Functional oncogene signatures guide rationally

www.impactjournals.com/oncotarget/

Oncotarget, Supplementary Materials 2016

Functional oncogene signatures guide rationally designed combination therapies to synergistically induce breast cancer cell death Supplementary Materials

Supplementary Figure S1: Targeting multiple drivers in the SUM-185 functional oncogene signature induces apoptotic cell morphology. Phase contrast images of SUM-185 cells treated with .05 uM PD173074, .1 uM Navitoclax, and .5 uM A66 for the indicated times.

Supplementary Table S1: SUM-52 cell line copy number amplified genes. Cell line SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

Symbol FLJ45717 ZNF669 VN1R5 ZNF670 ZNF124 TMSL3 BRI3 PTCD1 ZNF394 DYNC1I1 CPSF4 ARPC1A TRRAP

Gene name FLJ45717 protein zinc finger protein 669 vomeronasal 1 receptor 5 zinc finger protein 670 zinc finger protein 124 thymosin-like 3 brain protein I3 pentatricopeptide repeat domain 1 zinc finger protein 394 dynein, cytoplasmic 1, intermediate chain 1 cleavage and polyadenylation specific factor 4, 30kDa actin related protein 2/3 complex, subunit 1A, 41kDa transformation/transcription domain-associated protein

Chromosome 1 1 1 1 1 4 7 7 7 7 7 7 7

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

BUD31 PDAP1 SLC25A13 SHFM1 ACN9 DKFZP434B0335

7 7 7 7 7 7

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

ATP5J2 SMURF1 ZNF789 PON2 ZKSCAN5 ASNS BAIAP2L1 ZNF498 ARPC1B PON3 TMEM130 NPTX2 BHLHB8 PDK4 DLX6 ASB4 LMTK2 DLX5 LOC4951

SUM52 SUM52

TAC1 AKAP9

BUD31 homolog (S. cerevisiae) PDGFA associated protein 1 solute carrier family 25, member 13 (citrin) split hand/foot malformation (ectrodactyly) type 1 ACN9 homolog (S. cerevisiae) DKFZP434B0335 protein ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F2 SMAD specific E3 ubiquitin protein ligase 1 zinc finger protein 789 paraoxonase 2 zinc finger with KRAB and SCAN domains 5 asparagine synthetase BAI1-associated protein 2-like 1 zinc finger protein 498 actin related protein 2/3 complex, subunit 1B, 41kDa paraoxonase 3 transmembrane protein 130 neuronal pentraxin II basic helix-loop-helix domain containing, class B, 8 pyruvate dehydrogenase kinase, isozyme 4 distal-less homeobox 6 ankyrin repeat and SOCS box-containing 4 lemur tyrosine kinase 2 distal-less homeobox 5 parvalbumin tachykinin, precursor 1 (substance K, substance P, neurokinin 1, neurokinin 2, neuromedin L, neurokinin alpha, neuropeptide K, neuropeptide gamma) A kinase (PRKA) anchor protein (yotiao) 9

7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7

7 7

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

FLJ21062 PFTK1 GTPBP10 PEX1 MTERF KRIT1 CDK6 ANKIB1 GATAD1 PON2 STEAP1 FAM133B PEG10 STEAP2 DKFZP564O0523 SGCE PON3 CYP51A1 BET1 CCDC132 CASD1 GNG11

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

GNGT1 PON1 PPP1R9A FZD1 CALCR TFPI2 SAMD9L SAMD9 ZNF804B COL1A2 LOC253012 MGC26647

SUM52 SUM52

POP7 CYP3A7

SUM52 SUM52 SUM52 SUM52

TAF6 ARS2 PILRB MCM7

SUM52

COPS6

hypothetical protein FLJ21062 PFTAIRE protein kinase 1 GTP-binding protein 10 (putative) peroxisome biogenesis factor 1 mitochondrial transcription termination factor KRIT1, ankyrin repeat containing cyclin-dependent kinase 6 ankyrin repeat and IBR domain containing 1 GATA zinc finger domain containing 1 paraoxonase 2 six transmembrane epithelial antigen of the prostate 1 family with sequence similarity 133, member B paternally expressed 10 six transmembrane epithelial antigen of the prostate 2 hypothetical protein DKFZp564O0523 sarcoglycan, epsilon paraoxonase 3 cytochrome P450, family 51, subfamily A, polypeptide 1 BET1 homolog (S. cerevisiae) coiled-coil domain containing 132 CAS1 domain containing 1 guanine nucleotide binding protein (G protein), gamma 11 guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1 paraoxonase 1 protein phosphatase 1, regulatory (inhibitor) subunit 9A frizzled homolog 1 (Drosophila) calcitonin receptor tissue factor pathway inhibitor 2 sterile alpha motif domain containing 9-like sterile alpha motif domain containing 9 zinc finger protein 804B collagen, type I, alpha 2 hypothetical protein LOC253012 hypothetical protein MGC26647 processing of precursor 7, ribonuclease P/MRP subunit (S. cerevisiae) cytochrome P450, family 3, subfamily A, polypeptide 7 TAF6 RNA polymerase II, TATA box binding protein (TBP)associated factor, 80kDa ARS2 protein paired immunoglobin-like type 2 receptor beta minichromosome maintenance complex component 7 COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)

7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7

SUM52 SUM52

PILRA AP4M1

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

SLC12A9 ZKSCAN5 C7orf47 MEPCE TSC22D4 ZNHIT1 HRBL ZNF3 STAG3 ZKSCAN1 LOC255374 RABL5 ZCWPW1 ZNF498 CYP3A4


FIS1 MGC40499 MOSPD3 TRIM56 TRIM4 TFR2

SUM52 SUM52 SUM52 SUM52 SUM52

PVRIG AP1S1 ZSCAN21 ACTL6B ZAN

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

GNB2 EPO CYP3A5 ACHE EPHB4 MOGAT3 PLOD3 GJE1 GATS LOC402573 VGF C7orf43 GPC2

paired immunoglobin-like type 2 receptor alpha adaptor-related protein complex 4, mu 1 subunit solute carrier family 12 (potassium/chloride transporters), member 9 zinc finger with KRAB and SCAN domains 5 chromosome 7 open reading frame 47 methylphosphate capping enzyme TSC22 domain family, member 4 zinc finger, HIT type 1 HIV-1 Rev binding protein-like zinc finger protein 3 stromal antigen 3 zinc finger with KRAB and SCAN domains 1 similar to hypothetical protein MGC49416 RAB, member RAS oncogene family-like 5 zinc finger, CW type with PWWP domain 1 zinc finger protein 498 cytochrome P450, family 3, subfamily A, polypeptide 4 fission 1 (mitochondrial outer membrane) homolog (S. cerevisiae) PRotein Associated with Tlr4 motile sperm domain containing 3 tripartite motif-containing 56 tripartite motif-containing 4 transferrin receptor 2 poliovirus receptor related immunoglobulin domain containing adaptor-related protein complex 1, sigma 1 subunit zinc finger and SCAN domain containing 21 actin-like 6B zonadhesin guanine nucleotide binding protein (G protein), beta polypeptide 2 erythropoietin cytochrome P450, family 3, subfamily A, polypeptide 5 acetylcholinesterase (Yt blood group) EPH receptor B4 monoacylglycerol O-acyltransferase 3 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 gap junction protein, epsilon 1, 29kDa opposite strand transcription unit to STAG3 hypothetical LOC402573 VGF nerve growth factor inducible chromosome 7 open reading frame 43 glypican 2

7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7


SERPINE1 AZGP1 FBXO24 MYLC2PL PERQ1 CLDN15 CYP3A43 GAL3ST4 TRIP6 EMID2 C7orf51 MUC17 PCOLCE CD36 HGF

SUM52 SUM52

SEMA3E CACNA2D1


SEMA3C ZNF479 ZNF107 ZNF138 ZNF680 CHCHD2

SUM52

SEMA3A

SUM52

SEMA3D


SEMA3E GRM3 CACNA2D1 CUTL1 SH2B2 MYLC2PL EMID2 INDO C8orf4 PPAPDC1B TM2D2 EIF4EBP1 ADAM9

SUM52

LSM1

serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 alpha-2-glycoprotein 1, zinc-binding F-box protein 24 myosin light chain 2, precursor lymphocyte-specific PERQ amino acid rich, with GYF domain 1 claudin 15 cytochrome P450, family 3, subfamily A, polypeptide 43 galactose-3-O-sulfotransferase 4 thyroid hormone receptor interactor 6 EMI domain containing 2 chromosome 7 open reading frame 51 mucin 17, cell surface associated procollagen C-endopeptidase enhancer CD36 molecule (thrombospondin receptor) hepatocyte growth factor (hepapoietin A; scatter factor) sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E calcium channel, voltage-dependent, alpha 2/delta subunit 1 sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C zinc finger protein 479 zinc finger protein 107 zinc finger protein 138 zinc finger protein 680 coiled-coil-helix-coiled-coil-helix domain containing 2 sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E glutamate receptor, metabotropic 3 calcium channel, voltage-dependent, alpha 2/delta subunit 1 cut-like 1, CCAAT displacement protein (Drosophila) SH2B adaptor protein 2 myosin light chain 2, precursor lymphocyte-specific EMI domain containing 2 indoleamine-pyrrole 2,3 dioxygenase chromosome 8 open reading frame 4 phosphatidic acid phosphatase type 2 domain containing 1B TM2 domain containing 2 eukaryotic translation initiation factor 4E binding protein 1 ADAM metallopeptidase domain 9 (meltrin gamma) LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)

7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8 8

SUM52

ASH2L

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

BRF2 DDHD2 WHSC1L1 PROSC FKSG2 HTRA4 ERLIN2 BAG4 LETM2 STAR ZMAT4 GOT1L1 RAB11FIP1 GPR124 ZNF703 SFRP1 ADRB3 ADAM32

SUM52 SUM52 SUM52

PLEKHA2 TACC1 UNC5D


FGFR1 ADAM18 ADAM2 C8orf41 FUT10 RBM13 RNF122 FKSG2 WRN DUSP26 NRG1 UNC5D LY6E PYCRL LYNX1 PSCA C8orf30A C8orf55

SUM52

GPAA1

ash2 (absent, small, or homeotic)-like (Drosophila) BRF2, subunit of RNA polymerase III transcription initiation factor, BRF1-like DDHD domain containing 2 Wolf-Hirschhorn syndrome candidate 1-like 1 proline synthetase co-transcribed homolog (bacterial) apoptosis inhibitor HtrA serine peptidase 4 ER lipid raft associated 2 BCL2-associated athanogene 4 leucine zipper-EF-hand containing transmembrane protein 2 steroidogenic acute regulatory protein zinc finger, matrin type 4 glutamic-oxaloacetic transaminase 1-like 1 RAB11 family interacting protein 1 (class I) G protein-coupled receptor 124 zinc finger protein 703 secreted frizzled-related protein 1 adrenergic, beta-3-, receptor ADAM metallopeptidase domain 32 pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 2 transforming, acidic coiled-coil containing protein 1 unc-5 homolog D (C. elegans) fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2, Pfeiffer syndrome) ADAM metallopeptidase domain 18 ADAM metallopeptidase domain 2 (fertilin beta) chromosome 8 open reading frame 41 fucosyltransferase 10 (alpha (1,3) fucosyltransferase) RNA binding motif protein 13 ring finger protein 122 apoptosis inhibitor Werner syndrome dual specificity phosphatase 26 (putative) neuregulin 1 unc-5 homolog D (C. elegans) lymphocyte antigen 6 complex, locus E pyrroline-5-carboxylate reductase-like Ly6/neurotoxin 1 prostate stem cell antigen chromosome 8 open reading frame 30A chromosome 8 open reading frame 55 glycosylphosphatidylinositol anchor attachment protein 1 homolog (yeast)

8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8


LY6K GPT EPPK1 PPP1R16A


MAFA HSF1 CYHR1 TSTA3 DGAT1 CPSF1

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

EEF1D ZC3H3 ZFP41 SLC39A4 MAF1 ZNF707 JRK ARC EXOSC4 VPS28 TIGD5 C8orf31 CYC1 MAPK15


NFKBIL2 LY6H LY6D TOP1MT KIFC2 NAPRT1

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

GRINA KIAA1833 OPLAH PUF60 BOP1 SLURP1 RHPN1 GPR172A CYP11B1 FAM83H GML

lymphocyte antigen 6 complex, locus K glutamic-pyruvate transaminase (alanine aminotransferase) epiplakin 1 protein phosphatase 1, regulatory (inhibitor) subunit 16A v-maf musculoaponeurotic fibrosarcoma oncogene homolog A (avian) heat shock transcription factor 1 cysteine/histidine-rich 1 tissue specific transplantation antigen P35B diacylglycerol O-acyltransferase homolog 1 (mouse) cleavage and polyadenylation specific factor 1, 160kDa eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein) zinc finger CCCH-type containing 3 zinc finger protein 41 homolog (mouse) solute carrier family 39 (zinc transporter), member 4 MAF1 homolog (S. cerevisiae) zinc finger protein 707 jerky homolog (mouse) activity-regulated cytoskeleton-associated protein exosome component 4 vacuolar protein sorting 28 homolog (S. cerevisiae) tigger transposable element derived 5 chromosome 8 open reading frame 31 cytochrome c-1 mitogen-activated protein kinase 15 nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2 lymphocyte antigen 6 complex, locus H lymphocyte antigen 6 complex, locus D topoisomerase (DNA) I, mitochondrial kinesin family member C2 nicotinate phosphoribosyltransferase domain containing 1 glutamate receptor, ionotropic, N-methyl D-asparateassociated protein 1 (glutamate binding) hypothetical protein KIAA1833 5-oxoprolinase (ATP-hydrolysing) poly-U binding splicing factor 60KDa block of proliferation 1 secreted LY6/PLAUR domain containing 1 rhophilin, Rho GTPase binding protein 1 G protein-coupled receptor 172A cytochrome P450, family 11, subfamily B, polypeptide 1 family with sequence similarity 83, member H GPI anchored molecule like protein

8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

PLEC1 SCRT1 LYPD2 FBXL6 ZNF696 ZNF623 CYP11B2 NRBP2 LOC338328 ADCK5 SCRIB PARP10 GSDMDC1 FOXH1 GLI4 CEBPD MYST3 RNF170 VDAC3 THAP1 GOLGA7

