Supplementary Table 1. Genes altered by BMP4 in whole tumor samples. Genes in bold are associated with immune responses.
Probeset ID / Gene Symbol / Refseq Transcript ID / Gene Title / P-value(BMP/
Control) / Fold-Change(BMP/ Control)
Genes up-regulated 3-fold by BMP4
1449033_at / Tnfrsf11b / NM_008764 / Tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) / 0.0001 / 13.1012
1417618_at / Itih2 / NM_010582 / Inter-alpha trypsin inhibitor, heavy chain 2 / 0.0000 / 10.3141
1418449_at / Lad1 / NM_133664 / Ladinin / 0.0003 / 8.3478
1418318_at / Rnf128 / NM_023270 / Ring finger protein 128 / 0.0008 / 7.7834
1418726_a_at / Tnnt2 / NM_011619 / Troponin T2, cardiac / 0.0126 / 6.5654
1417597_at / Cd28 /// LOC100048845 / NM_007642 / CD28 antigen /// similar to CD28 antigen / 0.0033 / 6.1323
1436528_at / Kazald1 / NM_178929 / Kazal-type serine peptidase inhibitor domain 1 / 0.0000 / 5.9738
1425951_a_at / Clec4n / NM_020001 / C-type lectin domain family 4, member n / 0.0400 / 5.8961
1451721_a_at / H2-Ab1 / NM_207105 / Histocompatibility 2, class II antigen A, beta 1 / 0.0413 / 5.7859
1451941_a_at / Fcgr2b / NM_001077189 /// NM_010187 / Fc receptor, igg, low affinity iib / 0.0433 / 5.5694
1427329_a_at / Igh-6 / --- / Immunoglobulin heavy chain 6 (heavy chain of igm) / 0.0272 / 5.4721
1426869_at / Boc / NM_172506 / Biregional cell adhesion molecule-related / 0.0004 / 5.4518
1429246_a_at / Anxa6 / NM_013472 / Annexin A6 / 0.0191 / 5.1879
1430388_a_at / Sulf2 / NM_028072 / Sulfatase 2 / 0.0109 / 5.0392
1422978_at / Cybb / NM_007807 / Cytochrome b-245, beta polypeptide / 0.0341 / 4.9877
1419178_at / Cd3g / NM_009850 / CD3 antigen, gamma polypeptide / 0.0216 / 4.9109
1417171_at / Itk / NM_010583 / IL2-inducible T-cell kinase / 0.0097 / 4.5601
1452205_x_at / Tcrb-V13 / --- / T-cell receptor beta, variable 13 / 0.0052 / 4.5223
1427301_at / Cd48 / NM_007649 / CD48 antigen / 0.0255 / 4.4754
1426772_x_at / Tcrb-J / --- / T-cell receptor beta, joining region / 0.0034 / 4.4222
1449235_at / Fasl / NM_010177 / Fas ligand (TNF superfamily, member 6) / 0.0346 / 4.2798
1418770_at / Cd2 / NM_013486 / CD2 antigen / 0.0070 / 4.2693
1417894_at / Gpr97 / NM_173036 / G protein-coupled receptor 97 / 0.0123 / 4.2356
1418353_at / Cd5 / NM_007650 / CD5 antigen / 0.0050 / 4.2173
1448730_at / Cpa3 / NM_007753 / Carboxypeptidase A3, mast cell / 0.0487 / 4.1849
1421173_at / Irf4 / NM_013674 / Interferon regulatory factor 4 / 0.0110 / 4.0923
1448749_at / Plek / NM_019549 / Pleckstrin / 0.0232 / 4.0826
1449153_at / Mmp12 / NM_008605 / Matrix metallopeptidase 12 / 0.0199 / 4.0757
1422771_at / Smad6 / NM_008542 / MAD homolog 6 (Drosophila) / 0.0025 / 4.0740
1452815_at / P2ry10 / NM_172435 / Purinergic receptor P2Y, G-protein coupled 10 / 0.0078 / 4.0168
