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Figure S1.

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Figure S2.

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Figure S3.

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Figure S4.

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Figure S5.

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Figure S6.

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Figure S7.

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Table S1.

symbol accession no. status in arrays VEGF-A vascular endothelial AW473981 B VEGF-B vascular endothelial growth factor B U43368 B VEGF-C vascular endothelial growth factor C X94216 B VEGF-D vascular endothelial growth factor D NM_004469 B PlGF AI004656 MRSL VEGFR1 VEGF-receptor 1 X51602 MRSL VEGFR2 VEGF-receptor 2 aka KDR XM_015439 B VEGFR3 VEGF-receptor 3 aka FLT4 XM_003852 B FGF1 1 acidic X59065 B FGF2 fibroblast growth factor 2 basic NM_002006 B FGFR1 fibroblast 1 X66945 B FGFR2 fibroblast growth factor receptor 2 M87770 NM FGFR3 fibroblast growth factor receptor 3 AI378807 B FGFR4 fibroblast growth factor receptor 4 Y13901 NM TGFβ1 transforming growth factor, beta 1 NM_000660 NM TGFβ2 transforming growth factor, beta 2 Y00083 B TGFβ3 transforming growth factor, beta 3 X14885 B TGFβR1 transforming growth factor, beta receptor 1 L11695 B TGFβR2 transforming growth factor, beta receptor 2 D50683 PRO TGFβR3 transforming growth factor, beta receptor 3 AJ251961 B endoglin NM_000118 B PDGF-A platelet-derived growth factor alpha AV729452 B PDGF-B platelet-derived growth factor beta NM_002608 B PDGF-C platelet-derived growth factor C BF002799 B PDGFRα platelet-derived growth factor receptor alpha NM_006206 NM PDGFRβ platelet-derived growth factor receptor beta M21616 NM PF4 aka CXCL4 aka oncostatin A AI739539 NM CAN-05-3294 Glesne et al

PF4 variant1 platelet factor 4 variant 1 NM_002620 NM leptin U43653 NM leptinR leptin receptor U66496 B SDF-1 stromal cell-derived factor 1 aka CXCL12 AL137026 B SDF-2 stromal cell-derived factor 2 AW250288 B CXCR4 (SDF- stromal cell-derived factor receptor 1 NM_017455 B 1R) EDN-1 -1 S56805 B EDN-2 endothelin-2 XM_002065 NM EDN-3 endothelin-3 AL035250 NM endothelinRA endothelin receptor type A S57498 B endothelinRB endothelin receptor type B M74921 B endothelinCE endothelin converting 1 AL031005 B tissue factor CD142 aka coagulation factor III AI085165 B Factor V coagulation factor V aka labile factor Z99572 B Factor VII coagulation factor VII aka hemophilia A M90707 B thrombin coagulation factor II AU121309 B thrombinR coagulation factor II receptor M62424 B -1 D13628 B angiopoietin-2 NM_001147 B angiopoietinlike- aka angiopoietin-3 XM_009621 B 1 angiopoietin 4 aka murine angiopoietin-3 AF113708 NM Tie-1 with immunoglobulin and EGF homology domains-1 XM_002037 MRSL Tie-2 tyrosine kinase with immunoglobulin and EGF homology domains-2 XM_005480 B EphrinA1 M18391 B A2 XM_009246 NM NM_004093 MRSL Eph-A4 NM_004438 MRSL Eph-B4 NM_004444 B CAN-05-3294 Glesne et al

jagged-1 U61276 B frizzled-5 (Wnt XM_010838 NM R) Nogo (A,B + C) A,B and C come from 1 gene- isomorphs AJ251383 B -2 AB029496 MRSL semaphorin-3A aka semaphorin-1 NM_006080 B semaphorin-3C NM_006379.1 MRSL semaphorin-3F U38276 MRSL semaphorin-4C NM_017789 MRSL semaphorin-4D aka collapsin NM_006378.1 B semaphorin-4F AA523537 B semaphorin-5 NM_003966 NM semaphorin-7 NM_003612 NM neuropilin-1 AF145712 B neuropilin-2 AF022859 B N-cadherin neuronal cadherin XM_016157 B VE-cadherin vascular epithelium cadherin NM_001795 B , β1 fibronectin receptor beta polypeptide aka CD29 X07979 NM integrin, β3 CD61 M35999 B integrin, β4 BE735810 MRSL integrin, α1 X68742 B integrin, α2b CD41B M34480 B integrin, α3 CD49C D01038 B integrin, α5 fibronectin receptor alpha polypeptide M13918 MRSL integrin, α6 CD49f X53586 B integrin, αv receptor XM_002379 B IAP/CD47 integrin-associated signal transducer AI491762 B ADAM-15 A disintegrin and metalloproteinase domain 15 aka Metargidin NM_003815 PRO Thy-1 CDw90 aka CD90 antigen AI679251 B VCAM-1 vascular cell adhesion molecule 1 NM_001078 B CAN-05-3294 Glesne et al