8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8

AGPAT6 PLAT POLB C8orf40 FNTA

plectin 1, intermediate filament binding protein 500kDa scratch homolog 1, zinc finger protein (Drosophila) LY6/PLAUR domain containing 2 F-box and leucine-rich repeat protein 6 zinc finger protein 696 zinc finger protein 623 cytochrome P450, family 11, subfamily B, polypeptide 2 nuclear receptor binding protein 2 high density lipoprotein-binding protein aarF domain containing kinase 5 scribbled homolog (Drosophila) poly (ADP-ribose) polymerase family, member 10 gasdermin domain containing 1 forkhead box H1 GLI-Kruppel family member GLI4 CCAAT/enhancer binding protein (C/EBP), delta MYST histone acetyltransferase (monocytic leukemia) 3 ring finger protein 170 voltage-dependent anion channel 3 THAP domain containing, apoptosis associated protein 1 golgi autoantigen, golgin subfamily a, 7 inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta GINS complex subunit 4 (Sld5 homolog) solute carrier family 20 (phosphate transporter), member 2 adaptor-related protein complex 3, mu 2 subunit heparan-alpha-glucosaminide N-acetyltransferase 1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta) plasminogen activator, tissue polymerase (DNA directed), beta chromosome 8 open reading frame 40 farnesyltransferase, CAAX box, alpha


IKBKB GINS4 SLC20A2 AP3M2 HGSNAT

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

ZMAT4 FLJ23356 ANK1 HOOK3 CHRNA6 CHRNB3 SFRP1 DKK4 IKZF5 C10orf88 PSTK ACADSB

zinc finger, matrin type 4 hypothetical protein FLJ23356 ankyrin 1, erythrocytic hook homolog 3 (Drosophila) cholinergic receptor, nicotinic, alpha 6 cholinergic receptor, nicotinic, beta 3 secreted frizzled-related protein 1 dickkopf homolog 4 (Xenopus laevis) IKAROS family zinc finger 5 (Pegasus) chromosome 10 open reading frame 88 phosphoseryl-tRNA kinase acyl-Coenzyme A dehydrogenase, short/branched chain

8 8 8 8 8 8 8 8 10 10 10 10

8 8 8 8 8 8 8 8 8 8


FAM24B CUZD1 FAM24A HMX2 DMBT1 NHLRC2 DCLRE1A CASP7 C10orf81 C10orf118 NRAP ADRB1 ODZ4


PRKRIR C11orf30 UVRAG USP35 CLNS1A

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

ALG8 RSF1 INTS4 PHCA NARS2 THRSP TSKU


NDUFC2 RPS3 C11orf67 PAK1


GDPD5 GAB2 DGAT2 MOGAT2 ARRB1


B3GNT6 OMP FLJ33790 WNT11 MYO7A AQP11

family with sequence similarity 24, member B CUB and zona pellucida-like domains 1 family with sequence similarity 24, member A H6 family homeobox 2 deleted in malignant brain tumors 1 NHL repeat containing 2 DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae) caspase 7, apoptosis-related cysteine peptidase chromosome 10 open reading frame 81 chromosome 10 open reading frame 118 nebulin-related anchoring protein adrenergic, beta-1-, receptor odz, odd Oz/ten-m homolog 4 (Drosophila) protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor) chromosome 11 open reading frame 30 UV radiation resistance associated gene ubiquitin specific peptidase 35 chloride channel, nucleotide-sensitive, 1A asparagine-linked glycosylation 8 homolog (S. cerevisiae, alpha-1,3-glucosyltransferase) remodeling and spacing factor 1 integrator complex subunit 4 phytoceramidase, alkaline asparaginyl-tRNA synthetase 2, mitochondrial (putative) thyroid hormone responsive (SPOT14 homolog, rat) tsukushin NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2, 14.5kDa ribosomal protein S3 chromosome 11 open reading frame 67 p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast) glycerophosphodiester phosphodiesterase domain containing 5 GRB2-associated binding protein 2 diacylglycerol O-acyltransferase homolog 2 (mouse) monoacylglycerol O-acyltransferase 2 arrestin, beta 1 UDP-GlcNAc:betaGal beta-1,3-Nacetylglucosaminyltransferase 6 (core 3 synthase) olfactory marker protein hypothetical protein FLJ33790 wingless-type MMTV integration site family, member 11 myosin VIIA aquaporin 11

10 10 10 10 10 10 10 10 10 10 10 10 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

SUM52

GDPD4


SERPINH1 KCTD21 MAP6 LRRC32 MGC33846 CAPN5 C12orf29 WDR51B TMTC3 CEP290 DUSP6

SUM52 SUM52 SUM52

GALNT4 KITLG ATP2B1


MGAT4C C12orf50 C12orf12 CCT2

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

MDM1 LGR5 SLC35E3 NUP107 LEMD3 CCDC131 YEATS4 FRS2 CAND1 TMBIM4 TBC1D15 LYZ RAB3IP C12orf31 GLIPR1L2 PHLDA1


DYRK2 RAP1B CNOT2 PTPRR MSRB3

glycerophosphodiester phosphodiesterase domain containing 4 serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1) potassium channel tetramerisation domain containing 21 microtubule-associated protein 6 leucine rich repeat containing 32 hypothetical protein MGC33846 calpain 5 chromosome 12 open reading frame 29 WD repeat domain 51B transmembrane and tetratricopeptide repeat containing 3 centrosomal protein 290kDa dual specificity phosphatase 6 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4) KIT ligand ATPase, Ca++ transporting, plasma membrane 1 mannosyl (alpha-1,3-)-glycoprotein beta-1,4-Nacetylglucosaminyltransferase, isozyme C (putative) chromosome 12 open reading frame 50 chromosome 12 open reading frame 12 chaperonin containing TCP1, subunit 2 (beta) Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse) leucine-rich repeat-containing G protein-coupled receptor 5 solute carrier family 35, member E3 nucleoporin 107kDa LEM domain containing 3 coiled-coil domain containing 131 YEATS domain containing 4 fibroblast growth factor receptor substrate 2 cullin-associated and neddylation-dissociated 1 transmembrane BAX inhibitor motif containing 4 TBC1 domain family, member 15 lysozyme (renal amyloidosis) RAB3A interacting protein (rabin3) chromosome 12 open reading frame 31 GLI pathogenesis-related 1 like 2 pleckstrin homology-like domain, family A, member 1 dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2 RAP1B, member of RAS oncogene family CCR4-NOT transcription complex, subunit 2 protein tyrosine phosphatase, receptor type, R methionine sulfoxide reductase B3

11 11 11 11 11 11 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12


RASSF3 GNS CPSF6 TMEM19 TBK1

SUM52 SUM52

KCNC2 RAB21

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

KCNMB4 WIF1 IRAK3 IL26 CAPS2 CPM TPH2 IFNG GLIPR1

SUM52 SUM52

MDM2 XPOT

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

KRR1 IL22 HMGA2 THAP2 HELB GLIPR1L1 PTPRB BEST3 TSPAN8 TRHDE RNF111 ADAM10 FAM63B SLTM CCNB2 LIPC ALDH1A2 FAM81A AQP9 MYO1E LDHAL6B CCDC44 PSMC5

Ras association (RalGDS/AF-6) domain family 3 glucosamine (N-acetyl)-6-sulfatase (Sanfilippo disease IIID) cleavage and polyadenylation specific factor 6, 68kDa transmembrane protein 19 TANK-binding kinase 1 potassium voltage-gated channel, Shaw-related subfamily, member 2 RAB21, member RAS oncogene family potassium large conductance calcium-activated channel, subfamily M, beta member 4 WNT inhibitory factor 1 interleukin-1 receptor-associated kinase 3 interleukin 26 calcyphosine 2 carboxypeptidase M tryptophan hydroxylase 2 interferon, gamma GLI pathogenesis-related 1 (glioma) Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) exportin, tRNA (nuclear export receptor for tRNAs) KRR1, small subunit (SSU) processome component, homolog (yeast) interleukin 22 high mobility group AT-hook 2 THAP domain containing, apoptosis associated protein 2 helicase (DNA) B GLI pathogenesis-related 1 like 1 protein tyrosine phosphatase, receptor type, B bestrophin 3 tetraspanin 8 thyrotropin-releasing hormone degrading enzyme ring finger protein 111 ADAM metallopeptidase domain 10 family with sequence similarity 63, member B SAFB-like, transcription modulator cyclin B2 lipase, hepatic aldehyde dehydrogenase 1 family, member A2 family with sequence similarity 81, member A aquaporin 9 myosin IE lactate dehydrogenase A-like 6B coiled-coil domain containing 44 proteasome (prosome, macropain) 26S subunit, ATPase, 5

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 15 15 15 15 15 15 15 15 15 15 15 17 17


FTSJ3 TLK2 BCAS3 CCDC47 POLG2 DDX42

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

SMARCD2 TEX2 BRIP1 CCDC45 WDR68 INTS2 MED13 DDX5 NACA2 TBX2 CYB561 MAP3K3 LIMD2 LYK5 ACE SMURF2 SCN4A GH1 CD79B PECAM1


KCNH6 GH2 CSHL1 CSH2


CSH1 MRC2 LRRC37A3 TBX4 ERN1 10-Mar ICAM2 EFCAB3 ZNF813

SUM52 SUM52

NDUFA3 ZNF331

FtsJ homolog 3 (E. coli) tousled-like kinase 2 breast carcinoma amplified sequence 3 coiled-coil domain containing 47 polymerase (DNA directed), gamma 2, accessory subunit DEAD (Asp-Glu-Ala-Asp) box polypeptide 42 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 testis expressed 2 BRCA1 interacting protein C-terminal helicase 1 coiled-coil domain containing 45 WD repeat domain 68 integrator complex subunit 2 mediator complex subunit 13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 nascent polypeptide-associated complex alpha subunit 2 T-box 2 cytochrome b-561 mitogen-activated protein kinase kinase kinase 3 LIM domain containing 2 protein kinase LYK5 angiotensin I converting enzyme (peptidyl-dipeptidase A) 1 SMAD specific E3 ubiquitin protein ligase 2 sodium channel, voltage-gated, type IV, alpha subunit growth hormone 1 CD79b molecule, immunoglobulin-associated beta platelet/endothelial cell adhesion molecule (CD31 antigen) potassium voltage-gated channel, subfamily H (eag-related), member 6 growth hormone 2 chorionic somatomammotropin hormone-like 1 chorionic somatomammotropin hormone 2 chorionic somatomammotropin hormone 1 (placental lactogen) mannose receptor, C type 2 leucine rich repeat containing 37, member A3 T-box 4 endoplasmic reticulum to nucleus signaling 1 membrane-associated ring finger (C3HC4) 10 intercellular adhesion molecule 2 EF-hand calcium binding domain 3 zinc finger protein 813 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3, 9kDa zinc finger protein 331

17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 19 19 19

SUM52 SUM52 SUM52

CACNG6 TFPT CACNG8

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

PRPF31 PRKCG OSCAR MYADM CNOT3 NLRP12 BIRC8 CACNG7 ZNF180 SYNGR4

SUM52 SUM52

XRCC1 TMEM145


KDELR1 TRAPPC6A FLJ10781 SNRPD2 ZNF404 ZNF233 LIG1 AP2S1 CARD8 RPL18 SAE1


SLC8A2 SFRS16 ZNF226 IRF2BP1 GEMIN7 ZNF234 DMWD CALM3 SEPW1 RUVBL2 RTN2 LIN7B GYS1 FBXO46 CLPTM1

calcium channel, voltage-dependent, gamma subunit 6 TCF3 (E2A) fusion partner (in childhood Leukemia) calcium channel, voltage-dependent, gamma subunit 8 PRP31 pre-mRNA processing factor 31 homolog (S. cerevisiae) protein kinase C, gamma osteoclast associated, immunoglobulin-like receptor myeloid-associated differentiation marker CCR4-NOT transcription complex, subunit 3 NLR family, pyrin domain containing 12 baculoviral IAP repeat-containing 8 calcium channel, voltage-dependent, gamma subunit 7 zinc finger protein 180 synaptogyrin 4 X-ray repair complementing defective repair in Chinese hamster cells 1 transmembrane protein 145 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1 trafficking protein particle complex 6A hypothetical protein FLJ10781 small nuclear ribonucleoprotein D2 polypeptide 16.5kDa zinc finger protein 404 zinc finger protein 233 ligase I, DNA, ATP-dependent adaptor-related protein complex 2, sigma 1 subunit caspase recruitment domain family, member 8 ribosomal protein L18 SUMO1 activating enzyme subunit 1 solute carrier family 8 (sodium-calcium exchanger), member 2 splicing factor, arginine/serine-rich 16 zinc finger protein 226 interferon regulatory factor 2 binding protein 1 gem (nuclear organelle) associated protein 7 zinc finger protein 234 dystrophia myotonica, WD repeat containing calmodulin 3 (phosphorylase kinase, delta) selenoprotein W, 1 RuvB-like 2 (E. coli) reticulon 2 lin-7 homolog B (C. elegans) glycogen synthase 1 (muscle) F-box protein 46 cleft lip and palate associated transmembrane protein 1

19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19

SUM52 SUM52 SUM52

DMPK TMEM160 ZNF225

SUM52 SUM52 SUM52

PPFIA3 EXOC3L2 ZNF45


PSCD2 EMP3 CNFN ZNF224 PPP1R15A


PLA2G4C SYMPK CCDC9 STRN4 KIAA1183


ERCC1 ZNF223 NUCB1 LYPD5 CCDC8 PVRL2 GLTSCR2 CIC ZNF284


KCNJ14 ZNF575 ZNF230 ZNF227 APOC1 BCL3 DBP FTL GRWD1


SULT2A1 ZNF235 CCDC114 EML2 LYPD3

dystrophia myotonica-protein kinase transmembrane protein 160 zinc finger protein 225 protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3 exocyst complex component 3-like 2 zinc finger protein 45 pleckstrin homology, Sec7 and coiled-coil domains 2 (cytohesin-2) epithelial membrane protein 3 cornifelin zinc finger protein 224 protein phosphatase 1, regulatory (inhibitor) subunit 15A phospholipase A2, group IVC (cytosolic, calciumindependent) symplekin coiled-coil domain containing 9 striatin, calmodulin binding protein 4 KIAA1183 protein excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence) zinc finger protein 223 nucleobindin 1 LY6/PLAUR domain containing 5 coiled-coil domain containing 8 poliovirus receptor-related 2 (herpesvirus entry mediator B) glioma tumor suppressor candidate region gene 2 capicua homolog (Drosophila) zinc finger protein 284 potassium inwardly-rectifying channel, subfamily J, member 14 zinc finger protein 575 zinc finger protein 230 zinc finger protein 227 apolipoprotein C-I B-cell CLL/lymphoma 3 D site of albumin promoter (albumin D-box) binding protein ferritin, light polypeptide glutamate-rich WD repeat containing 1 sulfotransferase family, cytosolic, 2A, dehydroepiandrosterone (DHEA)-preferring, member 1 zinc finger protein 235 coiled-coil domain containing 114 echinoderm microtubule associated protein like 2 LY6/PLAUR domain containing 3

