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Home , ANGPT2, Ephrin A3, FGF1, ITGB3BP, PDGFA, PDGFB

Supplemental Data for Khatua et al.: Overexpression of the EGFR/FKBP12/HIF-2α Pathway Identified in Childhood Astrocytomas by Profiling

Expression summary for 133 pre-selected angiogenesis-related

Average d Percent Present Expressionb Gene Affymetrix Genbank High- Low c High- Low- P-value Total Functiona Probe Number Gene Description Grade Grade Grade Grade Adh 39071_at M14648 ITGAV , alpha V 2161 4295 0.010 100% 100% 100% Adh 40676_at U37139 ITGB3BP binding (beta3-endonexin) 313 42 0.025 33% 14% 23% Adh 2058_s_at M35011 ITGB5 Integrin, beta 5 1883 2846 0.053 83% 100% 92% Adh 37398_at AA100961 PECAM1 Platelet/endothelial cell adhesion molecule 868 750 0.625 83% 86% 85% ECM 34018_at D38163 collagen, type XIX, alpha 1 206 419 0.001 17% 71% 46% ECM 38427_at L25286 collagen, type XV, alpha 1 106 518 0.001 33% 100% 69% ECM 39925_at M95610 collagen, type IX, alpha 2 158 1266 0.002 0% 43% 23% ECM 37459_at X57527 collagen, type VIII, alpha 1 199 439 0.002 83% 100% 92% ECM 38729_at M88279 FK506-binding protein 4 (59kD) 3916 1597 0.002 100% 100% 100% ECM 38761_s_at AA487755 FK506-binding protein 9 (63 kD) 1672 1014 0.002 100% 100% 100% ECM 35168_f_at M92642 collagen, type XVI, alpha 1 912 3732 0.004 100% 100% 100% ECM 33409_at AA158243 FK506-binding protein 2 (13kD) 1614 2165 0.010 100% 100% 100% ECM 36091_at AF051323 (SAPS) SCAP2 Src family associated phosphoprotein 2 144 384 0.018 33% 100% 69% ECM 40850_at L37033 FK506-binding protein 8 (38kD) 39 299 0.024 0% 14% 8% ECM 37229_at U49844 FRP1, FRAP related protein 1054 799 0.027 100% 100% 100% ECM 31719_at X02761 FN1 Fibronectin 1 5815 2552 0.028 100% 100% 100% ECM 34598_at X98085 TNR Tenascin R (restrictin, janusin) 1664 982 0.034 0% 71% 38% ECM 36659_at X05610 collagen, type IV, alpha 2 5335 2686 0.041 100% 100% 100% ECM 39939_at D21337 collagen, type IV, alpha 6 218 102 0.061 50% 29% 38% ECM 33561_at X80031 collagen, type IV, alpha 3 108 137 0.069 33% 43% 38% ECM 32818_at X78565 HXB Hexabrachion (tenascin C, cytotactin) 5865 2701 0.071 100% 100% 100% ECM 32306_g_at J03464 collagen, type I, alpha 2 1673 673 0.149 100% 100% 100% ECM 34721_at U42031 FK506-binding protein 5 398 640 0.197 67% 86% 77% ECM 32667_at M58526 collagen, type IV, alpha 5 402 268 0.218 83% 100% 92% ECM 38420_at Y14690 collagen, type V, alpha 2 4403 1713 0.218 100% 100% 100% ECM 38722_at X15880 collagen, type VI, alpha 1 1815 1234 0.256 83% 100% 92% ECM 34388_at Y11710 collagen, type XIV, alpha 1 89 114 0.426 17% 0% 8% ECM 671_at J03040 SPARC Secreted protein, acidic, cysteine-rich () 12599 15440 0.456 100% 100% 100% ECM 35493_at X81053 collagen, type IV, alpha 4 64 80 0.480 0% 43% 23% ECM 880_at M34539 FK506-binding protein 1A (12kD) 3802 3327 0.513 100% 100% 100% ECM 37892_at J04177 collagen, type XI, alpha 1 2809 3797 0.516 67% 100% 85% ECM 38137_at AF038847 FK506-binding protein 6 (36kD) 204 266 0.572 17% 0% 8% ECM 35379_at X54412 collagen, type