1422188_s_at / Tcrg / --- / T-cell receptor gamma chain / 0.0461 / 3.9954
1423226_at / Ms4a1 / NM_007641 / Membrane-spanning 4-domains, subfamily A, member 1 / 0.0267 / 3.9630
1416271_at / Perp / NM_022032 / PERP, TP53 apoptosis effector / 0.0067 / 3.9085
1424443_at / Hdgfrp3 /// Tm6sf1 / NM_013886 /// NM_145375 / Hepatoma-derived growth factor, related protein 3 /// transmembrane 6 superfamil / 0.0265 / 3.9039
1437356_at / Ebi2 / NM_183031 / Epstein-Barr virus induced gene 2 / 0.0098 / 3.8388
1421404_at / Cxcl15 / NM_011339 / Chemokine (C-X-C motif) ligand 15 / 0.0012 / 3.8274
1428379_at / Slc17a6 / NM_080853 / Solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), m / 0.0402 / 3.8063
1418638_at / H2-dmb1 / NM_010387 / Histocompatibility 2, class II, locus Mb1 / 0.0384 / 3.7629
1423466_at / Ccr7 / NM_007719 / Chemokine (C-C motif) receptor 7 / 0.0107 / 3.7616
1431784_a_at / Bxdc5 / NM_027332 /// NM_027371 / Brix domain containing 5 / 0.0223 / 3.7355
1417837_at / Phlda2 / NM_009434 / Pleckstrin homology-like domain, family A, member 2 / 0.0009 / 3.6916
1418826_at / Ms4a6b / NM_027209 / Membrane-spanning 4-domains, subfamily A, member 6B / 0.0426 / 3.6630
1452431_s_at / H2-Aa / NM_010378 / Histocompatibility 2, class II antigen A, alpha / 0.0142 / 3.6599
1420249_s_at / Ccl6 / NM_009139 / Chemokine (C-C motif) ligand 6 / 0.0438 / 3.6403
1421315_s_at / Cttn / NM_007803 / Cortactin / 0.0181 / 3.6343
1440668_at / Adamtsl3 / XM_194370 / ADAMTS-like 3 / 0.0013 / 3.6148
1416007_at / Satb1 / NM_009122 / Special AT-rich sequence binding protein 1 / 0.0038 / 3.6089
1420819_at / Sla / NM_001029841 /// NM_009192 / Src-like adaptor / 0.0356 / 3.6065
1421014_a_at / Clybl / NM_029556 / Citrate lyase beta like / 0.0060 / 3.6043
1459713_s_at / Tmem16a / NM_178642 / Transmembrane protein 16A / 0.0017 / 3.6012
1439843_at / Camk4 / NM_009793 / Calcium/calmodulin-dependent protein kinase IV / 0.0044 / 3.6008
1422828_at / Cd3d / NM_013487 / CD3 antigen, delta polypeptide / 0.0096 / 3.5696
1416953_at / Ctgf / NM_010217 / Connective tissue growth factor / 0.0013 / 3.5610
1439141_at / Gpr18 / NM_182806 / G protein-coupled receptor 18 / 0.0109 / 3.5570
1423547_at / Lyzs / NM_017372 / Lysozyme / 0.0241 / 3.5424
1449078_at / St3gal6 / NM_018784 / ST3 beta-galactoside alpha-2,3-sialyltransferase 6 / 0.0067 / 3.5377
1449858_at / Cd86 / NM_019388 / CD86 antigen / 0.0273 / 3.5351
1417995_at / Ptpn22 / NM_008979 / Protein tyrosine phosphatase, non-receptor type 22 (lymphoid) / 0.0304 / 3.5157
1438439_at / Gpr171 / NM_173398 / G protein-coupled receptor 171 / 0.0100 / 3.5112
1416811_s_at / Ctla2a /// Ctla2b / NM_007796 /// XM_001477566 / Cytotoxic T lymphocyte-associated protein 2 alpha /// cytotoxic T lymphocyte-ass / 0.0010 / 3.5031