19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19

19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19


ZNF155 CGB1 HRC FOXA3 SULT2B1 APOC2 FAM83E ELSPBP1 PSG1


PAFAH1B3 LOC126147 CGB GPR77 C19orf7 QPCTL

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

RELB GRLF1 NTF5 FGF21 ZNF576 NAPA C19orf61 PPP1R13L

SUM52 SUM52 SUM52

DACT3 TMEM143 PPP5C


SLC1A5 DHX34 RASIP1 PGLYRP1 FOSB C5AR1 PSG11 NOVA2 GIPR MEIS3

SUM52 SUM52

TOMM40 FLJ10490

SUM52

FUT1

zinc finger protein 155 chorionic gonadotropin, beta polypeptide 1 histidine rich calcium binding protein forkhead box A3 sulfotransferase family, cytosolic, 2B, member 1 apolipoprotein C-II family with sequence similarity 83, member E epididymal sperm binding protein 1 pregnancy specific beta-1-glycoprotein 1 platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit 29kDa hypothetical protein BC018697 chorionic gonadotropin, beta polypeptide G protein-coupled receptor 77 chromosome 19 open reading frame 7 glutaminyl-peptide cyclotransferase-like v-rel reticuloendotheliosis viral oncogene homolog B, nuclear factor of kappa light polypeptide gene enhancer in B-cells 3 (avian) glucocorticoid receptor DNA binding factor 1 neurotrophin 5 (neurotrophin 4/5) fibroblast growth factor 21 zinc finger protein 576 N-ethylmaleimide-sensitive factor attachment protein, alpha chromosome 19 open reading frame 61 protein phosphatase 1, regulatory (inhibitor) subunit 13 like dapper, antagonist of beta-catenin, homolog 3 (Xenopus laevis) transmembrane protein 143 protein phosphatase 5, catalytic subunit solute carrier family 1 (neutral amino acid transporter), member 5 DEAH (Asp-Glu-Ala-His) box polypeptide 34 Ras interacting protein 1 peptidoglycan recognition protein 1 FBJ murine osteosarcoma viral oncogene homolog B complement component 5a receptor 1 pregnancy specific beta-1-glycoprotein 11 neuro-oncological ventral antigen 2 gastric inhibitory polypeptide receptor Meis homeobox 3 translocase of outer mitochondrial membrane 40 homolog (yeast) hypothetical protein FLJ10490 fucosyltransferase 1 (galactoside 2-alpha-Lfucosyltransferase, H blood group)

19 19 19 19 19 19 19 19 19 19 19 19 19 19 19

19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19


CEACAM8 CRX BAX CKM MARK4 ETHE1 ZNF228 ZNF342 GRIN2D

SUM52 SUM52

CEACAM1 PLAUR

SUM52 SUM52 SUM52

KCNA7 EHD2 SLC6A16


ERCC2 SPACA4 APOE TEX101 NPAS1 CD3EAP NKPD1 GNG8

SUM52 SUM52 SUM52

PLEKHA4 CADM4 BCAM


TRPM4 CABP5 PTGIR LHB CGB2 APOC4 KLC3 GLTSCR1 RSHL1 ZNF114 LIPE HIF3A PSG8 ZNF428 SIX5

carcinoembryonic antigen-related cell adhesion molecule 8 cone-rod homeobox BCL2-associated X protein creatine kinase, muscle MAP/microtubule affinity-regulating kinase 4 ethylmalonic encephalopathy 1 zinc finger protein 228 zinc finger protein 342 glutamate receptor, ionotropic, N-methyl D-aspartate 2D carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein) plasminogen activator, urokinase receptor potassium voltage-gated channel, shaker-related subfamily, member 7 EH-domain containing 2 solute carrier family 6, member 16 excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D) sperm acrosome associated 4 apolipoprotein E testis expressed 101 neuronal PAS domain protein 1 CD3e molecule, epsilon associated protein NTPase, KAP family P-loop domain containing 1 guanine nucleotide binding protein (G protein), gamma 8 pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4 cell adhesion molecule 4 basal cell adhesion molecule (Lutheran blood group) transient receptor potential cation channel, subfamily M, member 4 calcium binding protein 5 prostaglandin I2 (prostacyclin) receptor (IP) luteinizing hormone beta polypeptide chorionic gonadotropin, beta polypeptide 2 apolipoprotein C-IV kinesin light chain 3 glioma tumor suppressor candidate region gene 1 radial spokehead-like 1 zinc finger protein 114 lipase, hormone-sensitive hypoxia inducible factor 3, alpha subunit pregnancy specific beta-1-glycoprotein 8 zinc finger protein 428 SIX homeobox 5

19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19


CBLC MEGF8 BBC3 FUT2 VASP UNQ473 PRKD2


OPA3 DHDH PSG6 ZNF283 IRGC LOC339344 PSG5 ZNF221 TPRX1 CA11 CEACAM19 PVR IGFL2


KCNN4 KPTN PSG9 CD177


SNRP70 BCAT2 GPR4 HSD17B14 TULP2 IZUMO1 FKRP

SUM52 SUM52 SUM52

FLJ36070 PSG3 DNAJB1

SUM52

NDUFB7

SUM52 SUM52

EMR2 PTGER1

SUM52

EMR3

Cas-Br-M (murine) ecotropic retroviral transforming sequence c multiple EGF-like-domains 8 BCL2 binding component 3 fucosyltransferase 2 (secretor status included) vasodilator-stimulated phosphoprotein DMC protein kinase D2 optic atrophy 3 (autosomal recessive, with chorea and spastic paraplegia) dihydrodiol dehydrogenase (dimeric) pregnancy specific beta-1-glycoprotein 6 zinc finger protein 283 immunity-related GTPase family, cinema hypothetical protein LOC339344 pregnancy specific beta-1-glycoprotein 5 zinc finger protein 221 tetra-peptide repeat homeobox 1 carbonic anhydrase XI carcinoembryonic antigen-related cell adhesion molecule 19 poliovirus receptor IGF-like family member 2 potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 kaptin (actin binding protein) pregnancy specific beta-1-glycoprotein 9 CD177 molecule small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) branched chain aminotransferase 2, mitochondrial G protein-coupled receptor 4 hydroxysteroid (17-beta) dehydrogenase 14 tubby like protein 2 izumo sperm-egg fusion 1 fukutin related protein likely ortholog of MEF2-activating SAP transcriptional regulator pregnancy specific beta-1-glycoprotein 3 DnaJ (Hsp40) homolog, subfamily B, member 1 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7, 18kDa egf-like module containing, mucin-like, hormone receptorlike 2 prostaglandin E receptor 1 (subtype EP1), 42kDa egf-like module containing, mucin-like, hormone receptorlike 3

19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

GIPC1 DDX39 ZNF333 GPSN2 PKN1 NCR1 SYT5 TNNI3 EPS8L1 FCAR ISOC2 TMC4 TNNT1 TSEN34 TTYH1 ZNF444 LENG4 ZNF579 NLRP7 HSPBP1 ZNF784 RPS9 LAIR1 CDC42EP5 NLRP2 LENG9 TMEM86B PPP1R12C ZNF524 PTPRH

SUM52 SUM52

LILRB3 CNOT3


LILRB4 TMEM190 RDH13 UBE2S ZNF580

SUM52 SUM52 SUM52

LILRB5 IL11 SAPS1

SUM52

KIR2DL1

GIPC PDZ domain containing family, member 1 DEAD (Asp-Glu-Ala-Asp) box polypeptide 39 zinc finger protein 333 glycoprotein, synaptic 2 protein kinase N1 natural cytotoxicity triggering receptor 1 synaptotagmin V troponin I type 3 (cardiac) EPS8-like 1 Fc fragment of IgA, receptor for isochorismatase domain containing 2 transmembrane channel-like 4 troponin T type 1 (skeletal, slow) tRNA splicing endonuclease 34 homolog (S. cerevisiae) tweety homolog 1 (Drosophila) zinc finger protein 444 leukocyte receptor cluster (LRC) member 4 zinc finger protein 579 NLR family, pyrin domain containing 7 hsp70-interacting protein zinc finger protein 784 ribosomal protein S9 leukocyte-associated immunoglobulin-like receptor 1 CDC42 effector protein (Rho GTPase binding) 5 NLR family, pyrin domain containing 2 leukocyte receptor cluster (LRC) member 9 transmembrane protein 86B protein phosphatase 1, regulatory (inhibitor) subunit 12C zinc finger protein 524 protein tyrosine phosphatase, receptor type, H leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3 CCR4-NOT transcription complex, subunit 3 leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4 transmembrane protein 190 retinol dehydrogenase 13 (all-trans/9-cis) ubiquitin-conjugating enzyme E2S zinc finger protein 580 leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5 interleukin 11 SAPS domain family, member 1 killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 1

19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19


LILRA4 U2AF2 NAT14 ZNF581 RPL28

SUM52

KIR3DL3

SUM52 SUM52

KIR2DL4 COX6B2


KIR3DL1 GP6 ZNF787 SUV420H2 NLRP11 ZSCAN5 LENG8 ZNF582 CCDC106

SUM52 SUM52 SUM52

LILRB1 LENG1 ZNF628

SUM52

LILRB2


LILRA3 EPN1 NLRP4 LAIR2 FIZ1 BRSK1 NLRP5 NLRP9 NLRP13 NLRP8 GALP ZNF137 ZNF813 ZNF665 ZNF415 ZNF347 ZNF160 ZNF610

leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4 U2 small nuclear RNA auxiliary factor 2 N-acetyltransferase 14 zinc finger protein 581 ribosomal protein L28 killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 3 killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 4 cytochrome c oxidase subunit VIb polypeptide 2 (testis) killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1 glycoprotein VI (platelet) zinc finger protein 787 suppressor of variegation 4-20 homolog 2 (Drosophila) NLR family, pyrin domain containing 11 zinc finger and SCAN domain containing 5 leukocyte receptor cluster (LRC) member 8 zinc finger protein 582 coiled-coil domain containing 106 leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1 leukocyte receptor cluster (LRC) member 1 zinc finger protein 628 leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2 leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3 epsin 1 NLR family, pyrin domain containing 4 leukocyte-associated immunoglobulin-like receptor 2 FLT3-interacting zinc finger 1 BR serine/threonine kinase 1 NLR family, pyrin domain containing 5 NLR family, pyrin domain containing 9 NLR family, pyrin domain containing 13 NLR family, pyrin domain containing 8 galanin-like peptide precursor zinc finger protein 137 zinc finger protein 813 zinc finger protein 665 zinc finger protein 415 zinc finger protein 347 zinc finger protein 160 zinc finger protein 610

19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19


ZNF600 ZNF320 ZNF83 ZNF528 ZNF28 ZNF468 ZNF808 ZNF480 BIRC8 VN1R2 VN1R4 PEG3 ZNF304 ZNF264 ZNF17 ZIM3 ZNF543 AURKC BC37295_3 USP29 CABLES2 ADRM1 OSBPL2

SUM52

TAF4


SS18L1 LAMA5 RPS21 PSMA7 LSM14B GTPBP5 HRH3


C20orf151 GATA5 SERINC3 ADA


YWHAB C20orf121 STK4 SLPI WISP2 TOMM34

zinc finger protein 600 zinc finger protein 320 zinc finger protein 83 zinc finger protein 528 zinc finger protein 28 zinc finger protein 468 zinc finger protein 808 zinc finger protein 480 baculoviral IAP repeat-containing 8 vomeronasal 1 receptor 2 vomeronasal 1 receptor 4 paternally expressed 3 zinc finger protein 304 zinc finger protein 264 zinc finger protein 17 zinc finger, imprinted 3 zinc finger protein 543 aurora kinase C hypothetical BC37295_3 ubiquitin specific peptidase 29 Cdk5 and Abl enzyme substrate 2 adhesion regulating molecule 1 oxysterol binding protein-like 2 TAF4 RNA polymerase II, TATA box binding protein (TBP)associated factor, 135kDa synovial sarcoma translocation gene on chromosome 18-like 1 laminin, alpha 5 ribosomal protein S21 proteasome (prosome, macropain) subunit, alpha type, 7 LSM14B, SCD6 homolog B (S. cerevisiae) GTP binding protein 5 (putative) histamine receptor H3

19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 20 20 20

chromosome 20 open reading frame 151 GATA binding protein 5 serine incorporator 3 adenosine deaminase tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide chromosome 20 open reading frame 121 serine/threonine kinase 4 secretory leukocyte peptidase inhibitor WNT1 inducible signaling pathway protein 2 translocase of outer mitochondrial membrane 34

20 20 20 20

20 20 20 20 20 20 20 20

20 20 20 20 20 20


KCNS1 KCNK15 RIMS4 MATN4 PKIG SEMG2 PI3


RBPJL SEMG1 SDC4 WFDC12 WFDC5 DIDO1 ARFGAP1 STMN3

SUM52

PCMTD2


SRMS GATA5 C20orf195 TCEA2 YTHDF1 CHRNA4 C20orf11 ZNF512B


TNFRSF6B PRPF6 EEF1A2 BHLHB4 C20orf149 C20orf135 COL9A3 ARFRP1 SOX18 SLC2A4RG GMEB2 OGFR MYT1 LOC198437

SUM52 SUM52

KCNQ2 SAMD10

potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1 potassium channel, subfamily K, member 15 regulating synaptic membrane exocytosis 4 matrilin 4 protein kinase (cAMP-dependent, catalytic) inhibitor gamma semenogelin II peptidase inhibitor 3, skin-derived (SKALP) recombination signal binding protein for immunoglobulin kappa J region-like semenogelin I syndecan 4 WAP four-disulfide core domain 12 WAP four-disulfide core domain 5 death inducer-obliterator 1 ADP-ribosylation factor GTPase activating protein 1 stathmin-like 3 protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2 src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites GATA binding protein 5 chromosome 20 open reading frame 195 transcription elongation factor A (SII), 2 YTH domain family, member 1 cholinergic receptor, nicotinic, alpha 4 chromosome 20 open reading frame 11 zinc finger protein 512B tumor necrosis factor receptor superfamily, member 6b, decoy PRP6 pre-mRNA processing factor 6 homolog (S. cerevisiae) eukaryotic translation elongation factor 1 alpha 2 basic helix-loop-helix domain containing, class B, 4 chromosome 20 open reading frame 149 chromosome 20 open reading frame 135 collagen, type IX, alpha 3 ADP-ribosylation factor related protein 1 SRY (sex determining region Y)-box 18 SLC2A4 regulator glucocorticoid modulatory element binding protein 2 opioid growth factor receptor myelin transcription factor 1 bA299N6.3 potassium voltage-gated channel, KQT-like subfamily, member 2 sterile alpha motif domain containing 10

