Table S1A. Generic EMT signature for tumour

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1 Table S1A. Generic EMT signature for tumour Index Gene Symbol Gene Title GO Molecular Function Weight Weight.Zt ransform ed Category In Generic Cell Line EMT Signature = 1 1 KRT19 Keratin, type I cytoskeletal 19 structural constituent of cytoskeleton Epi 1 2 AGR2 Anterior gradient protein 2 homolog oxidoreductase activity Epi 1 3 RAB25 Ras-related protein Rab Epi 1 4 CDH1 cadherin 1, type 1, E-cadherin (epithelial) calcium ion binding Epi 1 5 ERBB3 Receptor tyrosine-protein kinase erbb-3 non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;growth factor activity Epi 1 6 FXYD3 7 SLC44A4 FXYD domain-containing ion transport regulator 3 solute carrier family 44, member 4 8 S100P Protein S100-P 9 SCNN1A 10 GALNT3 Amiloride-sensitive sodium channel subunit alpha Polypeptide N- acetylgalactosaminyltransferase 3 ion channel activity;protein binding Epi 1 phospholipid metabolic process Epi 0 calcium ion binding;receptor binding;calmodulin binding Epi 1 ion channel activity Epi 1 transferase activity, transferring glycosyl groups Epi 1 11 PRSS8 Prostasin serine-type peptidase activity Epi 1 12 ELF3 ETS-related transcription factor Elf-3 transcription factor activity;receptor binding;transcription factor activity Epi 1 13 CEACAM6 Carcinoembryonic antigenrelated cell adhesion molecule Epi 1 14 TMPRSS4 Transmembrane protease serine 4 serine-type peptidase activity Epi 1 15 CLDN7 Claudin Epi 1 16 TACSTD2 Tumour-associated calcium signal transducer 2 receptor activity Epi 1 17 CLDN3 Claudin Epi 0 18 EPCAM Epithelial cell adhesion molecule receptor activity Epi 1 19 SPINT1 Kunitz-type protease inhibitor 1 protein binding;serine-type endopeptidase inhibitor activity Epi 1 20 TSPAN1 Tetraspanin-1 receptor activity;receptor binding Epi 1 21 PLS1 Phospholipid scramblase Epi 1 22 TMEM30B Cell cycle control protein 50B Epi 1 23 PRR15L Proline-rich protein 15-like protein Epi 0 24 KRT8 Keratin, type II cytoskeletal 8 structural constituent of cytoskeleton Epi 1 25 ST14 Suppressor of Tumourigenicity 14 protein serine-type peptidase activity;receptor activity;calcium ion binding;hormone activity;calmodulin binding;calcium-dependent phospholipid binding;peptidase inhibitor activity Epi 1 26 RBM47 RNA-binding protein 47 RNA splicing factor activity, transesterification mechanism;structural constituent of ribosome;dna replication origin binding;singlestranded DNA binding;poly(a) RNA binding Epi 1 27 S100A14 Protein S100-A14 28 C1orf NQO1 30 TOX3 Uncharacterized protein C1orf106 NAD(P)H dehydrogenase [quinone] 1 TOX high mobility group box family member 3 calcium ion binding;receptor binding;calmodulin binding Epi Epi Epi 0 transcription factor activity;chromatin binding;receptor binding;transcription factor activity Epi 1 31 PTK6 Protein-tyrosine kinase 6 32 TFF1 Trefoil factor 1 non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;growth factor activity cytokine activity;hormone activity;growth factor activity Epi Epi 0

2 33 CLDN4 Claudin Epi 1 34 GPRC5A Retinoic acid-induced protein 3 G-protein coupled receptor activity Epi 0 35 TJP3 Tight junction protein ZO Epi 0 36 KRT18 Keratin, type I cytoskeletal 18 structural constituent of cytoskeleton Epi 1 37 MAP7 Ensconsin structural constituent of cytoskeleton;microtubule binding Epi 1 38 CKMT1A creatine kinase, mitochondrial 1A nucleotide binding Epi 1 39 ESRP1 Epithelial splicing regulatory protein 1 40 MUC1 mucin 1, cell surface associated 41 SPINT2 Kunitz-type protease inhibitor 2 42 ESRP2 43 CDS1 44 PPAP2C Epithelial splicing regulatory protein 2 Phosphatidate cytidylyltransferase 1 Lipid phosphate phosphohydrolase 2 structural constituent of ribosome;nucleic acid binding RNA polymerase II core promoter proximal region sequence-specific DNA binding protein binding;serine-type endopeptidase inhibitor activity structural constituent of ribosome;nucleic acid binding Epi Epi Epi Epi 1 nucleotidyltransferase activity Epi 1 pyrophosphatase activity Epi 0 45 CEACAM7 Carcinoembryonic antigenrelated cell adhesion molecule Epi 0 46 TTC39A Tetratricopeptide repeat protein 39A 47 OVOL2 Transcription factor Ovo-like 2 48 EHF ETS homologous factor Epi 1 transcription factor activity;transcription factor activity transcription factor activity;receptor binding;transcription factor activity Epi Epi 1 49 AP1M2 AP-1 complex subunit mu Epi 1 50 CEACAM5 Carcinoembryonic antigenrelated cell adhesion molecule Epi 0 51 LAD1 Ladinin-1 structural molecule activity Epi 1 52 ARHGAP8 Rho GTPase-activating protein 8 protein binding;small GTPase regulator activity Epi 1 53 TFF3 trefoil factor 3 (intestinal) molecular_function Epi 0 54 JUP junction plakoglobin transcription coactivator activity Epi 1 55 CD24 CD24 Molecular signal transducer activity Epi 0 56 TMC5 57 MLPH Melanophilin Transmembrane channel-like protein 5 ion channel activity Epi 0 motor activity;structural constituent of cytoskeleton;actin binding;small GTPase regulator activity Epi 0 58 ELMO3 engulfment and cell motility 3 binding Epi 1 59 ERBB2 Receptor tyrosine-protein kinase erbb-2 non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;growth factor activity Epi 1 60 LLGL2 Lethal(2) giant larvae protein homolog Epi 1 61 DDR1 Epithelial discoidin domaincontaining receptor 1 non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;growth factor activity Epi 1 62 FA2H Fatty acid 2-hydroxylase oxidoreductase activity Epi 1 63 CBLC Signal transduction protein CBL- C ligase activity Epi 1 64 TMPRSS2 Transmembrane protease serine 2 serine-type peptidase activity;receptor activity;calcium ion binding;hormone activity;calmodulin binding;calcium-dependent phospholipid binding;peptidase inhibitor activity Epi 1 65 LSR 66 PERP Lipolysis-stimulated lipoprotein receptor p53 apoptosis effector related to PMP Epi Epi 1 67 POF1B Protein POF1B Epi 1 68 MYO5C Unconventional myosin-vc motor activity;structural constituent of cytoskeleton;protein binding;small GTPase regulator activity Epi 1 69 RAB11FIP1 Rab11 family-interacting protein Epi 1

