Table S1 - Plos

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CDKN1A. Cyclin-Dependent Kinase Inhibitor 1A (p21, Cip1). 0.004. 55. LAMA4. Laminin, alpha 4. 0.004. 56. BST2. Bone marrow stromal cell antigen 2. 0.004.
Table S1 (Huijbers et al.) Table S1: List of 100 most upregulated genes in GBM versus grade III gliomas. Rank 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59

Gene symbol NNMT TncRNA PDPN IGFBP5 SOD2 MRC2/Endo180 SHC1 PLAT ITGA7 CD151 CALD1 VEGFA DDOST SERPINE1 ABCC3 ADM COL5A2 DNALI1 PRSS23 CSDA SP100 CAV1 GDF15 ITGA3 TM9SF1 MEOX2 PROS1 TGFB2 P4HB THBS1 COL1A2 CD44 FGFR1 PHC2 H2AFV PDIA5 TAGLN RGS6 TRIP6 MPZL2 IL1RAP C1R COL6A1 CA12 SFRP4 MCM4 DDB2 FKBP9 FN1 GNS UPP1 CRIP1 PLOD3 CDKN1A LAMA4 BST2 GUSB ELF4 HLA-DQB1

Gene name Nicotinamide n-methyltransferase Throphoblast-derived noncoding RNA Podoplanin Insulin-like growth factor binding protein 5 Superoxide dismutase 2 Mannose receptor, C-type 2; Endo180 Shc transforming protein Plasminogen activator, tissue Integrin, alpha 7 CD151 Caldesmon 1 Vascular Endothelial Growth Factor A Dolichyl-diphosphooligosaccharide-protein glycosyltransferase Serpin peptidase inhibitor, clade E; PAI-1 ATP-binding cassette, sub-family C (CFTR/MRP), member 3 Adrenomedullin Collagen, type V, alpha2 Dynein, axonemal, light intermediate chain 1 Protease, serine, 23 Cold shock domain protein A SP100 nuclear antigen Caveolin 1, caveolae protein, 22kDa Growth Differentiation Factor 15 Integrin, alpha 3 Transmembrane 9 superfamily member 1 Mesenchyme homeobox 2 Protein S (alpha) Transforming growth factor, beta 2 Proline 4-hydroxylase, beta Thrombospondin 1 Collagen, type I, alpha2 CD44 Fibroblast Growth Factor Receptor 1 Polyhomeotic homolog 2 (Drosophila) H2A histone family, member V Protein disulfide isomerase family A, member 5 Transgelin Regulator of G-protein signaling 6 Thyroid hormone receptor interactor 6 Myelin protein zero-like 2 Interleukin 1 receptor accessory protein Complement component 1, r subcomponent Collagen, type VI, alpha1 Carbonic Anhydrase XII Secreted frizzled-related protein 4 Minichromosome maintenance complex component 4 Damage-specific DNA binding protein 2, 48kDa FK506 binding protein 9, 63 kDa Fibronectin 1 Glucosamine (N-acetyl)-6-sulfatase (Sanfilippo disease IIID) Uridine phosphorylase 1 Cysteine-rich protein 1 (intestinal) Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 Cyclin-Dependent Kinase Inhibitor 1A (p21, Cip1) Laminin, alpha 4 Bone marrow stromal cell antigen 2 Glucuronidase, beta E74-like factor 4 (ets domain transcription factor) Major histocompatibility complex, class II, DQ beta 1

Up in GBM (p-value) -6 1.80 x 10 -6 2.22 x 10 -6 9.31 x 10 -5 1.96 x 10 -5 3.03 x 10 -5 5.56 x 10 -5 5.72 x 10 -4 1.12 x 10 -4 1.42 x 10 -4 1.71 x 10 -4 1.88 x 10 -4 2.21 x 10 -4 2.34 x 10 -4 3.02 x 10 -4 3.14 x 10 -4 4.33 x 10 -4 5.66 x 10 -4 5.76 x 10 -4 6.89 x 10 -4 7.04 x 10 -4 7.13 x 10 -4 7.77 x 10 -4 8.49 x 10 -4 9.82 x10 -4 9.94 x10 0.001 0.001 0.001 0.001 0.001 0.002 0.002 0.002 0.002 0.002 0.002 0.002 0.003 0.003 0.003 0.003 0.003 0.003 0.003 0.003 0.003 0.003 0.003 0.003 0.003 0.003 0.004 0.004 0.004 0.004 0.004 0.004 0.004 0.004