20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20


PRR17 ZBTB46 C20orf58 C20orf59 PTK6 NPBWR2 UCKL1 RGS19 OPRL1


PRIC285 C20orf20 BIRC7 TCFL5 C20orf200 LIME1 NTSR1 TPD52L2 COL20A1 SLCO4A1 C20orf166 NPEPL1

SUM52 SUM52 SUM52

TFAP2C C20orf106 TH1L


ATP5E SYCP2 RAB22A APCDD1L C20orf177

SUM52 SUM52 SUM52

TAF4 BMP7 TMEPAI


HMG1L1 GNAS CDH26 PPP1R3D


VAPB CTCFL CTSZ PCK1

proline rich 17 zinc finger and BTB domain containing 46 chromosome 20 open reading frame 58 chromosome 20 open reading frame 59 PTK6 protein tyrosine kinase 6 neuropeptides B/W receptor 2 uridine-cytidine kinase 1-like 1 regulator of G-protein signaling 19 opiate receptor-like 1 peroxisomal proliferator-activated receptor A interacting complex 285 chromosome 20 open reading frame 20 baculoviral IAP repeat-containing 7 (livin) transcription factor-like 5 (basic helix-loop-helix) chromosome 20 open reading frame 200 Lck interacting transmembrane adaptor 1 neurotensin receptor 1 (high affinity) tumor protein D52-like 2 collagen, type XX, alpha 1 solute carrier organic anion transporter family, member 4A1 chromosome 20 open reading frame 166 aminopeptidase-like 1 transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) chromosome 20 open reading frame 106 TH1-like (Drosophila) ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit synaptonemal complex protein 2 RAB22A, member RAS oncogene family adenomatosis polyposis coli down-regulated 1-like chromosome 20 open reading frame 177 TAF4 RNA polymerase II, TATA box binding protein (TBP)associated factor, 135kDa bone morphogenetic protein 7 (osteogenic protein 1) transmembrane, prostate androgen induced RNA high-mobility group (nonhistone chromosomal) protein 1-like 1 GNAS complex locus cadherin-like 26 protein phosphatase 1, regulatory (inhibitor) subunit 3D VAMP (vesicle-associated membrane protein)-associated protein B and C CCCTC-binding factor (zinc finger protein)-like cathepsin Z phosphoenolpyruvate carboxykinase 1 (soluble)

20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20


C20orf43 LSM14B RBM38 STX16 SLMO2 TUBB1 CDH4 RAE1 C20orf197 PHACTR3 C20orf85


SPO11 ZBP1 EDN3 SNX21 CD40 PTGIS

SUM52 SUM52 SUM52

SLC12A5 KCNG1 ZNF334


MMP9 ACOT8 UBE2V1 STAU1


ARFGEF2 ZNF313 ZSWIM1 ZSWIM3 TP53RK ELMO2 DNTTIP1

SUM52 SUM52

DBNDD2 SLC35C2

SUM52 SUM52 SUM52

SLC13A3 ADNP CTSA

SUM52 SUM52

KCNB1 NEURL2

chromosome 20 open reading frame 43 LSM14B, SCD6 homolog B (S. cerevisiae) RNA binding motif protein 38 syntaxin 16 slowmo homolog 2 (Drosophila) tubulin, beta 1 cadherin 4, type 1, R-cadherin (retinal) RAE1 RNA export 1 homolog (S. pombe) chromosome 20 open reading frame 197 phosphatase and actin regulator 3 chromosome 20 open reading frame 85 SPO11 meiotic protein covalently bound to DSB homolog (S. cerevisiae) Z-DNA binding protein 1 endothelin 3 sorting nexin family member 21 CD40 molecule, TNF receptor superfamily member 5 prostaglandin I2 (prostacyclin) synthase solute carrier family 12, (potassium-chloride transporter) member 5 potassium voltage-gated channel, subfamily G, member 1 zinc finger protein 334 matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase) acyl-CoA thioesterase 8 ubiquitin-conjugating enzyme E2 variant 1 staufen, RNA binding protein, homolog 1 (Drosophila) ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) zinc finger protein 313 zinc finger, SWIM-type containing 1 zinc finger, SWIM-type containing 3 TP53 regulating kinase engulfment and cell motility 2 deoxynucleotidyltransferase, terminal, interacting protein 1 dysbindin (dystrobrevin binding protein 1) domain containing 2 solute carrier family 35, member C2 solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3 activity-dependent neuroprotector homeobox cathepsin A potassium voltage-gated channel, Shab-related subfamily, member 1 neuralized homolog 2 (Drosophila)

20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20


B4GALT5 CSE1L ZNF335 WFDC3 BCAS4

SUM52 SUM52 SUM52

PREX1 PIGT C20orf175

SUM52 SUM52 SUM52

SLC9A8 SNAI1 CEBPB

SUM52

NFATC2


SLC2A10 C20orf10 UBE2C DDX27 MOCS3 WFDC8 WFDC13 ZNFX1 SPATA2

SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52 SUM52

DPM1 NCOA3 WFDC9 PTPN1 WFDC6 C20orf67 WFDC10B PARD6B WFDC11 C20orf165 PLTP NCOA5 SALL4 ZFP64 ATP9A TNNC2 CDH22

SUM52

RBPJL

UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5 CSE1 chromosome segregation 1-like (yeast) zinc finger protein 335 WAP four-disulfide core domain 3 breast carcinoma amplified sequence 4 phosphatidylinositol 3,4,5-trisphosphate-dependent RAC exchanger 1 phosphatidylinositol glycan anchor biosynthesis, class T chromosome 20 open reading frame 175 solute carrier family 9 (sodium/hydrogen exchanger), member 8 snail homolog 1 (Drosophila) CCAAT/enhancer binding protein (C/EBP), beta nuclear factor of activated T-cells, cytoplasmic, calcineurindependent 2 solute carrier family 2 (facilitated glucose transporter), member 10 chromosome 20 open reading frame 10 ubiquitin-conjugating enzyme E2C DEAD (Asp-Glu-Ala-Asp) box polypeptide 27 molybdenum cofactor synthesis 3 WAP four-disulfide core domain 8 WAP four-disulfide core domain 13 zinc finger, NFX1-type containing 1 spermatogenesis associated 2 dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit nuclear receptor coactivator 3 WAP four-disulfide core domain 9 protein tyrosine phosphatase, non-receptor type 1 WAP four-disulfide core domain 6 chromosome 20 open reading frame 67 WAP four-disulfide core domain 10B par-6 partitioning defective 6 homolog beta (C. elegans) WAP four-disulfide core domain 11 chromosome 20 open reading frame 165 phospholipid transfer protein nuclear receptor coactivator 5 sal-like 4 (Drosophila) zinc finger protein 64 homolog (mouse) ATPase, Class II, type 9A troponin C type 2 (fast) cadherin-like 22 recombination signal binding protein for immunoglobulin kappa J region-like

20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20


SULF2 ZMYND8 SDC4 EYA2


SPINLW1 WFDC10A POLA1 MAGEB6 ARX MAGEB18 MAGEB10 GEMIN8 OFD1 FANCB PRPS2 MOSPD2 TMEM27 GPM6B TRAPPC2 ACE2 TMSB4X PIR BMX


PIGA FRMPD4 RAB9A ASB9 EGFL6 TLR7 GLRA2

SUM52 SUM52 SUM52

FIGF FAM9C ASB11

sulfatase 2 zinc finger, MYND-type containing 8 syndecan 4 eyes absent homolog 2 (Drosophila) serine peptidase inhibitor-like, with Kunitz and WAP domains 1 (eppin) WAP four-disulfide core domain 10A polymerase (DNA directed), alpha 1 melanoma antigen family B, 6 aristaless related homeobox melanoma antigen family B, 18 melanoma antigen family B, 10 gem (nuclear organelle) associated protein 8 oral-facial-digital syndrome 1 Fanconi anemia, complementation group B phosphoribosyl pyrophosphate synthetase 2 motile sperm domain containing 2 transmembrane protein 27 glycoprotein M6B trafficking protein particle complex 2 angiotensin I converting enzyme (peptidyl-dipeptidase A) 2 thymosin, beta 4, X-linked pirin (iron-binding nuclear protein) BMX non-receptor tyrosine kinase phosphatidylinositol glycan anchor biosynthesis, class A (paroxysmal nocturnal hemoglobinuria) FERM and PDZ domain containing 4 RAB9A, member RAS oncogene family ankyrin repeat and SOCS box-containing 9 EGF-like-domain, multiple 6 toll-like receptor 7 glycine receptor, alpha 2 c-fos induced growth factor (vascular endothelial growth factor D) family with sequence similarity 9, member C ankyrin repeat and SOCS box-containing 11

20 20 20 20 20 20 X X X X X X X X X X X X X X X X X X X X X X X X X X X

Supplementary Table S2: SUM-185 cell line copy number amplified genes. Cell line SUM185

Symbol TACC3


FGFR3 CTBP1 MAEA CRIPAK FGFRL1 IDUA MGC21675 KIAA1530 TMEM129 LETM1 SLBP WHSC2 WHSC1 POLN TMEM175 SLC26A1 SPON2 MXD4 RNF212 NAT8L DGKQ CXCL3 CXCL2

SUM185

MTHFD2L


CXCL1 IL8 EPGN ALB ANKRD17

SUM185 SUM185 SUM185

COX18 PF4 AFP


ADAMTS3 RASSF6 CXCL5 AFM

SUM185

CXCL6

Gene name transforming, acidic coiled-coil containing protein 3 fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism) C-terminal binding protein 1 macrophage erythroblast attacher cysteine-rich PAK1 inhibitor fibroblast growth factor receptor-like 1 iduronidase, alpha-Lhypothetical protein MGC21675 KIAA1530 protein transmembrane protein 129 leucine zipper-EF-hand containing transmembrane protein 1 stem-loop (histone) binding protein Wolf-Hirschhorn syndrome candidate 2 Wolf-Hirschhorn syndrome candidate 1 polymerase (DNA directed) nu transmembrane protein 175 solute carrier family 26 (sulfate transporter), member 1 spondin 2, extracellular matrix protein MAX dimerization protein 4 ring finger protein 212 N-acetyltransferase 8-like diacylglycerol kinase, theta 110kDa chemokine (C-X-C motif) ligand 3 chemokine (C-X-C motif) ligand 2 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha) interleukin 8 epithelial mitogen homolog (mouse) albumin ankyrin repeat domain 17 COX18 cytochrome c oxidase assembly homolog (S. cerevisiae) platelet factor 4 (chemokine (C-X-C motif) ligand 4) alpha-fetoprotein ADAM metallopeptidase with thrombospondin type 1 motif, 3 Ras association (RalGDS/AF-6) domain family 6 chemokine (C-X-C motif) ligand 5 afamin chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic protein 2)

Chromosome 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4


PF4V1 PPBP LRAP RIOK2 LNPEP LIX1 RGMB FAM81B C5orf36 MCTP1 ANKRD32 VPS35 GPT2 LOC388272 DNAJA2 SHCBP1 PHKB ORC6L NETO2 ITFG1 MLCK


ABCC12 NLRP5 C19orf18 ZNF444 ZNF530 ZNF71 UBE2S NAT14 ZNF417 ZNF582 SUV420H2 ZNF543 ZNF587 ZNF274 ISOC2 ZNF580 ZSCAN5 ZNF418 ZNF304 FIZ1 VN1R1 ZNF552 ZNF549

platelet factor 4 variant 1 pro-platelet basic protein (chemokine (C-X-C motif) ligand 7) leukocyte-derived arginine aminopeptidase RIO kinase 2 (yeast) leucyl/cystinyl aminopeptidase Lix1 homolog (mouse) RGM domain family, member B family with sequence similarity 81, member B chromosome 5 open reading frame 36 multiple C2 domains, transmembrane 1 ankyrin repeat domain 32 vacuolar protein sorting 35 homolog (S. cerevisiae) glutamic pyruvate transaminase (alanine aminotransferase) 2 similar to RIKEN cDNA 4921524J17 DnaJ (Hsp40) homolog, subfamily A, member 2 SHC SH2-domain binding protein 1 phosphorylase kinase, beta origin recognition complex, subunit 6 like (yeast) neuropilin (NRP) and tolloid (TLL)-like 2 integrin alpha FG-GAP repeat containing 1 MLCK protein ATP-binding cassette, sub-family C (CFTR/MRP), member 12 NLR family, pyrin domain containing 5 chromosome 19 open reading frame 18 zinc finger protein 444 zinc finger protein 530 zinc finger protein 71 ubiquitin-conjugating enzyme E2S N-acetyltransferase 14 zinc finger protein 417 zinc finger protein 582 suppressor of variegation 4-20 homolog 2 (Drosophila) zinc finger protein 543 zinc finger protein 587 zinc finger protein 274 isochorismatase domain containing 2 zinc finger protein 580 zinc finger and SCAN domain containing 5 zinc finger protein 418 zinc finger protein 304 FLT3-interacting zinc finger 1 vomeronasal 1 receptor 1 zinc finger protein 552 zinc finger protein 549

4 4 5 5 5 5 5 5 5 5 5 16 16 16 16 16 16 16 16 16 16 16 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19

SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185

CCDC106 ZNF583 ZNF497 GALP ZNF8 ZNF17 ZNF628 SYT5 ZNF581 ZNF134 ZFP28 ZNF606 U2AF2 ZNF211 ZSCAN4 TNNI3 ZNF524 ZNF551 ZNF329 TMEM190 ZNF671 PPP1R12C ZNF776 ZSCAN22 SAPS1 ZNF667 ZNF416 ZNF419 ZNF264 ZNF784 NLRP11 ZNF787 ZNF256 EPS8L1 AURKC ZNF135 HSPBP1 ZNF579 ZNF471 TMEM86B RPL28


