 6 SMAD family member 6 NM_005585 GDF6 Growth differentiation factor 6 NM_001001557 BMP 1 BMP 1 2 Bone morphogenetic protein 1 NM_009755 BMP 2 BMP 2 1 Bone morphogenetic protein 2 NM_001200 BMP 3 Bone morphogenetic protein 3 NM_001201 BMP 4 BMP 4 1, 2 Bone morphogenetic protein 4 NM_001202 BMP 5 1, 2 Bone morphogenetic protein 5 NM_021073 BMP 6 BMP 6 1 Bone morphogenetic protein 6 NM_001718 BMP 7 BMP 7 1, 2 Bone morphogenetic protein 7 NM_001719 Intestine development/ Paneth cell lineage allocation FOXF 1 FOXF 1 FOXF 1 2 Forkhead box F1 NM_001451 FOXF 2 FOXF 2 2 Forkhead box F2 NM_001452 BMP 4 BMP 4 1, 2 Bone morphogenetic protein 4 NM_001202 WNT 5a 1 Wingless-related MMTV integration site 5a NM_003392 KLF 4 KLF 4 1 Kruppel-like factor 4 (gut) NM_004235 SOX 9 SOX 9 1, 2 SRY-related HMG-box 9 NM_000346 RSPO 1 R-spondin homolog 1 NM_001038633 RSPO 2 R-spondin homolog 2 NM_178565

Supplementary Table 3 (Part 2). The embryonic Wnt interactive network in mesenchymal precursor cells (3 pages) expressing SYTSSX2 and in synovial sarcoma tumors

Symbol Name Accession C2C12 hMSCs SS tumors Early mesenchyme determination LBH LBH Limb bud heart NM_030915 Gastrulation movements FGFR 2 FGFR 2 FGFR 2 1 Fibroblast growth factor receptor 2 NM_000141 FGFR 3 FGFR 3 FGFR 3 1, 2 Fibroblast growth factor receptor 3 NM_000142 Sex determination FGF 9 FGF 9 Fibroblast growth factor 9 NM_002010 SOX 9 SOX 9 1, 2 SRY-related HMG-box 9 NM_000346 Somitogenesis and paraxial mesoderm specification MEST MEST 1 Mesoderm specific transcript homolog NM_002402 GLI 2 GLI 2 1 Glioma-associated oncogene family zinc finger 2 NM_005270 RSPO 1 R-spondin homolog 1 NM_001038633 RSPO 2 R-spondin homolog 2 NM_178565 TCF 3 TCF 3 1, 2 Transcription factor 3 NM_003200 TCF 7 TCF 7 1, 2 Transcription factor 7 NM_003202 FOX C1 FOX C1 1, 2 Forkhead box protein C1 NM_002010 FOX C2 Forkhead box protein C2 NM_000346 NOTCH 1 NOTCH 1 1, 2 NOTCH (Drosophila) homolog 1 NM_017617 DLL 1 DLL 1 DLL1 1, 2 Delta-like 1 NM_005618 Dorso/ventral axis patterning SOX 17 SRY-related HMG-box 17 NM_022454 NOG Noggin NM_005450 SHH SHH Sonic hedgehog homolog NM_000193 GLI 2 GLI 2 1 GLI-Kruppel family member GLI2 NM_005270 WNT 4 WNT 4 Wingless-related MMTV integration site 4 NM_030761 WNT 7b WNT 7b Wingless-related MMTV integration site 7b NM_058238 WNT 11 WNT 11 Wingless-related MMTV integration site 11 NM_004626 A/P axis and early neural patterning/ specification DKK 3 Dickkopf homolog 3 NM_015814 FOXA 1 Forkhead box A1 NM_004496 FOXM 1 Forkhead box M1 NM_202002 FOXO 1 Forkhead box O1 NM_002015 FOXD 1 FOXD 1 1, 2 NM_004472 FOXG 1B 1 Forkhead box G1B NM_005249 MYC MYC MYC 1, 2 Myelocytomatosis oncogene NM_002467 PROX 1 PROX 1 Prospero homeobox 1 NM_002763 DLX 5 DLX 5 1 Distal-less homeobox 5 NM_005221 MSX 1 Msh homeobox 1 NM_010835

