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Supplementary Figure S11 and Tables S1-S3

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Supplementary Figure S11 and Tables S1-S3 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, genes 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 morphogenesis. 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 Frizzled 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 receptor-related protein 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 Transcription factor 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 kinase-like orphan receptor 2 NM_004560 RYK Receptor-like tyrosine kinase 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 Gene 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 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 G protein 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 Ephrin A1 NM_004428 EFN A3 EFN A3 Ephrin A3 NM_004952 EFN A4 EFN A4 2 Ephrin A4 NM_005227 EFN A5 Ephrin A5 NM_001962 EFN B1 EFN B1 Ephrin B1 NM_004429 EFN B2 1 Ephrin B2 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 Insulin-like growth factor 2 NM_000612 IGFBP2 IGFBP2 IGFBP2 1, 2 Insulin-like growth factor binding protein 2 NM_000597 SHH SHH Sonic hedgehog homolog NM_000193 GLI 2 GLI 2 1 Glioma-associated oncogene family zinc finger 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 Fibroblast growth factor 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 homeobox 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 Msh homeobox 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 Retinoic acid receptor 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 Gastrulation 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 growth factor receptor NM_005228 MET MET 2 Hepatocyte growth factor 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 Follistatin NM_006350 POSTN POSTN POSTN 2 Periostin NM_006475 PTN PTN 1 Pleiotrophin 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 Angiopoietin-like 4 NM_020581 UNC 5B UNC 5B 2 Unc-5 homolog b (C.elegans) NM_170744 SEMA 3A SEMA 3A SEMA 3A 2 Semaphorin 3A NM_006080 LAMC 2 1 Laminin gamma 2 NM_005562 FN 1 FN 1 Fibronectin 1 NM_212482 C3 C3 Complement component 3 NM_000064 IL8 Interleukin 8 NM_000584 IL6 1 Interleukin 6 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 Endothelin 1 NM_001955 CD44 1, 2 CD44 molecule
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