ZIK1 RDH13 BRSK1

coiled-coil domain containing 106 zinc finger protein 583 zinc finger protein 497 galanin-like peptide precursor zinc finger protein 8 zinc finger protein 17 zinc finger protein 628 synaptotagmin V zinc finger protein 581 zinc finger protein 134 zinc finger protein 28 homolog (mouse) zinc finger protein 606 U2 small nuclear RNA auxiliary factor 2 zinc finger protein 211 zinc finger and SCAN domain containing 4 troponin I type 3 (cardiac) zinc finger protein 524 zinc finger protein 551 zinc finger protein 329 transmembrane protein 190 zinc finger protein 671 protein phosphatase 1, regulatory (inhibitor) subunit 12C zinc finger protein 776 zinc finger and SCAN domain containing 22 SAPS domain family, member 1 zinc finger protein 667 zinc finger protein 416 zinc finger protein 419 zinc finger protein 264 zinc finger protein 784 NLR family, pyrin domain containing 11 zinc finger protein 787 zinc finger protein 256 EPS8-like 1 aurora kinase C zinc finger protein 135 hsp70-interacting protein zinc finger protein 579 zinc finger protein 471 transmembrane protein 86B ribosomal protein L28 zinc finger protein interacting with K protein 1 homolog (mouse) retinol dehydrogenase 13 (all-trans/9-cis) BR serine/threonine kinase 1

19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19

SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185

NLRP4 TNNT1 ZNF544 ZIM3 EPN1 ZSCAN1 PEG3 COX6B2 IL11 BC37295_3 PTPRH ZSCAN18 RPS5 NLRP9 NLRP13 NLRP8 USP29 ZNF14 ZNF486 UPF1 ZNF626 ISYNA1 ZNF253 CRLF1 GATAD2A ZNF682 KIAA0892 ZNF93 SF4 KLHL26 ATP13A1 ELL DDX49 COPE SFRS14 NDUFA13 SSBP4 GMIP TRA16 TMEM161A LASS1 RFXANK COMP CILP2 UBA52

NLR family, pyrin domain containing 4 troponin T type 1 (skeletal, slow) zinc finger protein 544 zinc finger, imprinted 3 epsin 1 zinc finger and SCAN domain containing 1 paternally expressed 3 cytochrome c oxidase subunit VIb polypeptide 2 (testis) interleukin 11 hypothetical BC37295_3 protein tyrosine phosphatase, receptor type, H zinc finger and SCAN domain containing 18 ribosomal protein S5 NLR family, pyrin domain containing 9 NLR family, pyrin domain containing 13 NLR family, pyrin domain containing 8 ubiquitin specific peptidase 29 zinc finger protein 14 zinc finger protein 486 UPF1 regulator of nonsense transcripts homolog (yeast) zinc finger protein 626 myo-inositol 1-phosphate synthase A1 zinc finger protein 253 cytokine receptor-like factor 1 GATA zinc finger domain containing 2A zinc finger protein 682 KIAA0892 zinc finger protein 93 splicing factor 4 kelch-like 26 (Drosophila) ATPase type 13A1 elongation factor RNA polymerase II DEAD (Asp-Glu-Ala-Asp) box polypeptide 49 coatomer protein complex, subunit epsilon splicing factor, arginine/serine-rich 14 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13 single stranded DNA binding protein 4 GEM interacting protein TR4 orphan receptor associated protein TRA16 transmembrane protein 161A LAG1 homolog, ceramide synthase 1 regulatory factor X-associated ankyrin-containing protein cartilage oligomeric matrix protein cartilage intermediate layer protein 2 ubiquitin A-52 residue ribosomal protein fusion product 1

19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19


FKBP8 ARMC6 HOMER3 ZNF101 NCAN


EDG4 SLC25A42 FLJ44894 PBX4 TM6SF2 TMEM59L TSSK6 HAPLN4 C19orf50


PRPF31 TFPT CNOT3


NDUFA3 CACNG8 CACNG7 OSCAR CACNG6 ZNF766 ZNF649 ZNF616 ZNF28 ZNF320 ZNF432 ZNF468 ZNF350 ZNF613 ZNF83 ZNF610 ZNF615 ZNF137 CLDND2 ZNF528 ZNF808


PPP2R1A ZNF480 ZNF577 ETFB

FK506 binding protein 8, 38kDa armadillo repeat containing 6 homer homolog 3 (Drosophila) zinc finger protein 101 neurocan endothelial differentiation, lysophosphatidic acid G-proteincoupled receptor, 4 solute carrier family 25, member 42 similar to zinc finger protein 91 pre-B-cell leukemia homeobox 4 transmembrane 6 superfamily member 2 transmembrane protein 59-like testis-specific serine kinase 6 hyaluronan and proteoglycan link protein 4 chromosome 19 open reading frame 50 PRP31 pre-mRNA processing factor 31 homolog (S. cerevisiae) TCF3 (E2A) fusion partner (in childhood Leukemia) CCR4-NOT transcription complex, subunit 3 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3, 9kDa calcium channel, voltage-dependent, gamma subunit 8 calcium channel, voltage-dependent, gamma subunit 7 osteoclast associated, immunoglobulin-like receptor calcium channel, voltage-dependent, gamma subunit 6 zinc finger protein 766 zinc finger protein 649 zinc finger protein 616 zinc finger protein 28 zinc finger protein 320 zinc finger protein 432 zinc finger protein 468 zinc finger protein 350 zinc finger protein 613 zinc finger protein 83 zinc finger protein 610 zinc finger protein 615 zinc finger protein 137 claudin domain containing 2 zinc finger protein 528 zinc finger protein 808 protein phosphatase 2 (formerly 2A), regulatory subunit A , alpha isoform zinc finger protein 480 zinc finger protein 577 electron-transfer-flavoprotein, beta polypeptide

19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19

SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185 SUM185

ZNF175 ZNF600 SIGLEC6 ZNF160 ZNF614 FPR1 FPRL1 NKG7 LIM2 SIGLEC5 FPRL2 FLJ40235 SIGLEC10 SIGLEC8 SIGLEC12 HAS1 PLAGL2 KIF3B TM9SF4 PDRG1 HM13 ASXL1 MYLK2 POFUT1 C20orf112 FKHL18 TPX2 C20orf160 BCL2L1


ID1 HCK COMMD7 REM1 COX4I2 DUSP15 C20orf3 GZF1 ABHD12 NAPB CST5 CST3 ACSS1 ZNF337 NKX2-2 RP4-691N24.1

zinc finger protein 175 zinc finger protein 600 sialic acid binding Ig-like lectin 6 zinc finger protein 160 zinc finger protein 614 formyl peptide receptor 1 formyl peptide receptor-like 1 natural killer cell group 7 sequence lens intrinsic membrane protein 2, 19kDa sialic acid binding Ig-like lectin 5 formyl peptide receptor-like 2 hypothetical protein FLJ40235 sialic acid binding Ig-like lectin 10 sialic acid binding Ig-like lectin 8 sialic acid binding Ig-like lectin 12 hyaluronan synthase 1 pleiomorphic adenoma gene-like 2 kinesin family member 3B transmembrane 9 superfamily protein member 4 p53 and DNA damage regulated 1 histocompatibility (minor) 13 additional sex combs like 1 (Drosophila) myosin light chain kinase 2, skeletal muscle protein O-fucosyltransferase 1 chromosome 20 open reading frame 112 forkhead-like 18 (Drosophila) TPX2, microtubule-associated, homolog (Xenopus laevis) chromosome 20 open reading frame 160 BCL2-like 1 inhibitor of DNA binding 1, dominant negative helix-loophelix protein hemopoietic cell kinase COMM domain containing 7 RAS (RAD and GEM)-like GTP-binding 1 cytochrome c oxidase subunit IV isoform 2 (lung) dual specificity phosphatase 15 chromosome 20 open reading frame 3 GDNF-inducible zinc finger protein 1 abhydrolase domain containing 12 N-ethylmaleimide-sensitive factor attachment protein, beta cystatin D cystatin C (amyloid angiopathy and cerebral hemorrhage) acyl-CoA synthetase short-chain family member 1 zinc finger protein 337 NK2 homeobox 2 KIAA0980 protein

19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20


NXT1 NANP GGTLA4


ENTPD6 THBD C20orf39 GINS1 PYGB FOXA2 VSX1 SSTR4 CST1 CD93 CST2 PAX1 CSTL1 CST11 CST8 CST9L CST9 CST7 DEFB118

NTF2-like export factor 1 N-acetylneuraminic acid phosphatase gamma-glutamyltransferase-like activity 4 ectonucleoside triphosphate diphosphohydrolase 6 (putative function) thrombomodulin chromosome 20 open reading frame 39 GINS complex subunit 1 (Psf1 homolog) phosphorylase, glycogen; brain forkhead box A2 visual system homeobox 1 somatostatin receptor 4 cystatin SN CD93 molecule cystatin SA paired box 1 cystatin-like 1 cystatin 11 cystatin 8 (cystatin-related epididymal specific) cystatin 9-like (mouse) cystatin 9 (testatin) cystatin F (leukocystatin) defensin, beta 118

20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20

Supplementary Table S3: SUM-190 cell line copy number amplified genes. Cell line SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190

Symbol OR10J5 DUSP23 APCS OR10J1 CRP CENPC1 TMPRSS11D UBE1L2 STAP1 GNRHR EPHA5 TMPRSS11A TMPRSS11F EPGN CXCL2 EREG CXCL3

SUM190

MTHFD2L

SUM190 SUM190

COX18 GRSF1


CXCL1 SAS10 MOBKL1A CXCL5


ADAMTS3 ANKRD17 DCK AFP ALB RUFY3 NPFFR2

SUM190 SUM190

SLC4A4 PF4

SUM190

IGJ


CXCL6 CXCL3 RASSF6

Gene name olfactory receptor, family 10, subfamily J, member 5 dual specificity phosphatase 23 amyloid P component, serum olfactory receptor, family 10, subfamily J, member 1 C-reactive protein, pentraxin-related centromere protein C 1 transmembrane protease, serine 11D ubiquitin-activating enzyme E1-like 2 signal transducing adaptor family member 1 gonadotropin-releasing hormone receptor EPH receptor A5 transmembrane protease, serine 11A transmembrane protease, serine 11F epithelial mitogen homolog (mouse) chemokine (C-X-C motif) ligand 2 epiregulin chemokine (C-X-C motif) ligand 3 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like COX18 cytochrome c oxidase assembly homolog (S. cerevisiae) G-rich RNA sequence binding factor 1 chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha) disrupter of silencing 10 MOB1, Mps One Binder kinase activator-like 1A (yeast) chemokine (C-X-C motif) ligand 5 ADAM metallopeptidase with thrombospondin type 1 motif, 3 ankyrin repeat domain 17 deoxycytidine kinase alpha-fetoprotein albumin RUN and FYVE domain containing 3 neuropeptide FF receptor 2 solute carrier family 4, sodium bicarbonate cotransporter, member 4 platelet factor 4 (chemokine (C-X-C motif) ligand 4) immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic protein 2) chemokine (C-X-C motif) ligand 3 Ras association (RalGDS/AF-6) domain family 6

Chromosome 1 1 1 1 1 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4


IL8 AMBN ENAM GC AFM PF4V1


PPBP ASPH CHD7


GGH RAB2A RLBP1L1 FAM77D YTHDF3 BHLHB5


GGH TTPA FAM77D NCALD DPYS

SUM190

OSGIN2


ATP6V0D2 PABPC1 EFCBP1 MATN2 TTC35 RIMS2


ATP6V1C1 RNF19A NPAL2 LAPTM4B UQCRB PGCP SLC26A7 INTS8 PMP2 GDF6 TMEM67 CA3 WWP1 SPAG1

interleukin 8 ameloblastin (enamel matrix protein) enamelin group-specific component (vitamin D binding protein) afamin platelet factor 4 variant 1 pro-platelet basic protein (chemokine (C-X-C motif) ligand 7) aspartate beta-hydroxylase chromodomain helicase DNA binding protein 7 gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase) RAB2A, member RAS oncogene family retinaldehyde binding protein 1-like 1 family with sequence similarity 77, member D YTH domain family, member 3 basic helix-loop-helix domain containing, class B, 5 gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase) tocopherol (alpha) transfer protein family with sequence similarity 77, member D neurocalcin delta dihydropyrimidinase oxidative stress induced growth inhibitor family member 2 ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2 poly(A) binding protein, cytoplasmic 1 EF-hand calcium binding protein 1 matrilin 2 tetratricopeptide repeat domain 35 regulating synaptic membrane exocytosis 2 ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1 ring finger protein 19A NIPA-like domain containing 2 lysosomal associated protein transmembrane 4 beta ubiquinol-cytochrome c reductase binding protein plasma glutamate carboxypeptidase solute carrier family 26, member 7 integrator complex subunit 8 peripheral myelin protein 2 growth differentiation factor 6 transmembrane protein 67 carbonic anhydrase III, muscle specific WW domain containing E3 ubiquitin protein ligase 1 sperm associated antigen 1

4 4 4 4 4 4 4 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8

SUM190 SUM190

RGS22 C8orf37


PPM2C TSPYL5 RPL30


PLEKHF2 OXR1 EIF3E


POLR2K HRSP12 SDC2 GRHL2 COX6C VPS13B ZNF706 RBM35A TM7SF4 KIAA1429 CA13 C8orf47 LRRCC1 OSR2 CHMP4C


POP1 NBN CA1 CA2 ANKRD46 RAD54B PSKH2 MMP16 SNX16 TMEM55A DECR1 ANGPT1 GEM BAALC LRP12 ZFPM2 CPNE3 IMPA1 WDSOF1

regulator of G-protein signaling 22 chromosome 8 open reading frame 37 protein phosphatase 2C, magnesium-dependent, catalytic subunit TSPY-like 5 ribosomal protein L30 pleckstrin homology domain containing, family F (with FYVE domain) member 2 oxidation resistance 1 eukaryotic translation initiation factor 3, subunit E polymerase (RNA) II (DNA directed) polypeptide K, 7.0kDa heat-responsive protein 12 syndecan 2 grainyhead-like 2 (Drosophila) cytochrome c oxidase subunit VIc vacuolar protein sorting 13 homolog B (yeast) zinc finger protein 706 RNA binding motif protein 35A transmembrane 7 superfamily member 4 KIAA1429 carbonic anhydrase XIII chromosome 8 open reading frame 47 leucine rich repeat and coiled-coil domain containing 1 odd-skipped related 2 (Drosophila) chromatin modifying protein 4C processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae) nibrin carbonic anhydrase I carbonic anhydrase II ankyrin repeat domain 46 RAD54 homolog B (S. cerevisiae) protein serine kinase H2 matrix metallopeptidase 16 (membrane-inserted) sorting nexin 16 transmembrane protein 55A 2,4-dienoyl CoA reductase 1, mitochondrial angiopoietin 1 GTP binding protein overexpressed in skeletal muscle brain and acute leukemia, cytoplasmic low density lipoprotein-related protein 12 zinc finger protein, multitype 2 copine III inositol(myo)-1(or 4)-monophosphatase 1 WD repeats and SOF1 domain containing