ZIC 2 ZIC 2 1 Zic finger protein of the 2 NM_007129 SIX 1 SIX 1 Sine oculis-related homeobox 1 NM_009189 GBX2 Gastrulation brain homeobox 2 NM_001485 OLIG 1 Oligodendrocyte transcription factor 1 NM_138983 OLIG 2 Oligodendrocyte transcription factor 2 NM_005806 MITF 1, 2 Microphthalmia-associated transcription factor NM_198159 TCF 3 TCF 3 1, 2 Transcription factor 3 NM_003200 NEUROD1 Neurogenic differentiation 1 NM_002500 NEUROG3 Neurogenin 3 NM_020999 PAX6 Paired box 6 NM_000280 SMAD 6 SMAD 6 SMAD family member 6 NM_005585 BMP 2 BMP 2 1 Bone morphogenetic protein 2 NM_001200 NOG Noggin NM_005450 SST Somatostatin NM_001048 GAS1 GAS1 1 Growth arrest specific 1 NM_002048 RET RET RET proto-oncogene NM_020975 GDNF 1 Glial cell-derived neurotrophic factor NM_010275 GFRA 1 GFRA 1 GFRA 1 1, 2 GDNF family receptor alpha 1 NM_005264 GFRA 2 GFRA 2 1 GDNF family receptor alpha 2 NM_001495 GFRA3 GDNF family receptor alpha 3 NM_001496 RARG RARG 1, 2 Retinoic acid receptor gamma NM_000966 NRP 1 Neuropilin 1 NM_008737 NRP 2 NRP 2 1, 2 Neuropilin 2 NM_201266 HGF HGF HGF 2 Hepatocyte growth factor NM_000601 MET MET 2 Hepatocyte growth factor receptor NM_001127500 FZD 3 FZD 3 Frizzled homolog 3 NM_017412 FZD 7 1, 2 Frizzled homolog 7 NM_003507 SHH SHH Sonic hedgehog homolog NM_000193 PTCH 1 PTCH1 PTCH1 2 Patched homolog 1 NM_001083603 HES 1 HES 1 Hairy and enhancer of split 1 NM_005524 NOTCH 1 NOTCH 1 2 NOTCH (Drosophila) homolog 1 NM_017617 RORA RAR-related orphan receptor A NM_134260 WNT 7a Wingless-related MMTV integration site 7a NM_009527 WNT 7b WNT 7b Wingless-related MMTV integration site 7b NM_058238 WNT 11 WNT 11 Wingless-related MMTV integration site 11 NM_004626 CYP26B1 CYP26B1 Cytochrome p450, family26, subfamilyb polypeptide1 NM_019885 Branching morphogenesis Kidney TGFB 2 TGFB 2 1, 2 Transforming growth factor, beta 2 NM_003238 BMP 2 BMP 2 1 Bone morphogenetic protein 2 NM_001200 WNT 4 WNT 4 Wingless-related MMTV integration site 4 NM_030761 WNT 11 WNT 11 Wingless-related MMTV integration site 11 NM_004626 MET MET 2 Hepatocyte growth factor receptor NM_001127500

HGF 1 HGF HGF 2 Hepatocyte growth factor NM_000601 RET RET RET proto-oncogene NM_020975 GDNF 1 Glial cell-derived neurotrophic factor NM_010275 GFRA 1 GFRA 1 GFRA 1 1, 2 GDNF family receptor alpha 1 NM_005264 GFRA 2 GFRA 2 1 GDNF family receptor alpha 2 NM_001495 GFRA 3 GDNF family receptor alpha 3 NM_001496 Lung FGF 9 FGF 9 Fibroblast growth factor 9 NM_002010 FGFR 1 1, 2 Fibroblast growth factor receptor 1 NM_023110 FGFR 2 FGFR 2 FGFR 2 1 Fibroblast growth factor receptor 2 NM_000141 WNT 2 1 Wingless-related MMTV integration site 2 NM_003391 WNT 5a 1 Wingless-related MMTV integration site 5a NM_003392 WNT 7a Wingless-related MMTV integration site 7a NM_009527 WNT 7b WNT 7b Wingless-related MMTV integration site 7b NM_058238 WNT 11 WNT 11 Wingless-related MMTV integration site 11 NM_004626 FZD 2 FZD 2 Frizzled homolog 2 NM_001466 BMP 4 BMP 4 1, 2 Bone morphogenetic protein 4 NM_001202 Vascular NRP 1 Neuropilin 1 NM_008737 NRP 2 NRP 2 1, 2 Neuropilin 2 NM_201266 NOTCH 1 NOTCH 1 2 NOTCH (Drosophila) homolog 1 NM_017617 NRARP Notch-regulated ankyrin repeat protein NM_001004354 CXCR 4 CXCR 4 CXCR 4 2 Chemokine receptor 4 NM_001008540

Underlined genes are downregulated. 1 indicates SS tumor microarray by Nielsen et al., 2002; 8 human SS tumors. 2 indicates SS tumor microarray by Francis et al., 2007; 32 human SS tumors.