1416778_at / Sdpr / NM_138741 / Serum deprivation response / 0.0003 / 3.4566
1424824_at / Slain1 / NM_198014 / SLAIN motif family, member 1 / 0.0025 / 3.4345
1426113_x_at / Tcra / --- / T-cell receptor alpha chain / 0.0027 / 3.4078
1451204_at / Scara5 / NM_028903 / Scavenger receptor class A, member 5 (putative) / 0.0055 / 3.4040
1437886_at / Klhl6 / NM_183390 / Kelch-like 6 (Drosophila) / 0.0077 / 3.3705
1433471_at / Tcf7 / NM_009331 / Transcription factor 7, T-cell specific / 0.0112 / 3.3632
1438467_at / Mgl2 / NM_145137 / Macrophage galactose N-acetyl-galactosamine specific lectin 2 / 0.0393 / 3.3619
1440837_at / H2-Ob / NM_010389 / Histocompatibility 2, O region beta locus / 0.0184 / 3.3618
1423345_at / Degs1 / NM_007853 / Degenerative spermatocyte homolog 1 (Drosophila) / 0.0019 / 3.3544
1430700_a_at / Pla2g7 / NM_013737 / Phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma) / 0.0032 / 3.3488
1421217_a_at / Lgals9 / NM_010708 / Lectin, galactose binding, soluble 9 / 0.0259 / 3.3456
1425832_a_at / Cxcr6 / NM_030712 / Chemokine (C-X-C motif) receptor 6 / 0.0203 / 3.3418
1418907_at / F5 / NM_007976 / Coagulation factor V / 0.0138 / 3.3271
1448713_at / Stat4 / NM_011487 / Signal transducer and activator of transcription 4 / 0.0123 / 3.2959
1417732_at / Anxa8 / NM_013473 / Annexin A8 / 0.0012 / 3.2773
1440173_x_at / Selp / NM_011347 / Selectin, platelet / 0.0497 / 3.2673
1422891_at / H2-Ea / NM_010381 / Histocompatibility 2, class II antigen E alpha / 0.0077 / 3.2669
1420743_a_at / Ppp3cc / NM_008915 / Protein phosphatase 3, catalytic subunit, gamma isoform / 0.0011 / 3.2540
1425396_a_at / Lck / NM_010693 / Lymphocyte protein tyrosine kinase / 0.0223 / 3.2513
1436858_at / Mbnl2 / NM_175341 /// NM_207515 / Muscleblind-like 2 / 0.0374 / 3.2177
1428557_a_at / Osgepl1 / NM_028091 / O-sialoglycoprotein endopeptidase-like 1 / 0.0154 / 3.1983
1450241_a_at / Evi2a / NM_001033711 / Ecotropic viral integration site 2a / 0.0324 / 3.1850
1437249_at / Skap1 / NM_001033186 / Src family associated phosphoprotein 1 / 0.0100 / 3.1347
1425546_a_at / Trf / NM_133977 / Transferrin / 0.0467 / 3.1230
1436735_at / Nsun3 / NM_178925 / NOL1/NOP2/Sun domain family 3 / 0.0299 / 3.1109
1454877_at / Sertad4 / NM_198247 / SERTA domain containing 4 / 0.0152 / 3.1106
1433930_at / Hpse / NM_152803 / Heparanase / 0.0336 / 3.1022
1419481_at / Sell / NM_011346 / Selectin, lymphocyte / 0.0103 / 3.0809
1439067_at / Lair1 / NM_178611 / Leukocyte-associated Ig-like receptor 1 / 0.0303 / 3.0797
1449361_at / Tbx21 / NM_019507 / T-box 21 / 0.0274 / 3.0739
1434945_at / Aytl1 / NM_173014 / Acyltransferase like 1 / 0.0319 / 3.0609