IX, alpha 1 649 756 0.594 0% 14% 8% ECM 36455_at L41162 collagen, type IX, alpha 3 2294 3054 0.611 50% 100% 77% ECM 355_s_at D38037 FK506-binding protein 1B (12.6 kD) 656 744 0.690 67% 86% 77% ECM 38077_at X52022 collagen, type VI, alpha 3 413 497 0.694 33% 100% 69% ECM 32488_at X14420 collagen, type III, alpha 1 625 447 0.740 50% 71% 62% ECM 38952_s_at M33653 collagen, type XIII, alpha 1 123 17 0.949 17% 0% 8% ECM 38508_s_at U89337 TNXB Tenascin XB 337 342 0.952 17% 14% 15% GF 996_at X59065 FGF1 (acidic FGF) 1130 4418 0.001 100% 100% 100% GF 38758_at R98910 PDGFA associated protein 1 (PDAP1) 5055 2823 0.001 100% 100% 100% GF 160025_at X70340 TGFA Transforming , alpha 99 726 0.001 33% 100% 69% GF 40422_at X16302 IGFBP2 -like growth factor binding protein 2 (36kD) 7087 504 0.001 100% 71% 85% GF 1593_at J04513 FGF2 2 (basic) 313 594 0.002 83% 100% 92% GF 1767_s_at X14885 TGFB3 Transforming growth factor, beta 3 460 687 0.024 67% 100% 85% GF 35703_at X06374 PDGFA Platelet-derived growth factor alpha polypeptide 2388 828 0.055 83% 86% 85% GF 36100_at AF022375 VEGF Vascular endothelial growth factor 6573 3142 0.162 100% 100% 100% GF 41445_at X02812 TGFB1 Transforming growth factor, beta 1 798 656 0.317 67% 29% 46% GF 1573_at M12783 PDGFB Platelet-derived growth factor beta polypeptide 161 63 0.319 0% 14% 8% GF 1591_s_at J03242 IGF2 427 134 0.795 17% 29% 23% GF 1542_at X04571 EGF (beta-urogastrone) 399 410 0.914 17% 14% 15% GF lig 34335_at AI765533 EFNB2 -B2 863 489 0.139 100% 100% 100% GF lig 469_at U66406 EFNB3 Ephrin-B3 878 653 0.232 33% 29% 31% GF lig 40425_at M57730 EFNA1 Ephrin-A1 1166 837 0.578 67% 86% 77% GF lig 188_at U09303 EFNB1 Ephrin-B1 555 537 0.870 33% 29% 31% GF lig 34573_at U14187 EFNA3 Ephrin-A3 1609 1645 0.876 83% 29% 54% Inhibitor 40664_at AB005299 brain-specific 3 (BAI3) 164 670 0.001 17% 71% 46% Inhibitor 36617_at X77956 ID1 4852 10707 0.001 100% 100% 100% Inhibitor 459_s_at U68485 BIN1 Bridging integrator 1 1053 2394 0.006 100% 100% 100% Inhibitor 1666_at J00210 alpha-d (INFA1) 45 113 0.008 0% 43% 23% Inhibitor 103_at Z19585 THBS4 4 1086 3368 0.017 83% 100% 92% Inhibitor 41116_at AI799802 BAI1-associated protein 3 1056 820 0.075 100% 100% 100% Inhibitor 36993_at M33210 ( Precursor) PLG Plasminogen 662 276 0.101 33% 14% 23% Inhibitor 37760_at AB015019 BAI1-associated protein 2 2461 1970 0.129 100% 100% 100% Inhibitor 1611_s_at J00219 interferon, gamma 18 40 0.201 0% 29% 15% Inhibitor 659_g_at L12350 THBS2 Thrombospondin 2 950 1301 0.286 100% 100% 100% Inhibitor 1022_f_at V00542 interferon, alpha 14 23 65 0.294 17% 0% 8% Inhibitor 1157_s_at J03171 interferon (alpha, beta and omega) receptor 1 144 109 0.340 0% 29% 15% Inhibitor 431_at X02530 SCYB10 Small inducible subfamily B, member 10 46 28 0.411 17% 0% 8% Inhibitor 33955_at M65291 IL12A 12A (natural killer cell stimulatory factor 1) 48 34 0.483 17% 14% 15% Inhibitor 427_f_at V00551 interferon, alpha 10 33 42 0.509 17% 29% 23% Inhibitor 32269_at W26805 BAI1-associated protein 1 642 726 0.540 33% 86% 