3 70 MAPK13 Mitogen-activated protein kinase 13 protein kinase activity Epi 1 71 KRT7 Keratin, type II cytoskeletal 7 structural constituent of cytoskeleton Epi 1 72 CEACAM1 Carcinoembryonic antigenrelated cell adhesion molecule Epi 1 73 CXADR 74 ATP2C2 75 RNF128 Coxsackievirus and adenovirus receptor Calcium-transporting ATPase type 2C member 2 E3 ubiquitin-protein ligase RNF MPZL2 Myelin protein zero-like protein 2 receptor activity Epi 0 hydrolase activity;cation transmembrane transporter activity;ion channel activity Epi 1 ubiquitin-protein ligase activity Epi 0 voltage-gated sodium channel activity;voltagegated sodium channel activity;cation channel activity Epi 1 77 EPS8L1 Epidermal growth factor receptor kinase substrate 8-like protein Epi 1 78 GALNT7 N- acetylgalactosaminyltransferase transferase activity, transferring glycosyl groups Epi CORO2A Coronin-2A structural constituent of cytoskeleton;actin binding Epi 0 80 BCAS1 Breast carcinoma-amplified sequence Epi 0 81 TPD52 Tumour protein D Epi 0 82 ARHGAP32 83 FUT2 84 OR7E14P Rho GTPase-activating protein 32 Galactoside 2-alpha-Lfucosyltransferase 2 olfactory receptor, family 7, subfamily E, member 14 pseudogene 85 GALE UDP-glucose 4-epimerase 86 GRHL2 Grainyhead-like protein 2 homolog protein binding;small GTPase regulator activity Epi 0 transferase activity, transferring glycosyl groups Epi Epi 1 oxidoreductase activity;hydro-lyase activity;racemase and epimerase activity transcription factor activity;transcription factor activity Epi Epi 1 87 BIK Bcl-2-interacting killer Epi 1 88 RAPGEFL1 Rap guanine nucleotide exchange factor-like 1 protein binding;small GTPase regulator activity;guanyl-nucleotide exchange factor activity Epi 0 89 STYK1 Tyrosine-protein kinase STYK1 non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity Epi 0 90 F11R Junctional adhesion molecule A receptor activity Epi 1 91 PKP3 Plakophilin-3 structural constituent of cytoskeleton;intermediate filament binding Epi 1 92 CYB561 Cytochrome b561 oxidoreductase activity Epi 1 93 SH3YL1 SH3 domain-containing YSC84- like protein 1 structural constituent of cytoskeleton;actin binding Epi 1 94 GDF15 Growth/differentiation factor 15 growth factor activity Epi 0 95 PSCA prostate stem cell antigen Epi 0 96 EZR Ezrin structural constituent of cytoskeleton Epi 0 97 TJP2 Tight junction protein ZO Epi 1 98 FGFR3 Fibroblast growth factor receptor 3 non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;growth factor activity Epi 0 99 FUT3 100 BSPRY Galactoside 3(4)-Lfucosyltransferase B box and SPRY domaincontaining protein 101 TOM1L1 TOM1-like protein IRF6 Interferon regulatory factor 6 transferase activity, transferring glycosyl groups Epi 0 ubiquitin-protein ligase activity;transcription factor activity;rna binding;transcription factor activity;transcription cofactor activity structural constituent of cytoskeleton;transmembrane transporter activity;protein binding;kinase activator activity;kinase regulator activity transcription factor activity;transcription factor activity Epi Epi Epi EPB41L4B Band 4.1-like protein 4B Epi SPDEF SAM pointed domain-containing Ets transcription factor transcription factor activity;receptor binding;transcription factor activity Epi 0