8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8


CALB1 C8orf38 RIPK2


KCNS2 TP53INP1 UBR5 RBM12B C8orf59


YWHAZ MTERFD1 RRM2B


RUNX1T1 DPY19L4 E2F5

SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190

SLC7A13 TMEM64 MGC39715 WDR21C CTHRC1 OTUD6B SLC25A32 FABP4 CCNE2 RSPO2 MTDH ZFAND1 PTDSS1 STK3 FAM82B FZD6 AZIN1 KLF10 RALYL REXO1L1 CNGB3 CNBD1 CDH17 ODF1 ABRA TMEM74 TRHR DNAJC12

calbindin 1, 28kDa chromosome 8 open reading frame 38 receptor-interacting serine-threonine kinase 2 potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2 tumor protein p53 inducible nuclear protein 1 ubiquitin protein ligase E3 component n-recognin 5 RNA binding motif protein 12B chromosome 8 open reading frame 59 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide MTERF domain containing 1 ribonucleotide reductase M2 B (TP53 inducible) runt-related transcription factor 1; translocated to, 1 (cyclin D-related) dpy-19-like 4 (C. elegans) E2F transcription factor 5, p130-binding solute carrier family 7, (cationic amino acid transporter, y+ system) member 13 transmembrane protein 64 hypothetical protein MGC39715 WD repeat domain 21C collagen triple helix repeat containing 1 OTU domain containing 6B solute carrier family 25, member 32 fatty acid binding protein 4, adipocyte cyclin E2 R-spondin 2 homolog (Xenopus laevis) metadherin zinc finger, AN1-type domain 1 phosphatidylserine synthase 1 serine/threonine kinase 3 (STE20 homolog, yeast) family with sequence similarity 82, member B frizzled homolog 6 (Drosophila) antizyme inhibitor 1 Kruppel-like factor 10 RALY RNA binding protein-like REX1, RNA exonuclease 1 homolog (S. cerevisiae)-like 1 cyclic nucleotide gated channel beta 3 cyclic nucleotide binding domain containing 1 cadherin 17, LI cadherin (liver-intestine) outer dense fiber of sperm tails 1 actin-binding Rho activating protein transmembrane protein 74 thyrotropin-releasing hormone receptor DnaJ (Hsp40) homolog, subfamily C, member 12

8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 10


SIRT1 MYPN HERC4 ATOH7 LRRTM3 PPME1 DKFZP586P0123 POLD3


SPCS2 UCP3 ARRB1 UCP2


P4HA3 CHRDL2 PGM2L1 NEU3

SUM190

SLCO2B1


KCNE3 C11orf30 TSKU PHCA

SUM190 SUM190

PRKRIR LRRC32


B3GNT6 MED19 C11orf31 TXNDC14 ZDHHC5


TIMM10 SLC43A1 CTNND1


CLP1 UBE2L6 RTN4RL2 YPEL4 OR1S2

SUM190

SERPING1

sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae) myopalladin hect domain and RLD 4 atonal homolog 7 (Drosophila) leucine rich repeat transmembrane neuronal 3 protein phosphatase methylesterase 1 hypothetical protein polymerase (DNA-directed), delta 3, accessory subunit signal peptidase complex subunit 2 homolog (S. cerevisiae) uncoupling protein 3 (mitochondrial, proton carrier) arrestin, beta 1 uncoupling protein 2 (mitochondrial, proton carrier) procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III chordin-like 2 phosphoglucomutase 2-like 1 sialidase 3 (membrane sialidase) solute carrier organic anion transporter family, member 2B1 potassium voltage-gated channel, Isk-related family, member 3 chromosome 11 open reading frame 30 tsukushin phytoceramidase, alkaline protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor) leucine rich repeat containing 32 UDP-GlcNAc:betaGal beta-1,3-Nacetylglucosaminyltransferase 6 (core 3 synthase) mediator complex subunit 19 chromosome 11 open reading frame 31 thioredoxin domain containing 14 zinc finger, DHHC-type containing 5 translocase of inner mitochondrial membrane 10 homolog (yeast) solute carrier family 43, member 1 catenin (cadherin-associated protein), delta 1 CLP1, cleavage and polyadenylation factor I subunit, homolog (S. cerevisiae) ubiquitin-conjugating enzyme E2L 6 reticulon 4 receptor-like 2 yippee-like 4 (Drosophila) olfactory receptor, family 1, subfamily S, member 2 serpin peptidase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary)

10 10 10 10 10 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11


LPXN TMEM126A C11orf73 CREBZF TMEM126B EED PICALM SYTL2 DLG2 CCDC83 PRSS23 ME3 CCDC81 CCDC89 ORAOV1


PPFIA1 CCND1 FADD CTTN


MYEOV TPCN2 DHCR7 FGF19 SHANK2

SUM190 SUM190

FGF3 TMEM16A


FGF4 THRSP INTS4


PAK1 C11orf67 CLNS1A

SUM190 SUM190

ALG8 RSF1


NDUFC2 AQP11 KCTD21 C11orf30 WNT11

leupaxin transmembrane protein 126A chromosome 11 open reading frame 73 CREB/ATF bZIP transcription factor transmembrane protein 126B embryonic ectoderm development phosphatidylinositol binding clathrin assembly protein synaptotagmin-like 2 discs, large homolog 2, chapsyn-110 (Drosophila) coiled-coil domain containing 83 protease, serine, 23 malic enzyme 3, NADP(+)-dependent, mitochondrial coiled-coil domain containing 81 coiled-coil domain containing 89 oral cancer overexpressed 1 protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 cyclin D1 Fas (TNFRSF6)-associated via death domain cortactin myeloma overexpressed gene (in a subset of t(11;14) positive multiple myelomas) two pore segment channel 2 7-dehydrocholesterol reductase fibroblast growth factor 19 SH3 and multiple ankyrin repeat domains 2 fibroblast growth factor 3 (murine mammary tumor virus integration site (v-int-2) oncogene homolog) transmembrane protein 16A fibroblast growth factor 4 (heparin secretory transforming protein 1, Kaposi sarcoma oncogene) thyroid hormone responsive (SPOT14 homolog, rat) integrator complex subunit 4 p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast) chromosome 11 open reading frame 67 chloride channel, nucleotide-sensitive, 1A asparagine-linked glycosylation 8 homolog (S. cerevisiae, alpha-1,3-glucosyltransferase) remodeling and spacing factor 1 NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2, 14.5kDa aquaporin 11 potassium channel tetramerisation domain containing 21 chromosome 11 open reading frame 30 wingless-type MMTV integration site family, member 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11

SUM190

UVRAG


PRKRIR C16orf71 NMRAL1 12-Sep ZNF174 MGRN1 HMOX2 ZNF500 ROGDI DNAJA3

SUM190

Magmas


ALG1 BTBD12 FAM100A ZNF205 C16orf5

SUM190 SUM190

ANKS3 DNASE1

SUM190

NUDT16L1


NAGPA UBN1 ZNF213 ZNF200 CREBBP C16orf68 ZNF75A ZNF434 ZNF263 N-PAC OR1F1 TIGD7 VASN TRAP1 CLUAP1 FLJ14154 ZSCAN10 ZNF597 CORO7

UV radiation resistance associated gene protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor) chromosome 16 open reading frame 71 NmrA-like family domain containing 1 septin 12 zinc finger protein 174 mahogunin, ring finger 1 heme oxygenase (decycling) 2 zinc finger protein 500 rogdi homolog (Drosophila) DnaJ (Hsp40) homolog, subfamily A, member 3 mitochondria-associated protein involved in granulocytemacrophage colony-stimulating factor signal transduction asparagine-linked glycosylation 1 homolog (S. cerevisiae, beta-1,4-mannosyltransferase) BTB (POZ) domain containing 12 family with sequence similarity 100, member A zinc finger protein 205 chromosome 16 open reading frame 5 ankyrin repeat and sterile alpha motif domain containing 3 deoxyribonuclease I nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1 N-acetylglucosamine-1-phosphodiester alpha-Nacetylglucosaminidase ubinuclein 1 zinc finger protein 213 zinc finger protein 200 CREB binding protein (Rubinstein-Taybi syndrome) chromosome 16 open reading frame 68 zinc finger protein 75a zinc finger protein 434 zinc finger protein 263 cytokine-like nuclear factor n-pac olfactory receptor, family 1, subfamily F, member 1 tigger transposable element derived 7 vasorin TNF receptor-associated protein 1 clusterin associated protein 1 hypothetical protein FLJ14154 zinc finger and SCAN domain containing 10 zinc finger protein 597 coronin 7

11 11 16 16 16 16 16 16 16 16 16

16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16


PPL MGC45438 ADCY9 A2BP1 GLIS2 NLRC3 OR2C1 FAM86A MEFV ABAT


TFAP4 GOSR1 CPD CRLF3 DKFZP434O047


ERBB2 C17orf37 PERLD1 GRB7 TCAP PNMT

SUM190 SUM190

STARD3 ORMDL3

SUM190

PSMD3


THRA GSDML MED24 NR1D1 GRB7 GSDM1 CSF3 MSL-1 IKZF3 ZPBP2 NBR1 TMEM106A BRCA1 IFI35 RND2 RPL27

SUM190

VAT1

periplakin hypothetical protein MGC45438 adenylate cyclase 9 ataxin 2-binding protein 1 GLIS family zinc finger 2 NLR family, CARD domain containing 3 olfactory receptor, family 2, subfamily C, member 1 family with sequence similarity 86, member A Mediterranean fever 4-aminobutyrate aminotransferase transcription factor AP-4 (activating enhancer binding protein 4) golgi SNAP receptor complex member 1 carboxypeptidase D cytokine receptor-like factor 3 DKFZP434O047 protein v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) chromosome 17 open reading frame 37 per1-like domain containing 1 growth factor receptor-bound protein 7 titin-cap (telethonin) phenylethanolamine N-methyltransferase StAR-related lipid transfer (START) domain containing 3 ORM1-like 3 (S. cerevisiae) proteasome (prosome, macropain) 26S subunit, nonATPase, 3 thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-erb-a) oncogene homolog, avian) gasdermin-like mediator complex subunit 24 nuclear receptor subfamily 1, group D, member 1 growth factor receptor-bound protein 7 gasdermin 1 colony stimulating factor 3 (granulocyte) male-specific lethal-1 homolog IKAROS family zinc finger 3 (Aiolos) zona pellucida binding protein 2 neighbor of BRCA1 gene 1 transmembrane protein 106A breast cancer 1, early onset interferon-induced protein 35 Rho family GTPase 2 ribosomal protein L27 vesicle amine transport protein 1 homolog (T. californica)

16 16 16 16 16 16 16 16 16 16 16 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17

SUM190

ZNF207


PSMD11 CDK5R1 TMEM98 MYO1D CCL2

SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190 SUM190

ACCN1 C17orf75 SPACA3 LGALS9 WSB1 NLK FAM27L FLJ40504 KSR1 NOS2A LIG3 CCT6B RFFL CCL7 CCDC16 CCL8 CCL2 NLE1 RAD51L3 CCL13 UNC45B SLFN5


ACCN1 CCL1 CCL11 FNDC8 AMAC1 KLHL22 ZNF74 SNAP29 MED15 PI4KA LZTR1 THAP7 MGC16703 CRKL DGCR6L

zinc finger protein 207 proteasome (prosome, macropain) 26S subunit, nonATPase, 11 cyclin-dependent kinase 5, regulatory subunit 1 (p35) transmembrane protein 98 myosin ID chemokine (C-C motif) ligand 2 amiloride-sensitive cation channel 1, neuronal (degenerin) chromosome 17 open reading frame 75 sperm acrosome associated 3 lectin, galactoside-binding, soluble, 9 (galectin 9) WD repeat and SOCS box-containing 1 nemo-like kinase family with sequence similarity 27-like hypothetical protein FLJ40504 kinase suppressor of ras 1 nitric oxide synthase 2A (inducible, hepatocytes) ligase III, DNA, ATP-dependent chaperonin containing TCP1, subunit 6B (zeta 2) ring finger and FYVE-like domain containing 1 chemokine (C-C motif) ligand 7 coiled-coil domain containing 16 chemokine (C-C motif) ligand 8 chemokine (C-C motif) ligand 2 notchless homolog 1 (Drosophila) RAD51-like 3 (S. cerevisiae) chemokine (C-C motif) ligand 13 unc-45 homolog B (C. elegans) schlafen family member 5 amiloride-sensitive cation channel 1, neuronal (degenerin) chemokine (C-C motif) ligand 1 chemokine (C-C motif) ligand 11 fibronectin type III domain containing 8 acyl-malonyl condensing enzyme 1 kelch-like 22 (Drosophila) zinc finger protein 74 synaptosomal-associated protein, 29kDa mediator complex subunit 15 phosphatidylinositol 4-kinase, catalytic, alpha leucine-zipper-like transcription regulator 1 THAP domain containing 7 tubulin, alpha pseudogene v-crk sarcoma virus CT10 oncogene homolog (avian)-like DiGeorge syndrome critical region gene 6-like

17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 22 22 22 22 22 22 22 22 22 22