E-selectin endothelial adhesion molecule 1 AL021940 B P-selectin CD62 aka granule membrane 140kD M25322 B PECAM-1 CD31 aka platelet/endothelial cell adhesion molecule M37780 B JAM-1 junctional adhesion molecule 1 AF172398 B VE-JAM vascular endothelial junction-associated molecule NM_021219 MRSL MCAM melanoma adhesion molecule XM_006077 B fibronectin AW385690 B thrombospondin- XM_007606 PRO 1 TSP receptor CD36 aka thrombospondin receptor type I receptor NM_005505 PRO tenascin-C cytotactin aka hexabrachion XM_005348 MRSL tenascin-X tenascin XB NM_019105 MRSL osteopontin bone sialoprotein BC007016 PRO vitronectin AF382388 B collagen I A1 AW577407 NM collagen I A2 NM_000089 B collagen II A3 AW410427 NM collagen IV A1 NM_001845 B collagen IV A3 Goodpasture antigen M81379 MRSL collagen IV A4 NM_000092 NM collagen IV A5 M58526 MRSL collagen IV A6 a basement membrane protein BC070203 B collagen V A2 AU117484 B collagen VI A1 X99135 NM collagen VI A2 AI635289 MRSL collagen VII A1 NM_000094 NM collagen VIII A1 NM_001850 B collagen IX A1 BF196880 NM collagen IX A2 AF019406 B collagen IX A3 L41162 NM CAN-05-3294 Glesne et al

collagen X A1 X98568 NM collagen XI A1 J04177 B collagen XI A2 AL031228 B collagen XII A1 U73778 NM collagen XIII A1 AF018081 B collagen XIV A1 undulin M64108 NM collagen XV A1 L01697 MRSL collagen XVI A1 S57132 NM collagen XIX A1 L12347 NM nidogen aka entactin NM_002508 B lumican AU118364 NM claudin-1 AI300819 NM claudin-4 BF036516 MRSL claudin-5 NM_003277 MRSL claudin-6 BC008934 NM claudin-7 AI151456 MRSL claudin-10 AI355429 B FGL-2 aka fibroleukin NM_006682 MRSL MMP-1 interstitial collagenase M13509 B MMP-2 gelatinase A J03210 MRSL MMP-3 stromelysin 1 XM_006271 NM MMP-7 matrilysin, uterine X07819 B MMP-9 gelatinase B NM_004994 B MMP-10 stromelysin 2 NM_002425 B MMP-11 stromelysin 3 AI189375 B MMP-12 macrophage elastase U78045 PRO MMP-13 collagenase 3 X81334 NM MMP-14 membrane-inserted AW628280 B MMP-15 membrane-inserted Z48482 NM MMP-16 membrane-inserted AI192539 B CAN-05-3294 Glesne et al