4 105 OCLN Occludin transcription factor activity;transcription factor activity;transcription cofactor activity Epi LRRC1 Leucine-rich repeat-containing protein 1 adenylate cyclase activity;receptor activity;growth factor activity;kinase regulator activity Epi C19orf ABHD EPS8L2 Uncharacterized protein C19orf21 Abhydrolase domain-containing protein 11 Epidermal growth factor receptor kinase substrate 8-like protein Epi 1 serine-type peptidase activity Epi Epi MYO6 Unconventional myosin-vi motor activity;structural constituent of cytoskeleton;protein binding;small GTPase regulator activity Epi TSPAN8 Tetraspanin-8 receptor activity;receptor binding Epi MST1R Macrophage-stimulating protein receptor non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;growth factor activity Epi SLC16A5 Monocarboxylate transporter 6 transmembrane transporter activity Epi GPR56 G-protein coupled receptor 56 G-protein coupled receptor activity Epi AZGP1 Zinc-alpha-2-glycoprotein receptor activity Epi TOB1 Protein Tob Epi SLC35A3 118 TRPM4 119 PHLDA2 120 VAMP8 121 SLC22A AKR1B10 UDP-N-acetylglucosamine transporter Transient receptor potential cation channel subfamily M member 4 Pleckstrin homology-like domain family A member 2 Vesicle-associated membrane protein 8 Solute carrier family 22 member 18 Aldo-keto reductase family 1 member B10 transmembrane transporter activity Epi 0 receptor activity;ion channel activity Epi Epi 0 SNAP receptor activity Epi 1 transmembrane transporter activity Epi 0 oxidoreductase activity;transporter activity Epi VAV3 Guanine nucleotide exchange factor VAV3 receptor binding;small GTPase regulator activity;guanyl-nucleotide exchange factor activity Epi SPAG1 Sperm-associated antigen Epi ABCC3 ATP-binding cassette, sub-family C (CFTR/MRP), member nucleotide binding Epi SYNGR2 Synaptogyrin Epi STAP2 Signal-transducing adaptor protein 2 transmembrane receptor protein kinase activity;transmembrane receptor protein kinase activity Epi C4orf19 Uncharacterized protein C4orf Epi PPL Periplakin structural constituent of cytoskeleton;intermediate filament binding Epi PLLP Plasmolipin structural constituent of myelin sheath Epi DSG2 Desmoglein-2 calcium ion binding Epi HDHD3 Haloacid dehalogenase-like hydrolase domain-containing protein 3 hydrolase activity Epi CD2AP CD2-associated protein receptor binding Epi MANSC1 MANSC domain-containing protein Epi DHCR24 Delta(24)-sterol reductase oxidoreductase activity Epi EPN3 Epsin Epi TUFT1 Tuftelin Epi GMDS GDP-mannose 4,6 dehydratase oxidoreductase activity;hydro-lyase activity;racemase and epimerase activity Epi EXPH5 Exophilin Epi DSP Dentin phosphoprotein Epi SDC4 Syndecan IL20RA Interleukin-20 receptor subunit alpha structural constituent of cytoskeleton;receptor binding Epi 0 interferon receptor activity Epi 1

5 143 FAM174B 144 PTPRF family with sequence similarity 174, member B Receptor-type tyrosine-protein phosphatase F Epi 0 phosphoprotein phosphatase activity;phosphoprotein phosphatase activity;receptor activity Epi SORD Sorbitol dehydrogenase oxidoreductase activity Epi GAS1 Growth arrest-specific protein Mes CXCL12 SDF-1-alpha(3-67) Mes ZEB1 Zinc finger E-box-binding homeobox Mes GLYR1 Putative oxidoreductase GLYR1 oxidoreductase activity Mes FHL1 Four and a half LIM domains protein 1 structural constituent of cytoskeleton;transcription factor activity;rna binding;transcription factor activity Mes FERMT2 Fermitin family homolog Mes C1S Complement C1s subcomponent oxidoreductase activity;serine-type peptidase activity;calcium ion binding;calmodulin binding;calcium-dependent phospholipid binding Mes FYN Tyrosine-protein kinase Fyn non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity Mes WIPF1 WAS/WASL-interacting protein family member Mes CYP1B1 Cytochrome P450, family 1, subfamily B, polypeptide 1, oxidoreductase activity Mes 0 isoform CRA_a 156 SERPING1 Plasma protease C1 inhibitor protein binding;serine-type endopeptidase inhibitor activity Mes 0 protein binding;serine-type endopeptidase 157 SERPINF1 Pigment epithelium-derived factor inhibitor activity Mes VCAM1 Vascular cell adhesion protein 1 phosphoprotein phosphatase activity;phosphoprotein phosphatase activity;receptor activity Mes MAP1B MAP1 light chain LC1 160 TCF4 Transcription factor 4 structural constituent of cytoskeleton;microtubule binding transcription factor activity;transcription factor activity Mes Mes SRPX Sushi repeat-containing protein SRPX serine-type peptidase activity;metallopeptidase activity;receptor activity;lipid transporter activity Mes EMP3 Epithelial membrane protein 3 structural constituent of cytoskeleton Mes DPT Dermatopontin Mes CALD1 Caldesmon structural constituent of cytoskeleton;actin binding Mes PTGIS Prostacyclin synthase oxidoreductase activity;isomerase activity Mes VIM Vimentin structural constituent of cytoskeleton Mes CD C1R Scavenger receptor cysteine-rich type 1 protein M130 Complement C1r subcomponent heavy chain oxidoreductase activity;serine-type peptidase activity;receptor activity oxidoreductase activity;serine-type peptidase activity;calcium ion binding;calmodulin binding;calcium-dependent phospholipid binding Mes Mes FBN1 Fibrillin-1 receptor activity;extracellular matrix structural constituent;calcium ion binding;receptor binding;calcium-dependent phospholipid binding Mes FN1 Anastellin hydrolase activity;deaminase activity;receptor binding;kinase regulator activity Mes FXYD6 FXYD domain-containing ion transport regulator 6 ion channel activity;protein binding Mes 0