62% Inhibitor 41140_at U05875 receptor 2 (interferon gamma transducer 1) 2753 3036 0.545 100% 100% 100% Inhibitor 33785_at AB005298 brain-specific angiogenesis inhibitor 2 (BAI2) 1366 1176 0.571 100% 86% 92% Inhibitor 41215_s_at D13891 ID2 4919 4451 0.580 100% 100% 100% Inhibitor 1434_at U92436 Phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 184 204 0.587 50% 86% 69% Inhibitor 32670_at L38969 THBS3 Thrombospondin 3 257 246 0.757 17% 0% 8% Inhibitor 1075_f_at M28585 interferon, alpha 16 52 44 0.772 17% 0% 8% Onc 1564_at M63167 AKT1 V-akt murine thymoma viral oncogene homolog 1 2409 429 0.095 67% 43% 54% Onc 33218_at M11730 ERBB2 V-erb-b2 erythroblastic leukemia viral oncogene homolog 2 268 162 0.342 50% 0% 23% Onc 1585_at M34309 ERBB3 V-erb-b2 erythroblastic leukemia viral oncogene homolog 3 925 1227 0.774 67% 100% 85% Pro/Inh 37310_at X02419 PLAU Plasminogen activator, urokinase 628 1488 0.002 67% 100% 85% Pro/Inh 1482_g_at L23808 matrix metalloproteinase 12 (macrophage elastase) 72 10 0.003 17% 0% 8% Pro/Inh 819_at U76456 TIMP4 Tissue inhibitor of metalloproteinase 4 695 3235 0.004 67% 100% 85% Pro/Inh 40759_at D83646 matrix metalloproteinase 16 (membrane-inserted) 511 1542 0.006 33% 86% 62% Pro/Inh 160020_at Z48481 matrix metalloproteinase 14 (membrane-inserted) 3839 2275 0.148 67% 57% 62% Pro/Inh 38852_at D79989 (PIKE) centaurin, gamma 1 62 24 0.257 17% 0% 8% Pro/Inh 1693_s_at D11139 TIMP1 Tissue inhibitor of metalloproteinase 1 7070 9197 0.475 100% 100% 100% Pro/Inh 1034_at U14394 TIMP3 Tissue inhibitor of metalloproteinase 3 673 1203 0.548 50% 100% 77% Pro/Inh 1375_s_at M32304 TIMP2 Tissue inhibitor of metalloproteinase 2 861 994 0.587 67% 57% 62% Pro/Inh 38181_at X57766 matrix metalloproteinase 11 (stromelysin 3) 591 552 0.612 100% 100% 100% Pro/Inh 31859_at J05070 matrix metalloproteinase 9 (gelatinase B) 257 164 0.679 33% 14% 23% Pro/Inh 40139_at U88966 FRAP1 FK506 binding protein 12-rapamycin associated protein 1 851 892 0.772 100% 100% 100% Pro/Inh 38125_at M14083 SERPINE1 Serine (or cysteine) proteinase inhibitor, clade E, member 1 633 577 0.800 67% 100% 85% Pro/Inh 681_at J05556 matrix metalloproteinase 8 (neutrophil collagenase) 35 44 0.972 0% 14% 8% Rec 35048_at U10301 GRIA3 Glutamate receptor (flip isoform), ionotrophic, AMPA 3 274 712 0.002 83% 100% 92% Rec 1351_at U07695 EphB4 B4 238 27 0.002 50% 29% 38% Rec 1537_at X00588 EGFR Epidermal 2389 44 0.003 67% 0% 31% Rec 37573_at AF007150 ANGPTL2 -like 2 858 2220 0.003 33% 100% 69% Rec 1368_at M27492 IL1R1 Interleukin 1 receptor, type I 178 999 0.005 33% 100% 69% Rec 1596_g_at L06139 Tie-2/Tek 121 791 0.018 50% 100% 77% Rec 1438_at X75208 EphB3 Ephrin Receptor B3 376 120 0.022 17% 0% 8% Rec 41678_at AF025304 EphB2 Ephrin Receptor B2 1225 661 0.040 100% 86% 92% Rec 1815_g_at D50683 TGFBR2 Transforming growth factor, beta receptor II 953 1790 0.052 83% 100% 92% Rec 39315_at D13628 ANGPT1 362 877 0.088 50% 86% 69% Rec 31805_at M64347 FGFR3 Fibroblast growth factor receptor 3 651 1087 0.157 50% 100% 77% Rec 