SUM190 SUM190

RTN4R KIAA1666


SERPIND1 SCARF2 AIFM3 MPP1 VBP1 BRCC3 GAB3 CLIC2 F8A1 SPRY3 RAB39B


F8 MTCP1 H2AFB2 DKC1 FUNDC2 TMLHE PLXNB3 ABCD1

SUM190 SUM190

PNCK SRPK3

SUM190

SSR4


SLC6A8 IDH3G L1CAM


MAGEA1 PDZD4 FAM58A TREX2 ATP2B3 BCAP31 UCHL5IP BGN DUSP9

reticulon 4 receptor KIAA1666 protein serpin peptidase inhibitor, clade D (heparin cofactor), member 1 scavenger receptor class F, member 2 apoptosis-inducing factor, mitochondrion-associated, 3 membrane protein, palmitoylated 1, 55kDa von Hippel-Lindau binding protein 1 BRCA1/BRCA2-containing complex, subunit 3 GRB2-associated binding protein 3 chloride intracellular channel 2 coagulation factor VIII-associated (intronic transcript) 1 sprouty homolog 3 (Drosophila) RAB39B, member RAS oncogene family coagulation factor VIII, procoagulant component (hemophilia A) mature T-cell proliferation 1 H2A histone family, member B2 dyskeratosis congenita 1, dyskerin FUN14 domain containing 2 trimethyllysine hydroxylase, epsilon plexin B3 ATP-binding cassette, sub-family D (ALD), member 1 pregnancy upregulated non-ubiquitously expressed CaM kinase SFRS protein kinase 3 signal sequence receptor, delta (translocon-associated protein delta) solute carrier family 6 (neurotransmitter transporter, creatine), member 8 isocitrate dehydrogenase 3 (NAD+) gamma L1 cell adhesion molecule melanoma antigen family A, 1 (directs expression of antigen MZ2-E) PDZ domain containing 4 family with sequence similarity 58, member A three prime repair exonuclease 2 ATPase, Ca++ transporting, plasma membrane 3 B-cell receptor-associated protein 31 UCHL5 interacting protein biglycan dual specificity phosphatase 9

22 22 22 22 22 X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X X

Supplementary Table S4: SUM-225 cell line copy number amplified genes. Cell line SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225

Symbol CXCL5 VDP ART3 SDAD1 SCARB2 C4orf26 BTC ANKRD17

SUM225

G3BP2

SUM225 SUM225

COX18 NUP54


RCHY1 CXCL9 DKFZP564O0823 CXCL10 CXCL11 THAP6 ALB AFP

SUM225 SUM225

CDKL2 EPGN


CXCL6 SHROOM3 IL8


MTHFD2L EREG STBD1 CXCL3

SUM225

PF4

SUM225 SUM225

ASAHL RASSF6

SUM225

CXCL1

SUM225

ADAMTS3

SUM225

AREG

Gene name chemokine (C-X-C motif) ligand 5 vesicle docking protein p115 ADP-ribosyltransferase 3 SDA1 domain containing 1 scavenger receptor class B, member 2 chromosome 4 open reading frame 26 betacellulin ankyrin repeat domain 17 GTPase activating protein (SH3 domain) binding protein 2 COX18 cytochrome c oxidase assembly homolog (S. cerevisiae) nucleoporin 54kDa ring finger and CHY zinc finger domain containing 1 chemokine (C-X-C motif) ligand 9 DKFZP564O0823 protein chemokine (C-X-C motif) ligand 10 chemokine (C-X-C motif) ligand 11 THAP domain containing 6 albumin alpha-fetoprotein cyclin-dependent kinase-like 2 (CDC2-related kinase) epithelial mitogen homolog (mouse) chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic protein 2) shroom family member 3 interleukin 8 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like epiregulin starch binding domain 1 chemokine (C-X-C motif) ligand 3 platelet factor 4 (chemokine (C-X-C motif) ligand 4) N-acylsphingosine amidohydrolase (acid ceramidase)-like Ras association (RalGDS/AF-6) domain family 6 chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha) ADAM metallopeptidase with thrombospondin type 1 motif, 3 amphiregulin (schwannoma-derived growth factor)

Chromosome 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4


CXCL2 11-Sep AFM PF4V1

SUM225

PPBP

SUM225

PPEF2


CYP51A1 CASD1 CCDC132 FAM133B FZD1 SAMD9L ANKIB1 MTERF CDK6 DKFZP564O0523 KRIT1 SAMD9 GATAD1 BET1 PEX1 CALCR SGCE AKAP9

SUM225 SUM225

GNG11 TFPI2


GNGT1 COL1A2 LOC253012 PFTK1 PDK4 PON3 PON2 PON1 SLC25A13


PPP1R9A ASB4 PEG10 DYNC1I1 RAB11FIP1

chemokine (C-X-C motif) ligand 2 septin 11 afamin platelet factor 4 variant 1 pro-platelet basic protein (chemokine (C-X-C motif) ligand 7) protein phosphatase, EF-hand calcium binding domain 2 cytochrome P450, family 51, subfamily A, polypeptide 1 CAS1 domain containing 1 coiled-coil domain containing 132 family with sequence similarity 133, member B frizzled homolog 1 (Drosophila) sterile alpha motif domain containing 9-like ankyrin repeat and IBR domain containing 1 mitochondrial transcription termination factor cyclin-dependent kinase 6 hypothetical protein DKFZp564O0523 KRIT1, ankyrin repeat containing sterile alpha motif domain containing 9 GATA zinc finger domain containing 1 BET1 homolog (S. cerevisiae) peroxisome biogenesis factor 1 calcitonin receptor sarcoglycan, epsilon A kinase (PRKA) anchor protein (yotiao) 9 guanine nucleotide binding protein (G protein), gamma 11 tissue factor pathway inhibitor 2 guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1 collagen, type I, alpha 2 hypothetical protein LOC253012 PFTAIRE protein kinase 1 pyruvate dehydrogenase kinase, isozyme 4 paraoxonase 3 paraoxonase 2 paraoxonase 1 solute carrier family 25, member 13 (citrin) protein phosphatase 1, regulatory (inhibitor) subunit 9A ankyrin repeat and SOCS box-containing 4 paternally expressed 10 dynein, cytoplasmic 1, intermediate chain 1 RAB11 family interacting protein 1 (class I)

4 4 4 4 4 4 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 8

SUM225 SUM225

FKSG2 ERLIN2

SUM225

BRF2


PROSC ZNF703 GPR124 GOT1L1 C8orf4 ZMAT4 INDO ADAM2 EXOSC4 HSF1 PUF60

SUM225

CPSF1

SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225

SLC39A4 KIAA1833 ZNF16 ZNF7 COMMD5 ZNF623 ZNF707 OPLAH C8orf30A ZNF34 PYCRL GPR172A CYHR1 EPPK1 FBXL6 C8orf33 KIAA1688 GLI4 MAF1 LY6E

SUM225

PPP1R16A


EEF1D VPS28 ZNF696 ADCK5

apoptosis inhibitor ER lipid raft associated 2 BRF2, subunit of RNA polymerase III transcription initiation factor, BRF1-like proline synthetase co-transcribed homolog (bacterial) zinc finger protein 703 G protein-coupled receptor 124 glutamic-oxaloacetic transaminase 1-like 1 chromosome 8 open reading frame 4 zinc finger, matrin type 4 indoleamine-pyrrole 2,3 dioxygenase ADAM metallopeptidase domain 2 (fertilin beta) exosome component 4 heat shock transcription factor 1 poly-U binding splicing factor 60KDa cleavage and polyadenylation specific factor 1, 160kDa solute carrier family 39 (zinc transporter), member 4 hypothetical protein KIAA1833 zinc finger protein 16 zinc finger protein 7 COMM domain containing 5 zinc finger protein 623 zinc finger protein 707 5-oxoprolinase (ATP-hydrolysing) chromosome 8 open reading frame 30A zinc finger protein 34 pyrroline-5-carboxylate reductase-like G protein-coupled receptor 172A cysteine/histidine-rich 1 epiplakin 1 F-box and leucine-rich repeat protein 6 chromosome 8 open reading frame 33 KIAA1688 protein GLI-Kruppel family member GLI4 MAF1 homolog (S. cerevisiae) lymphocyte antigen 6 complex, locus E protein phosphatase 1, regulatory (inhibitor) subunit 16A eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein) vacuolar protein sorting 28 homolog (S. cerevisiae) zinc finger protein 696 aarF domain containing kinase 5

8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8


RPL8 CYC1 RHPN1 SCRIB


DGAT1 NRBP2 ZNF250

SUM225

NFKBIL2

SUM225

NAPRT1


GRINA TSTA3 LRRC24 ZFP41 KIFC2


GPAA1 RECQL4 PARP10 FAM83H TOP1MT ZC3H3


CYP11B1 LOC338328 BOP1 LY6H

SUM225 SUM225

PLEC1 TIGD5

SUM225

SCRT1


GPT MFSD3 C8orf31 MAPK15


MAFA FOXH1 GSDMDC1 ZNF251

SUM225

CYP11B2

ribosomal protein L8 cytochrome c-1 rhophilin, Rho GTPase binding protein 1 scribbled homolog (Drosophila) diacylglycerol O-acyltransferase homolog 1 (mouse) nuclear receptor binding protein 2 zinc finger protein 250 nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2 nicotinate phosphoribosyltransferase domain containing 1 glutamate receptor, ionotropic, N-methyl D-asparate-associated protein 1 (glutamate binding) tissue specific transplantation antigen P35B leucine rich repeat containing 24 zinc finger protein 41 homolog (mouse) kinesin family member C2 glycosylphosphatidylinositol anchor attachment protein 1 homolog (yeast) RecQ protein-like 4 poly (ADP-ribose) polymerase family, member 10 family with sequence similarity 83, member H topoisomerase (DNA) I, mitochondrial zinc finger CCCH-type containing 3 cytochrome P450, family 11, subfamily B, polypeptide 1 high density lipoprotein-binding protein block of proliferation 1 lymphocyte antigen 6 complex, locus H plectin 1, intermediate filament binding protein 500kDa tigger transposable element derived 5 scratch homolog 1, zinc finger protein (Drosophila) glutamic-pyruvate transaminase (alanine aminotransferase) major facilitator superfamily domain containing 3 chromosome 8 open reading frame 31 mitogen-activated protein kinase 15 v-maf musculoaponeurotic fibrosarcoma oncogene homolog A (avian) forkhead box H1 gasdermin domain containing 1 zinc finger protein 251 cytochrome P450, family 11, subfamily B, polypeptide 2

8 8 8 8 8 8 8 8 8

8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8


PXMP3 ZFHX4 HNF4G


PKIA WDR21C TMEM65 EIF2C2 LYNX1


TRMT12 SLC26A7 SQLE JRK AZIN1

SUM225

SLC30A8

SUM225

KHDRBS3

SUM225

POLR2K


ATP6V1C1 RNF139 TTC35 DERL1


EBAG9 DPYS WDSOF1


SNTB1 FBXO32 FAM91A1


YWHAZ ZNF572 LY6D RNF19A DEPDC6 C8orf37 ZHX1 SLC45A4 KIAA0143 ADCY8

peroxisomal membrane protein 3, 35kDa (Zellweger syndrome) zinc finger homeobox 4 hepatocyte nuclear factor 4, gamma protein kinase (cAMP-dependent, catalytic) inhibitor alpha WD repeat domain 21C transmembrane protein 65 eukaryotic translation initiation factor 2C, 2 Ly6/neurotoxin 1 tRNA methyltransferase 12 homolog (S. cerevisiae) solute carrier family 26, member 7 squalene epoxidase jerky homolog (mouse) antizyme inhibitor 1 solute carrier family 30 (zinc transporter), member 8 KH domain containing, RNA binding, signal transduction associated 3 polymerase (RNA) II (DNA directed) polypeptide K, 7.0kDa ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1 ring finger protein 139 tetratricopeptide repeat domain 35 Der1-like domain family, member 1 estrogen receptor binding site associated, antigen, 9 dihydropyrimidinase WD repeats and SOF1 domain containing syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1) F-box protein 32 family with sequence similarity 91, member A1 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide zinc finger protein 572 lymphocyte antigen 6 complex, locus D ring finger protein 19A DEP domain containing 6 chromosome 8 open reading frame 37 zinc fingers and homeoboxes 1 solute carrier family 45, member 4 KIAA0143 protein adenylate cyclase 8 (brain)

8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8

8 8 8 8 8 8 8 8 8 8


HAS2 C8orf53 ANGPT1 TRIB1


NSMCE2 TMEM67 TSPYL5 INTS8 RAD21 ZNF706 C8orf76 ANXA13 RIMS2 STK3 FAM49B PTP4A3 KLF10 PABPC1 PHF20L1 ZFAT1 PTK2 TSNARE1

SUM225

TAF2


WWP1 RPL30 ARC NDRG1

SUM225

UBR5


PPM2C OSR2 OTUD6B NIBP NPAL2

SUM225

TNFRSF11B


RUNX1T1 CHRAC1 COL22A1 MRPL13

SUM225

NDUFB9

hyaluronan synthase 2 chromosome 8 open reading frame 53 angiopoietin 1 tribbles homolog 1 (Drosophila) non-SMC element 2, MMS21 homolog (S. cerevisiae) transmembrane protein 67 TSPY-like 5 integrator complex subunit 8 RAD21 homolog (S. pombe) zinc finger protein 706 chromosome 8 open reading frame 76 annexin A13 regulating synaptic membrane exocytosis 2 serine/threonine kinase 3 (STE20 homolog, yeast) family with sequence similarity 49, member B protein tyrosine phosphatase type IVA, member 3 Kruppel-like factor 10 poly(A) binding protein, cytoplasmic 1 PHD finger protein 20-like 1 ZFAT zinc finger 1 PTK2 protein tyrosine kinase 2 t-SNARE domain containing 1 TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa WW domain containing E3 ubiquitin protein ligase 1 ribosomal protein L30 activity-regulated cytoskeleton-associated protein N-myc downstream regulated gene 1 ubiquitin protein ligase E3 component n-recognin 5 protein phosphatase 2C, magnesium-dependent, catalytic subunit odd-skipped related 2 (Drosophila) OTU domain containing 6B NIK and IKK{beta} binding protein NIPA-like domain containing 2 tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) runt-related transcription factor 1; translocated to, 1 (cyclin D-related) chromatin accessibility complex 1 collagen, type XXII, alpha 1 mitochondrial ribosomal protein L13 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9, 22kDa