Table S1 (Huijbers et al.) 60 61 62 63 64 65 66 67 68 69 70 71

EMP3 COL4A1 EYA2 MMP9 HSPG2 LIMS1 COL4A2 MOXD1 TGFB1 TGFBR1 TAP1 HIST1H2BD

Epithelial membrane protein 3 0.004 Collagen, type IV, alpha 1 0.004 Eyes absent homolog 2 (Drosophila) 0.004 Matrix metallopeptidase 9 0.004 Heparan sulfate proteoglycan 2 0.005 LIM and senescent cell antigen-like domains 1 0.005 Collagen, type IV, alpha 2 0.005 Monooxygenase, DBH-like 1 0.005 Transforming growth factor, beta-induced 0.006 Transforming growth factor, beta receptor I 0.006 Transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) 0.006 Histone cluster 1, H2bd 0.006 Solute carrier family 22 (organic cation transporter), member 72 SLC22A18 0.006 18 73 CDC25B Cell division cycle 25 homolog B (S. pombe) 0.006 74 MR1 Major histocompatibility complex, class I-related 0.006 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein 75 KDELR1 0.006 retention receptor 1 76 TSPAN4 Tetraspanin 4 0.006 77 CFLAR CASP8 and FADD-like apoptosis regulator 0.006 78 RARRES2 Retinoic acid receptor responder (tazarotene induced) 2 0.006 79 GPX7 Glutathione peroxidase 7 0.006 80 FAM114A1 Family with sequence similarity 114, member A1 0.007 81 PLA2G2A Phospholipase A2, group IIA (platelets, synovial fluid) 0.007 82 MXRA5 Matrix-remodelling associated 5 0.007 83 GLB1 Galactosidase, beta 1 0.007 84 RBPMS RNA binding protein with multiple splicing 0.007 85 DIRAS3 DIRAS family, GTP-binding RAS-like 3 0.007 86 ANGPT2 Angiopoietin 2 0.007 87 RAB27A RAB27A, member RAS oncogene family 0.008 88 CCR1 Chemokine (C-C motif) receptor 1 0.008 89 HEXA Hexosaminidase A (alpha polypeptide) 0.008 90 BGN Biglycan 0.008 Runt-related transcription factor 1 (acute myeloid leukemia 1; 91 RUNX1 0.008 aml1 oncogene) 92 ARL4C ADP-ribosylation factor-like 4C 0.008 93 FEM1C Fem-1 homolog c (C. elegans) 0.008 94 STAT1 Signal transducer and activator of transcription 1, 91kDa 0.008 95 WEE1 WEE1 homolog (S. pombe) 0.009 96 OAS2 2'-5'-oligoadenylate synthetase 2, 69/71kDa 0.009 97 HLA-A Major histocompatibility complex, class I, A 0.009 98 TRADD TNFRSF1A-associated via death domain 0.009 99 KLF10 Kruppel-like factor 10 0.009 100 DPYD Dihydropyrimidine dehydrogenase 0.010 TM An ONCOMINE profile search for glioblastoma comparing 5 independent studies; Shai_brain, Liang_brain, Sun_brain and Bredel_brain_2 and Freye_brain was undertaken (see Figure 1A). A ranked list of genes differentially expressed between grade III and IV tumors across all of these studies was compiled and pvalues calculated by T statistics. Highlighted are Endo180 (MRC2, green), genes involved in TGF-β signaling (orange) and ECM proteins, ECM receptors and ECM proteases (yellow).