1379_at M59371 EphA2 Ephrin Receptor A2 439 123 0.192 67% 29% 46% Rec 1731_at M21574 PDGFRA Platelet-derived growth factor receptor, alpha polypeptide 9958 6896 0.218 100% 100% 100% Rec 1001_at X60957 Tie/Tie1 158 213 0.299 17% 29% 23% Rec 1606_at L36645 EphA4 Ephrin Receptor A4 241 149 0.326 33% 43% 38% Rec 1964_g_at U01134 fms-related 1 (vascular endothelial growth factor receptor) 225 179 0.343 33% 57% 46% Rec 1771_s_at J03278 PDGFRB Platelet-derived growth factor receptor, beta polypeptide 600 489 0.457 67% 43% 54% Rec 1954_at AF035121 KDR Kinase insert domain receptor (a type III ) 265 218 0.499 50% 71% 62% Rec 1363_at M87770 FGFR2 Fibroblast growth factor receptor 2 667 451 0.529 67% 43% 54% Rec 1605_g_at L36644 EphA5 Ephrin Receptor A5 33 48 0.541 17% 14% 15% Rec 34331_at L40636 EphB1 Ephrin Receptor B1 345 508 0.542 17% 86% 54% Rec 2057_g_at M34641 FGFR1 Fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2) 5201 5491 0.732 100% 100% 100% Rec 1951_at AF004327 ANGPT2 Angiopoietin 2 248 277 0.755 100% 71% 85% Rec 32903_at L11695 TGFBR1 Transforming growth factor, beta receptor I 43 38 0.893 0% 29% 15% TF 35352_at AB002305 ARNT2 Aryl-hydrocarbon receptor nuclear translocator 2 3573 8377 0.001 100% 100% 100% TF 32767_at M74558 TAL1 (SCL) interrupting locus 423 93 0.001 100% 86% 92% TF 41425_at M98833 FLI1 Friend leukemia virus integration 1 88 205 0.012 33% 100% 69% TF 38230_at U81984 Endothelial PAS domain protein 1 (HIF-2A) 1152 697 0.038 17% 14% 15% TF 36896_s_at AF044288 ARNTL Aryl hydrocarbon receptor nuclear translocator-like 319 117 0.107 67% 57% 62% TF 507_s_at U43189 (NERF-2) ELF2 E74-like factor 2 (ets domain transcription factor) 891 706 0.150 100% 100% 100% TF 1039_s_at U22431 HIF-1A Hypoxia-inducible factor 1, alpha subunit 3872 4675 0.185 100% 100% 100% TF 35968_s_at AF001307 (HIF-1b) ARNT Aryl hydrocarbon receptor nuclear translocator 252 199 0.374 17% 29% 23% TF 789_at X52541 EGR1 Early growth response 1 540 468 0.448 83% 71% 77% TF 38491_at U11732 ETV6 Ets variant gene 6 (TEL oncogene) 217 251 0.555 33% 29% 31% TF 40507_at K03195 Glut1/SLC2A1 673 766 0.600 33% 43% 38% TF 37194_at M68891 GATA binding protein 2 261 319 0.628 17% 29% 23% TF 39548_at U77970 NPAS2 Neuronal PAS domain protein 2 227 210 0.675 50% 57% 54% TF 38293_s_at Y09980 HOXD3 Homeo box D3 99 81 0.921 33% 14% 23% a Genes are grouped according to their functions- Adh: adhesion molecules; ECM: ; GF: growth factor; GF lig: growth factor ; Inhibitor: inhibitor of angiogenesis; Onc: oncogene; Pro/Inh: protease or protease inhibitor; Rec: receptor; TF: transcription factor. b Average expression is in arbitrary expression units generated by Affymetrix Microarray Suite Version 4.0 software. c P-value is generated via permutation testing based on the T-test. Genes with P-values below 0.05 (highlighted) were considered to be differentially expressed candidate genes. d Percentage of HGA and LGA samples with above-threshold as determined by Affymetrix Microarray Suite Version 4.0 software.