6 172 IGF1 Insulin-like growth factor I hormone activity;growth factor activity Mes NAP1L3 Nucleosome assembly protein 1- like 3 protein binding;phosphatase inhibitor activity;phosphatase regulator activity Mes MRC1 Macrophage mannose receptor 1 receptor activity Mes QKI Protein quaking RNA splicing factor activity, transesterification mechanism;transcription factor activity;mrna binding;transcription factor activity;transcription cofactor activity Mes MS4A4A Membrane-spanning 4-domains subfamily A member 4A receptor activity Mes DCN Decorin receptor activity Mes LOX Protein-lysine 6-oxidase 179 RECK Reversion-inducing cysteine-rich protein with Kazal motifs oxidoreductase activity;serine-type peptidase activity;receptor activity protein binding;serine-type endopeptidase inhibitor activity Mes Mes ANK2 Ankyrin-2 structural constituent of cytoskeleton Mes LY96 Lymphocyte antigen Mes ZFPM2 Zinc finger protein ZFPM2 183 CSRP2 Cysteine and glycine-rich protein 2 transcription factor activity;transcription factor activity Mes 0 structural constituent of cytoskeleton Mes EFEMP1 EGF-containing fibulin-like extracellular matrix protein 1 receptor activity;extracellular matrix structural constituent;calcium ion binding;receptor binding;calmodulin binding;calcium-dependent phospholipid binding Mes RARRES2 186 PTPRC 187 PLEKHO1 Retinoic acid receptor responder protein 2 Receptor-type tyrosine-protein phosphatase C Pleckstrin homology domaincontaining family O member Mes 0 phosphoprotein phosphatase activity;phosphoprotein phosphatase activity;receptor activity Mes Mes RGS2 Regulator of G-protein signaling 2 protein binding;small GTPase regulator activity Mes F13A1 Coagulation factor XIII A chain acyltransferase activity Mes JAM2 Junctional adhesion molecule B receptor activity Mes CHRDL1 Chordin-like protein 1 receptor binding Mes TUBA1A Tubulin alpha-1a chain structural constituent of cytoskeleton Mes AP1S2 AP-1 complex subunit sigma Mes MYLK Myosin light chain kinase, smooth muscle protein kinase activity Mes DDR2 Discoidin domain-containing receptor 2 non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;growth factor activity Mes DSE Dermatan-sulfate epimerase Mes SACS Sacsin Mes GLIPR1 Glioma pathogenesis-related protein Mes CXCL13 C-X-C motif chemokine 13 chemokine activity Mes FLRT2 Leucine-rich repeat transmembrane protein FLRT2 receptor activity Mes PTX3 Pentraxin-related protein PTX Mes AKT3 RAC-gamma serine/threonineprotein kinase protein kinase activity;calcium ion binding;calmodulin binding;calcium-dependent phospholipid binding Mes COL6A2 Collagen alpha-2(vi) chain receptor activity;extracellular matrix structural constituent;transmembrane transporter activity Mes DPYSL3 Dihydropyrimidinase-related protein CDH11 Cadherin PDZRN3 207 ZEB2 E3 ubiquitin-protein ligase PDZRN3 Zinc finger E-box-binding homeobox 2 hydrolase activity Mes 0 G-protein coupled receptor activity;calcium ion binding Mes Mes Mes 0

7 208 CCL2 C-C motif chemokine 2 chemokine activity Mes MAFB Transcription factor MafB 210 SFRP1 211 C14orf139 Secreted frizzled-related protein 1 chromosome 14 open reading frame 139 transcription factor activity;transcription factor activity G-protein coupled receptor activity;receptor binding Mes Mes Mes MFAP4 Microfibril-associated glycoprotein 4 hydrolase activity;deaminase activity;receptor binding;kinase regulator activity Mes MAF Transcription factor Maf 214 UCHL1 Ubiquitin carboxyl-terminal hydrolase isozyme L1 transcription factor activity;transcription factor activity Mes 0 cysteine-type peptidase activity Mes TUBB6 Tubulin beta-6 chain structural constituent of cytoskeleton Mes SRGN Serglycin Mes HEG1 Protein HEG homolog Mes KCNJ8 ATP-sensitive inward rectifier potassium channel 8 voltage-gated potassium channel activity;voltagegated potassium channel activity;cation channel activity Mes AKAP12 A-kinase anchor protein Mes EVI2A Protein EVI2A receptor activity Mes COL14A1 Collagen alpha-1(xiv) chain receptor activity;extracellular matrix structural constituent;transmembrane transporter activity Mes AXL Tyrosine-protein kinase receptor UFO non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;growth factor activity Mes ECM2 Extracellular matrix protein 2 receptor activity Mes FSTL1 Follistatin-related protein 1 protein binding Mes PLN Cardiac phospholamban Mes MYL9 Myosin regulatory light polypeptide 9 structural constituent of cytoskeleton;calcium ion binding;calmodulin binding Mes OLFML3 Olfactomedin-like protein 3 receptor activity;structural molecule activity Mes STON1 Stonin Mes SLIT2 Slit homolog 2 protein receptor activity Mes BICC1 Protein bicaudal C homolog 1 lipid transporter activity;rna binding Mes SOBP Sine oculis-binding protein homolog Mes CLIC4 Chloride intracellular channel protein 4 oxidoreductase activity;transferase activity;racemase and epimerase activity;structural constituent of cytoskeleton;anion channel activity;translation factor activity, nucleic acid binding;receptor binding;translation elongation factor activity Mes ENPP2 Ectonucleotide pyrophosphatase activity;nucleotide phosphatase pyrophosphatase/phosphodiester activity;nucleotide phosphatase activity ase family member Mes SAMSN1 SAM domain-containing protein SAMSN Mes TPM2 Tropomyosin beta chain motor activity;structural constituent of cytoskeleton Mes ASPN Asporin receptor activity Mes COL6A1 Collagen alpha-1(vi) chain receptor activity;extracellular matrix structural constituent;transmembrane transporter activity Mes IGFBP5 239 MOXD1 Insulin-like growth factor-binding --- protein Mes 0 DBH-like monooxygenase protein oxidoreductase activity Mes AKAP2 A-kinase anchor protein Mes SLC2A3 Solute carrier family 2, facilitated glucose transporter member 3 carbohydrate transmembrane transporter activity;transmembrane transporter activity Mes 0