MMP-17 TNFα-CE U86755 NM MMP-19 U37791 NM TIMP-1 tissue inhibitor of metalloproteinase 1 AI831659 MRSL TIMP-2 tissue inhibitor of metalloproteinase 2 XM_012690 MRSL TIMP-3 tissue inhibitor of metalloproteinase 3 AI095372 B u-PA plasminogen activator, urokinase M15476 MRSL u-PAR plasminogen activator, urokinase receptor BF129898 B t-PA plasminogen activator, tissue M15518 MRSL PAI-1 plasminogen activator inhibitor-1 X04744 B PAI-2 plasminogen activator inhibitor-2 Y00630 NM MAPK-3 mitogen-activated protein kinase 3 X60188 B MAPK-6 mitogen-activated protein kinase 6 BE883563 B MEKK-3 mitogen-activated protein kinase-activated protein kinase 3 U43784 B MEKK-4 mitogen-activated protein kinase-activated protein kinase 4 D86968 B MEKK-5 mitogen-activated protein kinase-activated protein kinase 5 BE784522 B ALK-1 activin receptor-like kinase 1 AH005451 PRO K-ras Kirsten murine sarcoma virus 2 NM_005086 NM H-ras Harvey murine sarcoma virus oncogene J00277 B Cdc42 cell division cycle 42 XM_017159 PRO TIAM-1 T-cell lymphoma invasion and metastasis 1 NM_003253 NM Rac-1 ras-related C3 botulinum toxin substrate 1 XM_016309 B Rac-2 ras-related C3 botulinum toxin substrate 2 XM_015214 NM Rho-A L25080 B PAK-1 p21/Cdc42/Rac1-activated kinase 1 XM_012031 NM COX-2 prostaglandin-endoperoxide synthase 2 D28235 B c-src c-src tyrosine kinase X59932 B PKCα protein kinase C, alpha X52479 NM PKCβ1 protein kinase C, beta 1 AC002299 NM PKCδ protein kinase C,delta D10495 B PKCγ protein kinase C, gamma Z15114 NM CAN-05-3294 Glesne et al

PKCη protein kinase C, eta NM_006255 B PKCε protein kinase C, epsilon NM_005400 NM PKCµ protein kinase C, mu NM_002742 B PKCν protein kinase C, nu AW149880 B PKCθ protein kinase C, theta AL137145 NM PKCζ protein kinase C, zeta NM_002744 MRSL PLCβ1 phosphoinositide-specific phospholipase C-beta 1 AB011153 MRSL PLCβ4 phosphoinositide-specific phospholipase C-beta 4 AA351454 NM PLCγ2 phosphoinositide-specific phospholipase C-gamma 2 X14034 B SMAD-5 mothers against decapentaplegic homolog 5 NM_005903 PRO eNOS-3 endothelial cell nitric oxide synthase 3 M95296 MRSL AKT-1 aka protein kinase B XM_015191 B AKT-2 aka protein kinase B beta XM_009203 NM AKT-3 protein kinase B, gamma XM_001729 PRO PI3K-p85 phosphoinositide-3-kinase, regulatory subunit aka p85 beta aka PIK3R2 XM_010504 B PI3K-p110 phosphoinositide-3-kinase, catalytic subunit aka p110 gamma aka NM_002649 NM PIK3CG PTEN phosphatase and tensin homolog U93051 B HIF-1α hypoxia-inducible factor 1, alpha subunit AI559451 B IKK-α IκB kinase-a AF080157 B IKK-β IκB kinase-b AF080158 B NF-κB p50 nuclear factor kB DNA-binding subunit p50 NM_002502 B NF-κB p65 nuclear factor kB DNA-binding subunit p65 L19067 B Id-1 inhibitor of DNA binding 1 NM_002165 B Id-2 inhibitor of differentiation 2 AF270493 B Id-3 inhibitor of DNA binding 3 NM_002167 B LMO-2 LIM domain only 2 (rhombotin-like 1) BC042426 MRSL HOX-B3 homeo box B3 W01448 NM HOX-D3 homeo box D3 AA434183 NM COUP TF-II COUP transcription factor 2 aka apolipoprotein AI regulatory protein-1 NM_021005 B CAN-05-3294 Glesne et al

aka ARP-1 LIM-2 LIM-homeodomain protein HLHX2 (LHX2) AI570565 NM

Table S3. no. Predicted gene no. No. MRSLs Probability per pair 1 2610 24 0.21149 2 1748 21 0.24114 3 1381 11 0.07867 4 1024 5 0.01963 5 1190 16 0.20141 6 1394 12 0.09610 7 1378 8 0.04122 8 927 9 0.07627 9 1076 13 0.14405 10 983 9 0.07301 11 1692 16 0.14178 12 1268 10 0.07052 13 496 3 0.01196 14 1173 8 0.04867 15 906 10 0.09913 16 1032 3 0.00583 17 1394 11 0.07945 18 400 2 0.00515 19 1592 15 0.13229 20 710 8 0.07761 21 337 4 0.03422 22 701 7 0.06033 23 1141 5 0.01737