1416794_at / Arl6ip2 / NM_019717 /// NM_178050 / ADP-ribosylation factor-like 6 interacting protein 2 / 0.0290 / 3.0475
1416246_a_at / Coro1a / NM_009898 / Coronin, actin binding protein 1A / 0.0319 / 3.0387
1422537_a_at / Id2 / NM_010496 / Inhibitor of DNA binding 2 / 0.0264 / 3.0297
1422527_at / H2-dma / NM_010386 / Histocompatibility 2, class II, locus dma / 0.0068 / 3.0106
1420924_at / Timp2 / NM_011594 / Tissue inhibitor of metalloproteinase 2 / 0.0109 / 3.0038
Genes down-regulated >3-fold by BMP4
1418147_at / Tcfap2c / NM_009335 / Transcription factor AP-2, gamma / 0.0042 / -3.0891
1439380_x_at / Gtl2 / NR_003633 /// XR_035480 /// XR_035483 /// XR_035484 / GTL2, imprinted maternally expressed untranslated mrna / 0.0486 / -3.1389
1452249_at / Prickle1 / NM_001033217 / Prickle like 1 (Drosophila) / 0.0068 / -3.1582
1443954_at / Rad18 / NM_021385 / RAD18 homolog (S. Cerevisiae) / 0.0054 / -3.1810
1454655_at / Dgkd / XM_906228 / Diacylglycerol kinase, delta / 0.0375 / -3.2054
1420380_at / Ccl2 / NM_011333 / Chemokine (C-C motif) ligand 2 / 0.0187 / -3.2134
1419077_at / Mpp3 / NM_007863 / Membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3) / 0.0021 / -3.2593
1441216_at / St3gal1 / NM_009177 / ST3 beta-galactoside alpha-2,3-sialyltransferase 1 / 0.0016 / -3.2998
1452114_s_at / Igfbp5 / NM_010518 / Insulin-like growth factor binding protein 5 / 0.0158 / -3.3006
1457492_at / Trio / NM_001081302 /// XM_001474968 /// XM_908972 / Triple functional domain (PTPRF interacting) / 0.0271 / -3.3152
1441321_at / LOC552911 / --- / Hypothetical LOC552911 / 0.0373 / -3.4591
1438590_at / Rapgef3 / NM_144850 / Rap guanine nucleotide exchange factor (GEF) 3 / 0.0023 / -3.4956
1446509_at / Smox / NM_145533 / Spermine oxidase / 0.0150 / -3.5216
1447853_x_at / Kif13a / NM_010617 / Kinesin family member 13A / 0.0089 / -3.5913
1441013_at / C81521 / --- / Expressed sequence C81521 / 0.0240 / -3.7592
1448573_a_at / Ceacam10 / NM_007675 / CEA-related cell adhesion molecule 10 / 0.0012 / -3.8338
1416980_at / Mettl7b / NM_027853 / Methyltransferase like 7B / 0.0003 / -3.9623
1421979_at / Phex / NM_011077 / Phosphate regulating gene with homologies to endopeptidases on the X chromosome / 0.0103 / -4.0427
1440227_at / Slc5a3 / NM_017391 / Solute carrier family 5 (inositol transporters), member 3 / 0.0272 / -4.5026
1455029_at / Kif21a / NM_016705 / Kinesin family member 21A / 0.0003 / -4.5364
1451888_a_at / Odz4 / NM_011858 / Odd Oz/ten-m homolog 4 (Drosophila) / 0.0003 / -4.9619
1446284_at / Mtss1 / NM_144800 / Metastasis suppressor 1 / 0.0274 / -9.1961
1427868_x_at / Myh1 / NM_030679 / Myosin, heavy polypeptide 1, skeletal muscle, adult / 0.0000 / -10.6742
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