8 242 OLFML2B Olfactomedin-like protein 2B receptor activity;structural molecule activity Mes ANGPTL2 Angiopoietin-related protein 2 hydrolase activity;deaminase activity;receptor binding;kinase regulator activity Mes PCOLCE Procollagen C-endopeptidase enhancer 1 oxidoreductase activity;serine-type peptidase activity;metallopeptidase activity;receptor activity;lipid transporter activity;transmembrane transporter activity;receptor binding;enzyme regulator activity Mes COLEC12 Collectin-12 receptor activity;transmembrane transporter activity Mes CTSK Cathepsin K cysteine-type peptidase activity Mes TAGLN Transgelin 248 CDH2 Cadherin IL10RA 250 C1orf54 Interleukin-10 receptor subunit alpha chromosome 1 open reading frame 54 structural constituent of cytoskeleton;actin binding G-protein coupled receptor activity;calcium ion binding Mes Mes 0 interferon receptor activity Mes Mes CEP170 Centrosomal protein of 170 kda Mes TNS1 Tensin CLEC2B C-type lectin domain family 2 member B phosphoprotein phosphatase activity;phosphoprotein phosphatase activity;structural constituent of cytoskeleton;actin binding Mes 0 receptor activity;receptor binding Mes JAM3 Junctional adhesion molecule C receptor activity Mes SEPT6 Septin-6 GTPase activity;structural constituent of cytoskeleton;protein binding Mes GREM1 Gremlin Mes VCAN Versican core protein Mes ZCCHC24 zinc finger, CCHC domain containing Mes CRYAB Alpha-crystallin B chain structural molecule activity Mes SFRP4 Secreted frizzled-related protein RUNX1T1 Protein CBFA2T1 G-protein coupled receptor activity;receptor binding transcription factor activity;transcription factor activity;transcription cofactor activity Mes Mes FGL2 Fibroleukin hydrolase activity;deaminase activity;receptor binding;kinase regulator activity Mes MS4A6A Membrane-spanning 4-domains subfamily A member 6A receptor activity Mes PTRF Polymerase I and transcript release factor transcription factor activity;transcription factor activity Mes GIMAP4 GTPase IMAP family member Mes TWIST1 Twist-related protein GFPT2 Glucosamine--fructose-6- phosphate aminotransferase [isomerizing] 2 transcription factor activity;transcription factor activity Mes 0 transaminase activity Mes LHFP Lipoma HMGIC fusion partner Mes CXCR4 C-X-C chemokine receptor type 4 G-protein coupled receptor activity Mes SPOCK1 Testican-1 calcium ion binding;protein binding;cysteine-type endopeptidase inhibitor activity Mes SPARC SPARC growth factor activity Mes VSIG4 273 GPM6B 274 TRPC1 V-set and immunoglobulin domain-containing protein Mes 0 Neuronal membrane glycoprotein structural constituent of myelin sheath M6-b Mes 0 Short transient receptor potential ion channel activity channel Mes 1

9 275 SNAI2 Zinc finger protein SNAI2 276 GUCY1B3 277 PLXNC1 Plexin-C1 guanylate cyclase 1, soluble, beta 3 transcription factor activity;transcription factor activity Mes 0 nucleotide binding Mes 0 transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;receptor binding Mes SYT11 Synaptotagmin Mes FLI1 Friend Leukaemia integration 1 transcription factor transcription factor activity;receptor binding;transcription factor activity Mes MYH10 Myosin-10 motor activity;structural constituent of cytoskeleton;protein binding;small GTPase regulator activity Mes CSF2RB Cytokine receptor common subunit beta cytokine receptor activity Mes TNC Tenascin hydrolase activity;deaminase activity;receptor binding;kinase regulator activity Mes PMP22 Peripheral myelin protein 22 structural constituent of cytoskeleton Mes COL5A2 Collagen alpha-2(v) chain receptor activity;extracellular matrix structural constituent;transmembrane transporter activity Mes MMP2 72 kda type IV collagenase metallopeptidase activity Mes GNG11 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-11 GTPase activity;protein binding Mes CAV1 Caveolin-1 structural molecule activity;protein binding;small GTPase regulator activity Mes CDK14 Cyclin-dependent kinase 14 non-membrane spanning protein tyrosine kinase activity Mes SDC2 Syndecan-2 structural constituent of cytoskeleton;receptor binding Mes PTGDS Prostaglandin-H2 D-isomerase isomerase activity;binding Mes NR3C1 Glucocorticoid receptor ligand-dependent nuclear receptor activity;transcription factor activity;transcription Mes 0 factor activity 292 SYNM Probable asparagine--trna ligase, mitochondrial aminoacyl-trna ligase activity;rna binding Mes FAP Glomulin structural molecule activity;receptor binding Mes NUAK1 NUAK family SNF1-like kinase 1 protein kinase activity Mes WWTR1 WW domain-containing transcription regulator protein 1 transcription factor activity;protein binding;kinase regulator activity;transcription factor activity;transcription cofactor activity Mes FBLN1 Fibulin-1 receptor activity;extracellular matrix structural constituent;calcium ion binding;receptor binding;calmodulin binding;calcium-dependent phospholipid binding Mes MPDZ Multiple PDZ domain protein structural constituent of cytoskeleton Mes SYNE1 Nesprin-1 structural constituent of cytoskeleton;calcium ion binding;actin binding Mes EFEMP2 EGF-containing fibulin-like extracellular matrix protein 2 receptor activity;extracellular matrix structural constituent;calcium ion binding;receptor binding;calmodulin binding;calcium-dependent phospholipid binding Mes GIMAP6 GTPase IMAP family member Mes KIAA cell adhesion Mes CCL8 C-C motif chemokine 8 chemokine activity Mes COL15A1 Collagen alpha-1(xv) chain receptor activity;extracellular matrix structural constituent;transmembrane transporter activity Mes CHN1 N-chimaerin protein binding;small GTPase regulator activity Mes 1