Expression summary for 11 HIF-related genes

Average Expressionb Percent Presentd Gene Affymetrix Genbank High- Low High- Low- Functiona Probe Number Gene Description Grade Grade P-valuec Grade Grade Total Inhibitor 33219_at AB029020 pVHL-interacting deubiquitinating enzyme 1 3079 3631 0.172 100% 100% 100% Rec 37324_at X01060 transferrin receptor (p90, CD71) 4003 788 0.001 100% 100% 100% TF 37677_at V00572 (PGK1) phosphoglycerate kinase 1 17998 9964 0.001 100% 100% 100% TF 1399_at L34587 transcription elongation factor B (SIII), polypeptide 1 (15kD, elongin C) 4524 3330 0.007 100% 100% 100% TF 35373_at M61906 PI3K p85 regulatory 1 (GRB1) 533 1743 0.015 67% 100% 85% TF 39184_at AI857469 transcription elongation factor B (SIII), polypeptide 2 (18kD, elongin B) 6010 4632 0.033 100% 100% 100% TF 1000_at X60188 p44 MAPK (ERK1, MAPK3) 1686 2034 0.111 83% 100% 92% TF 32336_at X05236 aldolase A, fructose-bisphosphate 4571 3593 0.560 100% 100% 100% TF 37894_at U83410 cullin 2 949 885 0.673 100% 86% 92% TF 36287_at X83368 PI3K catalytic, gamma polypeptide 109 120 0.721 33% 14% 23% TF 976_s_at Z11695 p42 MAPK (ERK2, MAPK1) 227 227 0.994 50% 57% 54% a The genes are grouped according to their functions- Inhibitor: inhibitor of angiogenesis; Rec: receptor; TF: transcription factor. b Average expression is in arbitrary expression units generated by Affymetrix Microarray Suite Version 4.0 software. c P-value is generated via permutation testing based on the T-test. Genes with P-values below 0.05 (highlighted) were considered to be differentially expressed candidate genes. d Percentage of HGA and LGA samples with above-threshold gene expression as determined by Affymetrix Microarray Suite Version 4.0 software.

Most frequently occurring ontologies of differentially expressed genesa

Number of Biological Process Annotations GO:7165 signal transduction 29 GO:7048 oncogenesis 19 GO:8283 cell proliferation 19 GO:6366 transcription from Pol II promoter 14 GO:6281 DNA repair 13 GO:74 cell cycle control 13 GO:7155 cell adhesion 11 GO:7399 neurogenesis 10 GO:6371 mRNA splicing 8 GO:9405 pathogenesis 8 GO:6832 small molecule transport 7 GO:6899 non-selective vesicle transport 7 GO:7275 developmental processes 7 GO:6260 DNA replication 6 GO:6357 transcription regulation from Pol II promoter 6

Number of Cell Component Annotations GO:5634 nucleus 42 GO:5887 integral plasma membrane protein 33 GO:5737 cytoplasm 29 GO:5886 plasma membrane 17 GO:5615 extracellular space 14 GO:5624 membrane fraction 12 GO:16021 integral membrane protein 11 GO:157 peripheral plasma membrane protein 9 GO:5829 cytosol 8 GO:5739 mitochondrion 7 GO:15629 actin cytoskeleton 6 GO:5856 cytoskeleton 6 GO:5681 spliceosome 5 GO:5764 lysosome 5 GO:5783 endoplasmic reticulum 5

Number of Molecular Function Annotations GO:3677 DNA binding 17 GO:3700 transcription factor 14 GO:8181 tumor suppressor 11 GO:3702 RNA polymerase II transcription factor 8 GO:3723 RNA binding 8 GO:5515 protein binding 8 GO:5194 cell adhesion 7 GO:5489 electron transporter 7 GO:4002 adenosinetriphosphatase 6 GO:4672 protein kinase 6 GO:5102 ligand 6 GO:3734 small nuclear ribonucleoprotein 5 GO:4674 protein serine/threonine kinase 5 GO:3754 chaperone 4 GO:3779 actin binding 4 a annotations for the 500 genes with the lowest permutational P-value were obtained from the Affymetrix NetAffx website (http://www.affymetrix.com).