10 305 CRISPLD2 Cysteine-rich secretory protein LCCL domain-containing Mes PDGFC Platelet-derived growth factor C oxidoreductase activity;serine-type peptidase activity;metallopeptidase activity;receptor activity;lipid transporter activity;transmembrane transporter activity;growth factor activity;enzyme regulator activity Mes GEM GTP-binding protein GEM GTPase activity;protein binding Mes ISLR Immunoglobulin superfamily containing leucine-rich repeat protein receptor activity Mes GZMK Granzyme K serine-type peptidase activity;calcium ion binding;growth factor activity;calmodulin binding;calcium-dependent phospholipid binding Mes SPARCL1 SPARC-like protein 1 growth factor activity Mes BNC2 Zinc finger protein basonuclin-2 transcription factor activity;transcription factor activity Mes BGN Biglycan receptor activity Mes MEOX2 Homeobox protein MOX-2 transcription factor activity;transcription factor activity Mes ITM2A Integral membrane protein 2A Mes IFFO1 Intermediate filament family orphan Mes 0

11 Table S1B. Generic EMT signature for cell line Index Gene Symbol Gene Title GO Molecular Function 1 CDH1 cadherin 1, type 1, E-cadherin (epithelial) 2 AGR2 Anterior gradient protein 2 homolog 3 EPCAM Epithelial cell adhesion molecule Weight Weight.Zt ransform ed Epi/Mes In Generic Tumour EMT Signature = 1 calcium ion binding Epi 1 oxidoreductase activity Epi 1 receptor activity Epi 1 4 KRT19 Keratin, type I cytoskeletal 19 structural constituent of cytoskeleton Epi 1 5 RAB25 Ras-related protein Rab Epi 1 6 TACSTD2 Tumour-associated calcium signal transducer 2 receptor activity Epi 1 7 S100P Protein S100-P calcium ion binding;receptor binding;calmodulin binding Epi 1 Carcinoembryonic antigenrelated 8 CEACAM6 cell adhesion molecule Epi GALNT3 Polypeptide N- transferase activity, transferring acetylgalactosaminyltransferas glycosyl groups e Epi 1 10 FXYD3 FXYD domain-containing ion transport regulator 3 ion channel activity;protein binding Epi 1 11 SPINT2 Kunitz-type protease inhibitor 2 protein binding;serine-type endopeptidase inhibitor activity Epi 1 12 TMEM30B Cell cycle control protein 50B Epi 1 13 SCNN1A Amiloride-sensitive sodium channel subunit alpha ion channel activity Epi 1 14 ST14 Suppressor of Tumourigenicity 14 protein serine-type peptidase activity;receptor activity;calcium ion binding;hormone activity;calmodulin binding;calciumdependent phospholipid binding;peptidase inhibitor activity Epi 1 15 ESRP1 Epithelial splicing regulatory protein 1 16 S100A14 Protein S100-A14 structural constituent of ribosome;nucleic acid binding calcium ion binding;receptor binding;calmodulin binding Epi Epi 1 17 CLDN7 Claudin Epi 1 18 ERBB3 Receptor tyrosine-protein kinase erbb-3 non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;growth factor activity Epi 1 19 RBM47 RNA-binding protein SPINT1 Kunitz-type protease inhibitor 1 RNA splicing factor activity, transesterification mechanism;structural constituent of ribosome;dna replication origin binding;single-stranded DNA binding;poly(a) RNA binding protein binding;serine-type endopeptidase inhibitor activity Epi Epi 1 21 ELF3 ETS-related transcription factor Elf-3 transcription factor activity;receptor binding;transcription factor activity Epi 1 22 CLDN4 Claudin Epi 1 23 PRSS8 Prostasin serine-type peptidase activity Epi 1 24 SH3YL1 SH3 domain-containing YSC84-like protein 1 structural constituent of cytoskeleton;actin binding Epi 1 25 EHF ETS homologous factor transcription factor activity;receptor binding;transcription factor activity Epi 1 26 LCN2 Neutrophil gelatinaseassociated lipocalin isomerase activity;binding Epi 0 27 JUP junction plakoglobin transcription coactivator activity Epi 1

12 28 VAMP8 Vesicle-associated membrane protein 8 SNAP receptor activity Epi 1 29 KRT8 Keratin, type II cytoskeletal 8 structural constituent of cytoskeleton Epi 1 30 C1orf106 Uncharacterized protein C1orf Epi 1 31 KRT7 Keratin, type II cytoskeletal 7 structural constituent of cytoskeleton Epi 1 32 DSP Dentin phosphoprotein Epi 1 33 CDS1 Phosphatidate cytidylyltransferase 1 nucleotidyltransferase activity Epi 1 34 ITGB4 Integrin beta-4 receptor activity Epi 0 Transmembrane protease 35 TMPRSS4 serine-type peptidase activity Epi 1 serine 4 Lipolysis-stimulated lipoprotein 36 LSR Epi 1 receptor receptor activity;transmembrane 37 SORL1 Sortilin-related receptor Epi 0 transporter activity;lipid binding 38 GRHL2 Grainyhead-like protein 2 homolog transcription factor activity;transcription factor activity Epi 1 39 PPL Periplakin 40 C1orf116 Specifically androgenregulated gene protein structural constituent of cytoskeleton;intermediate filament binding Epi Epi 0 41 TSPAN1 Tetraspanin-1 receptor activity;receptor binding Epi 1 42 MAP7 Ensconsin 43 SLPI Antileukoproteinase structural constituent of cytoskeleton;microtubule binding protein binding;serine-type endopeptidase inhibitor activity Epi Epi 0 44 TOX3 TOX high mobility group box family member 3 transcription factor activity;chromatin binding;receptor binding;transcription factor activity Epi 1 45 ARHGAP8 46 F11R Rho GTPase-activating protein 8 Junctional adhesion molecule A protein binding;small GTPase regulator activity Epi 1 receptor activity Epi 1 47 LAD1 Ladinin-1 structural molecule activity Epi 1 48 GPX2 Glutathione peroxidase 2 oxidoreductase activity;peroxidase activity Epi 0 49 CTSH Cathepsin H cysteine-type peptidase activity Epi 0 50 GPR56 G-protein coupled receptor 56 G-protein coupled receptor activity Epi 1 51 FA2H Fatty acid 2-hydroxylase oxidoreductase activity Epi 1 52 KLF5 Krueppel-like factor 5 transcription factor activity;transcription factor activity Epi 0 53 AREG Amphiregulin growth factor activity Epi 0 54 KRT18 Keratin, type I cytoskeletal 18 structural constituent of cytoskeleton Epi 1 55 SCEL Sciellin Epi 0 56 CDH3 Cadherin-15 G-protein coupled receptor activity;calcium ion binding Epi 0 57 UGT1A1 UDP-glucuronosyltransferase 1-1 transferase activity, transferring glycosyl groups Epi 0 58 MPZL2 Myelin protein zero-like protein 2 voltage-gated sodium channel activity;voltage-gated sodium channel activity;cation channel activity Epi 1 59 AIM1 Absent in melanoma 1 protein structural molecule activity Epi 0 60 OVOL2 Transcription factor Ovo-like 2 transcription factor activity;transcription factor activity Epi 1 61 LLGL2 62 ESRP2 Lethal(2) giant larvae protein homolog 2 Epithelial splicing regulatory protein Epi 1 structural constituent of ribosome;nucleic acid binding Epi 1

13 63 MYO5C Unconventional myosin-vc motor activity;structural constituent of cytoskeleton;protein binding;small GTPase regulator activity Epi 1 64 DDR1 Epithelial discoidin domaincontaining receptor 1 non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;growth factor activity Epi 1 65 VGLL1 Transcription cofactor vestigiallike protein 1 activity;transcription factor transcription factor activity Epi 0 66 IRF6 Interferon regulatory factor 6 transcription factor activity;transcription factor activity Epi 1 67 SFN Oligoribonuclease, mitochondrial exoribonuclease activity;nucleic acid binding Epi 0 68 TSPAN13 Tetraspanin-13 receptor activity;receptor binding Epi 0 69 KCNK1 Potassium channel subfamily K member 1 voltage-gated potassium channel activity;voltage-gated potassium channel activity;cation channel activity Epi 0 70 MYO1D Unconventional myosin-id 71 PKP3 Plakophilin-3 motor activity;structural constituent of cytoskeleton;protein binding;enzyme regulator activity structural constituent of cytoskeleton;intermediate filament binding Epi Epi 1 72 ITGB6 Integrin beta-6 receptor activity Epi 0 73 LY75 Lymphocyte antigen 75 receptor activity Epi 0 74 MAPK13 75 TTC39A Mitogen-activated protein kinase 13 Tetratricopeptide repeat protein 39A protein kinase activity Epi Epi 1 76 ELMO3 engulfment and cell motility 3 binding Epi 1 77 CEACAM1 Carcinoembryonic antigenrelated cell adhesion molecule Epi 1 78 DTX4 Protein deltex-4 transcription factor activity;transcription factor activity;transcription cofactor activity Epi 0 79 ERBB2 Receptor tyrosine-protein kinase erbb-2 non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;growth factor activity Epi 1 80 RAB11FIP1 81 ATP2C2 Rab11 family-interacting protein 1 Calcium-transporting ATPase type 2C member Epi 1 hydrolase activity;cation transmembrane transporter activity;ion channel activity Epi 1 82 MST1R Macrophage-stimulating protein receptor non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;growth factor activity Epi 1 83 AP1M2 AP-1 complex subunit mu Epi 1 84 TGFA Protransforming growth factor alpha cytokine activity;growth factor activity Epi 0

14 85 MYO6 Unconventional myosin-vi motor activity;structural constituent of cytoskeleton;protein binding;small GTPase regulator activity Epi 1 86 PTK6 Protein-tyrosine kinase 6 non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;growth factor activity Epi 1 87 OAS1 2'-5'-oligoadenylate synthase 1 nucleotidyltransferase activity;nucleic acid binding Epi 0 88 FBP1 fructose-1,6-bisphosphatase 1 protein binding Epi 0 89 AQP3 Aquaporin-3 transmembrane transporter activity Epi 0 90 CBLC Signal transduction protein CBL-C ligase activity Epi 1 91 EPHA1 Ephrin type-a receptor 1 non-membrane spanning protein tyrosine kinase activity;transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;growth factor activity Epi 0 92 BSPRY 93 SH2D3A 94 EPS8L1 95 GRB7 96 C4orf19 B box and SPRY domaincontaining protein SH2 domain-containing protein 3A Epidermal growth factor receptor kinase substrate 8- like protein 1 Growth factor receptor-bound protein 7 Uncharacterized protein C4orf19 ubiquitin-protein ligase activity;transcription factor activity;rna binding;transcription factor activity;transcription cofactor activity Epi Epi Epi Epi Epi 1 97 KLK6 Kallikrein-6 serine-type peptidase activity Epi 0 98 TJP2 Tight junction protein ZO Epi 1 99 PLS1 Phospholipid scramblase Epi DENND2D 101 EPS8L2 102 IL20RA DENN domain-containing protein 2D Epidermal growth factor receptor kinase substrate 8- like protein 2 Interleukin-20 receptor subunit alpha Epi Epi 1 interferon receptor activity Epi HES1 Transcription factor HES-1 transcription factor activity;transcription factor activity Epi IL1RN Interleukin-1 receptor antagonist protein hematopoietin/interferon-class (D200- domain) cytokine receptor binding Epi EXPH5 Exophilin Epi ARHGDIB 107 C19orf CAMK2N1 Rho GDP-dissociation inhibitor 2 Uncharacterized protein C19orf21 Calcium/calmodulin-dependent protein kinase II inhibitor 1 receptor binding;small GTPase regulator activity Epi Epi Epi HPGD 15-hydroxyprostaglandin dehydrogenase [NAD(+)] oxidoreductase activity Epi SYNGR2 Synaptogyrin Epi C10orf PERP 113 MANSC1 chromosome 10 open reading frame 116 p53 apoptosis effector related to PMP-22 MANSC domain-containing protein 1 molecular_function Epi Epi Epi 1

15 114 DSC2 Desmocollin-2 calcium ion binding Epi POF1B Protein POF1B Epi SERINC5 Serine incorporator Epi BIK Bcl-2-interacting killer Epi ANXA9 Annexin A9 calcium ion binding;calciumdependent phospholipid binding Epi MALL MAL-like protein structural constituent of myelin sheath Epi EPN3 Epsin Epi STAP2 Signal-transducing adaptor protein 2 transmembrane receptor protein kinase activity;transmembrane receptor protein kinase activity Epi FOXA1 Hepatocyte nuclear factor 3- alpha transcription factor activity;transcription factor activity Epi PYCARD cysteine-type peptidase Apoptosis-associated specklike protein containing a CARD activity;protein binding;peptidase inhibitor activity Epi ZNF165 Zinc finger protein 165 transcription factor activity;transcription factor activity Epi SLC37A1 Glycerol-3-phosphate transporter cation transmembrane transporter activity Epi ANK3 Ankyrin-3 structural constituent of cytoskeleton Epi TSPAN15 Tetraspanin-15 receptor activity;receptor binding Epi HNMT Histamine N-methyltransferase Epi ABCC3 130 SDC1 Syndecan CKMT1A ATP-binding cassette, subfamily C (CFTR/MRP), member creatine kinase, mitochondrial 1A nucleotide binding Epi 1 structural constituent of cytoskeleton;receptor binding Epi 0 nucleotide binding Epi TOB1 Protein Tob Epi B3GNT3 134 TMC6 UDP-GlcNAc:betaGal beta-1,3- N- transferase activity, transferring acetylglucosaminyltransferase glycosyl groups 3 Transmembrane channel-like protein Epi 0 ion channel activity Epi CD9 CD9 antigen receptor activity;receptor binding Epi ADAP1 Arf-GAP with dual PH domaincontaining protein 1 nucleic acid binding;protein binding;small GTPase regulator activity Epi ATP1B1 Sodium/potassiumtransporting ATPase subunit beta-1 cation transmembrane transporter activity;hydrogen ion transmembrane transporter activity Epi SHANK2 SH3 and multiple ankyrin repeat domains protein Epi CYB561 Cytochrome b561 oxidoreductase activity Epi ERMP1 Endoplasmic reticulum metallopeptidase 1 metallopeptidase activity Epi RAB20 Ras-related protein Rab Epi MYH14 myosin, heavy chain 14, nonmuscle 143 CAPN1 Calpain-1 catalytic subunit 144 ALDH3B2 Aldehyde dehydrogenase family 3 member B2 microfilament motor activity Epi 0 cysteine-type peptidase activity;calcium ion binding;calmodulin binding;calcium-dependent phospholipid binding Epi 0 oxidoreductase activity Epi TRIM31 E3 ubiquitin-protein ligase TRIM31 ubiquitin-protein ligase activity;structural constituent of cytoskeleton;transcription factor activity;rna binding;cytoskeletal protein binding;transcription factor activity;transcription cofactor activity Epi 0

16 146 ARAP2 Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 2 nucleic acid binding;protein binding;small GTPase regulator activity Epi SSH3 Protein phosphatase Slingshot homolog 3 phosphoprotein phosphatase activity;phosphoprotein phosphatase activity;protein binding;kinase inhibitor activity;kinase regulator activity Epi ICA1 Islet cell autoantigen Epi ARHGEF5 Rho guanine nucleotide exchange factor Epi ALOX5 Arachidonate 5-lipoxygenase oxidoreductase activity Epi RHOD Rho-related GTP-binding protein RhoD GTPase activity;protein binding Epi TMPRSS2 Transmembrane protease serine 2 serine-type peptidase activity;receptor activity;calcium ion binding;hormone activity;calmodulin binding;calciumdependent phospholipid binding;peptidase inhibitor activity Epi MTUS1 154 CYP4F3 Microtubule-associated Tumour suppressor 1 Leukotriene-B(4) omegahydroxylase Epi 0 oxidoreductase activity Epi PPFIBP2 Liprin-beta Epi RABGAP1L 157 PLXNB2 Plexin-B2 158 MGST2 159 OR7E14P 160 EVPL Envoplakin Rab GTPase-activating protein 1-like Microsomal glutathione S- transferase 2 olfactory receptor, family 7, subfamily E, member 14 pseudogene 161 CD46 Membrane cofactor protein hydrolase activity;protein binding;small GTPase regulator activity transmembrane receptor protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane receptor protein kinase activity;receptor binding Epi Epi 0 transferase activity Epi Epi 1 structural constituent of cytoskeleton;intermediate filament binding serine-type peptidase activity;metallopeptidase activity;receptor activity;lipid transporter activity Epi Epi KRT15 Keratin, type I cytoskeletal 15 structural constituent of cytoskeleton Epi CNKSR1 Connector enhancer of kinase suppressor of ras 1 protein binding;kinase regulator activity Epi BLNK B-cell linker protein receptor binding Epi COMT Catechol O-methyltransferase methyltransferase activity Epi ANXA4 annexin A4 phospholipase inhibitor activity Epi TNFSF13 Tumour necrosis factor ligand superfamily member Epi OCLN Occludin transcription factor activity;transcription factor activity;transcription cofactor activity Epi SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF Epi XBP1 X-box-binding protein 1 transcription factor activity;transcription factor activity Epi VIM Vimentin structural constituent of cytoskeleton Mes ZEB1 Zinc finger E-box-binding homeobox Mes EMP3 Epithelial membrane protein 3 structural constituent of cytoskeleton Mes SACS Sacsin Mes 1