8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8


LOC441376 FAM84B KIAA1429


DDEF1 GDF6 ANKRD46 MTERFD1


KCNQ3 PGCP (2X) RIPK2 RBM12B

SUM225

EIF3E

SUM225

LAPTM4B

SUM225 SUM225

MLZE UQCRB


EIF3H RGS22 C8orf47 FLJ43860 CCNE2 SPAG1 C8orf55 MMP16 LY6K


PLEKHF2 ATAD2 EFCBP1 TG SLA DENND3 PSCA KIAA0196 NUDCD1 COL14A1 FZD6


SLC7A13 SLC25A32 ST3GAL1 OXR1

AARD protein family with sequence similarity 84, member B KIAA1429 development and differentiation enhancing factor 1 growth differentiation factor 6 ankyrin repeat domain 46 MTERF domain containing 1 potassium voltage-gated channel, KQT-like subfamily, member 3 plasma glutamate carboxypeptidase receptor-interacting serine-threonine kinase 2 RNA binding motif protein 12B eukaryotic translation initiation factor 3, subunit E lysosomal associated protein transmembrane 4 beta melanoma-derived leucine zipper, extra-nuclear factor ubiquinol-cytochrome c reductase binding protein eukaryotic translation initiation factor 3, subunit H regulator of G-protein signaling 22 chromosome 8 open reading frame 47 FLJ43860 protein cyclin E2 sperm associated antigen 1 chromosome 8 open reading frame 55 matrix metallopeptidase 16 (membrane-inserted) lymphocyte antigen 6 complex, locus K pleckstrin homology domain containing, family F (with FYVE domain) member 2 ATPase family, AAA domain containing 2 EF-hand calcium binding protein 1 thyroglobulin Src-like-adaptor DENN/MADD domain containing 3 prostate stem cell antigen KIAA0196 NudC domain containing 1 collagen, type XIV, alpha 1 (undulin) frizzled homolog 6 (Drosophila) solute carrier family 7, (cationic amino acid transporter, y+ system) member 13 solute carrier family 25, member 32 ST3 beta-galactoside alpha-2,3-sialyltransferase 1 oxidation resistance 1

8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8


TMEM55A NBN CPNE3 SDC2 TMEM71 C8orf38


ATP6V0D2 GRHL2 C8orf32 ZFPM2 TP53INP1 SLURP1 ZHX2 BAALC DPY19L4 COX6C WDR67 KCNK9 WISP1 GOLSYN HRSP12 PTDSS1 MGC39715 VPS13B EXT1

SUM225

MTBP


OSGIN2 MAL2 RAD54B NOV MTSS1 CTHRC1 GPR20 CSMD3 TM7SF4 MATN2 ENY2 GML FAM83A

SUM225

ENPP2

SUM225

PKHD1L1

transmembrane protein 55A nibrin copine III syndecan 2 transmembrane protein 71 chromosome 8 open reading frame 38 ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2 grainyhead-like 2 (Drosophila) chromosome 8 open reading frame 32 zinc finger protein, multitype 2 tumor protein p53 inducible nuclear protein 1 secreted LY6/PLAUR domain containing 1 zinc fingers and homeoboxes 2 brain and acute leukemia, cytoplasmic dpy-19-like 4 (C. elegans) cytochrome c oxidase subunit VIc WD repeat domain 67 potassium channel, subfamily K, member 9 WNT1 inducible signaling pathway protein 1 Golgi-localized protein heat-responsive protein 12 phosphatidylserine synthase 1 hypothetical protein MGC39715 vacuolar protein sorting 13 homolog B (yeast) exostoses (multiple) 1 Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa oxidative stress induced growth inhibitor family member 2 mal, T-cell differentiation protein 2 RAD54 homolog B (S. cerevisiae) nephroblastoma overexpressed gene metastasis suppressor 1 collagen triple helix repeat containing 1 G protein-coupled receptor 20 CUB and Sushi multiple domains 3 transmembrane 7 superfamily member 4 matrilin 2 enhancer of yellow 2 homolog (Drosophila) GPI anchored molecule like protein family with sequence similarity 83, member A ectonucleotide pyrophosphatase/ phosphodiesterase 2 (autotaxin) polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1

8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8


COLEC10 RBM35A LRRC6 DECR1


MYC LYPD2 FAM82B TATDN1 NCALD


GEM TMEM64 CALB1 TRPS1 RSPO2


DCC1 TMEM74 MED30


POP1 LRP12 MTDH RRM2B BAI1 PSKH2 CNGB3 CNBD1 CDH17


KCNS2 ODF1 ABRA TRHR KCNV1 FAM135B YARS2 DNM1L SYT10


ALG10 FGD4 PKP2 BICD1 ERGIC2

collectin sub-family member 10 (C-type lectin) RNA binding motif protein 35A leucine rich repeat containing 6 2,4-dienoyl CoA reductase 1, mitochondrial v-myc myelocytomatosis viral oncogene homolog (avian) LY6/PLAUR domain containing 2 family with sequence similarity 82, member B TatD DNase domain containing 1 neurocalcin delta GTP binding protein overexpressed in skeletal muscle transmembrane protein 64 calbindin 1, 28kDa trichorhinophalangeal syndrome I R-spondin 2 homolog (Xenopus laevis) defective in sister chromatid cohesion homolog 1 (S. cerevisiae) transmembrane protein 74 mediator complex subunit 30 processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae) low density lipoprotein-related protein 12 metadherin ribonucleotide reductase M2 B (TP53 inducible) brain-specific angiogenesis inhibitor 1 protein serine kinase H2 cyclic nucleotide gated channel beta 3 cyclic nucleotide binding domain containing 1 cadherin 17, LI cadherin (liver-intestine) potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2 outer dense fiber of sperm tails 1 actin-binding Rho activating protein thyrotropin-releasing hormone receptor potassium channel, subfamily V, member 1 family with sequence similarity 135, member B tyrosyl-tRNA synthetase 2, mitochondrial dynamin 1-like synaptotagmin X asparagine-linked glycosylation 10 homolog (yeast, alpha-1,2-glucosyltransferase) FYVE, RhoGEF and PH domain containing 4 plakophilin 2 bicaudal D homolog 1 (Drosophila) ERGIC and golgi 2

8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 12 12 12 12 12 12 12 12

SUM225 SUM225

IPO8 MLSTD1


TMTC1 CCDC91 CX3CL1

SUM225 SUM225

POLR2C DOK4

SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225 SUM225

NUDT21 BRD7 NDRG4 COQ9 NIP30 MMP15 HEATR3 N4BP1 IRX6 NKD1 BBS2 PAPD5 ITFG1 C16orf80 CNOT1 PHKB IRX3 CBLN1 DNAJA2 LONP2 CYLD FLJ10815 CIAPIN1 SIAH1


OGFOD1 NLRC5 ZNF319 NUP93 CCDC102A CHD9


GOT2 TMEM188 CCL17 GPR56

SUM225

HERPUD1

importin 8 male sterility domain containing 1 transmembrane and tetratricopeptide repeat containing 1 coiled-coil domain containing 91 chemokine (C-X3-C motif) ligand 1 polymerase (RNA) II (DNA directed) polypeptide C, 33kDa docking protein 4 nudix (nucleoside diphosphate linked moiety X)type motif 21 bromodomain containing 7 NDRG family member 4 coenzyme Q9 homolog (S. cerevisiae) NEFA-interacting nuclear protein NIP30 matrix metallopeptidase 15 (membrane-inserted) HEAT repeat containing 3 Nedd4 binding protein 1 iroquois homeobox 6 naked cuticle homolog 1 (Drosophila) Bardet-Biedl syndrome 2 PAP associated domain containing 5 integrin alpha FG-GAP repeat containing 1 chromosome 16 open reading frame 80 CCR4-NOT transcription complex, subunit 1 phosphorylase kinase, beta iroquois homeobox 3 cerebellin 1 precursor DnaJ (Hsp40) homolog, subfamily A, member 2 lon peptidase 2, peroxisomal cylindromatosis (turban tumor syndrome) amino acid transporter cytokine induced apoptosis inhibitor 1 seven in absentia homolog 1 (Drosophila) 2-oxoglutarate and iron-dependent oxygenase domain containing 1 NLR family, CARD domain containing 5 zinc finger protein 319 nucleoporin 93kDa coiled-coil domain containing 102A chromodomain helicase DNA binding protein 9 glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2) transmembrane protein 188 chemokine (C-C motif) ligand 17 G protein-coupled receptor 56 homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1

12 12 12 12 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16

SUM225 SUM225

C16orf57 CES7


GPT2 FTO GINS3 KATNB1 LOC388272

SUM225 SUM225

ABCC11 AKTIP


NOD2 IRX5 RBL2 MT1F SALL1 CSNK2A2 MT1M CPNE2 AMFR RPGRIP1L CNGB1 AYTL1 CCDC113 GPR114 KIFC3


MMP2 NETO2 SETD6 CAPNS2 MT3


CES1 TEPP ARL2BP ZNF423 MT2A GPR97 MT1X MT1H ADCY7 MT1A MT1G CETP

chromosome 16 open reading frame 57 carboxylesterase 7 glutamic pyruvate transaminase (alanine aminotransferase) 2 fat mass and obesity associated GINS complex subunit 3 (Psf3 homolog) katanin p80 (WD repeat containing) subunit B 1 similar to RIKEN cDNA 4921524J17 ATP-binding cassette, sub-family C (CFTR/MRP), member 11 AKT interacting protein nucleotide-binding oligomerization domain containing 2 iroquois homeobox 5 retinoblastoma-like 2 (p130) metallothionein 1F sal-like 1 (Drosophila) casein kinase 2, alpha prime polypeptide metallothionein 1M copine II autocrine motility factor receptor RPGRIP1-like cyclic nucleotide gated channel beta 1 acyltransferase like 1 coiled-coil domain containing 113 G protein-coupled receptor 114 kinesin family member C3 matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase) neuropilin (NRP) and tolloid (TLL)-like 2 SET domain containing 6 calpain, small subunit 2 metallothionein 3 carboxylesterase 1 (monocyte/macrophage serine esterase 1) testis/prostate/placenta-expressed protein ADP-ribosylation factor-like 2 binding protein zinc finger protein 423 metallothionein 2A G protein-coupled receptor 97 metallothionein 1X metallothionein 1H adenylate cyclase 7 metallothionein 1A metallothionein 1G cholesteryl ester transfer protein, plasma

16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16

SUM225 SUM225

MT1B CCDC135

SUM225

SLC12A3


GNAO1 MT1E C16orf78 PLLP

SUM225 SUM225

ABCC12 SLIC1


SLC6A2 MT4 CCL22 Klkbl4 CDH8 C16orf70 CENPT PSKH1 HSPC171


WWP2 HSF4 DYNC1LI2


GFOD2 FHOD1 DPEP3

SUM225 SUM225

SMPD3 LOC653319

SUM225

CMTM2


ATP6V0D1 LRRC36 RANBP10

SUM225 SUM225

NOL3 NQO1

SUM225

SLC9A5

SUM225

SLC7A6

SUM225

SNTB2

metallothionein 1B coiled-coil domain containing 135 solute carrier family 12 (sodium/chloride transporters), member 3 guanine nucleotide binding protein (G protein), alpha activating activity polypeptide O metallothionein 1E chromosome 16 open reading frame 78 plasma membrane proteolipid (plasmolipin) ATP-binding cassette, sub-family C (CFTR/MRP), member 12 selectin ligand interactor cytoplasmic-1 solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2 metallothionein 4 chemokine (C-C motif) ligand 22 plasma kallikrein-like protein 4 cadherin 8, type 2 chromosome 16 open reading frame 70 centromere protein T protein serine kinase H1 HSPC171 protein WW domain containing E3 ubiquitin protein ligase 2 heat shock transcription factor 4 dynein, cytoplasmic 1, light intermediate chain 2 glucose-fructose oxidoreductase domain containing 2 formin homology 2 domain containing 1 dipeptidase 3 sphingomyelin phosphodiesterase 3, neutral membrane (neutral sphingomyelinase II) hypothetical protein LOC653319 CKLF-like MARVEL transmembrane domain containing 2 ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1 leucine rich repeat containing 36 RAN binding protein 10 nucleolar protein 3 (apoptosis repressor with CARD domain) NAD(P)H dehydrogenase, quinone 1 solute carrier family 9 (sodium/hydrogen exchanger), member 5 solute carrier family 7 (cationic amino acid transporter, y+ system), member 6 syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2)

16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16

SUM225

GOT2

SUM225

PLEKHG4

SUM225 SUM225

CYB5B HSD11B2

SUM225 SUM225

VPS4A CTCF

SUM225

NFATC3

SUM225 SUM225

CMTM4 LONP2

SUM225

NFAT5


PSMB10 RBM35B DDX28 CDH3 APPBP1 CDH1 COG8 CES2 AGRP CES3 TERF2


RLTPR RRAD PDP2 MGC4655 E2F4 THAP11 CKLF

SUM225 SUM225

CMTM3 TK2


CDH5 EDC4 CIRH1A LYPLA3 FAM96B C16orf48

glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2) pleckstrin homology domain containing, family G (with RhoGef domain) member 4 cytochrome b5 type B (outer mitochondrial membrane) hydroxysteroid (11-beta) dehydrogenase 2 vacuolar protein sorting 4 homolog A (S. cerevisiae) CCCTC-binding factor (zinc finger protein) nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3 CKLF-like MARVEL transmembrane domain containing 4 core-binding factor, beta subunit nuclear factor of activated T-cells 5, tonicityresponsive proteasome (prosome, macropain) subunit, beta type, 10 RNA binding motif protein 35B DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 cadherin 3, type 1, P-cadherin (placental) amyloid beta precursor protein binding protein 1 cadherin 1, type 1, E-cadherin (epithelial) component of oligomeric golgi complex 8 carboxylesterase 2 (intestine, liver) agouti related protein homolog (mouse) carboxylesterase 3 (brain) telomeric repeat binding factor 2 RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein Ras-related associated with diabetes pyruvate dehydrogenase phosphatase isoenzyme 2 hypothetical protein MGC4655 E2F transcription factor 4, p107/p130-binding THAP domain containing 11 chemokine-like factor CKLF-like MARVEL transmembrane domain containing 3 thymidine kinase 2, mitochondrial cadherin 5, type 2, VE-cadherin (vascular epithelium) enhancer of mRNA decapping 4 cirrhosis, autosomal recessive 1A (cirhin) lysophospholipase 3 (lysosomal phospholipase A2) family with sequence similarity 96, member B chromosome 16 open reading frame 48

16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16

SUM225

TMCO7


DUS2L CDH11 NIP7

SUM225

LOC388284


PDPR NUTF2 TSNAXIP1 CDH16 FLJ37464

SUM225 SUM225

CTF8 HAS3

SUM225

TMED6


PARD6A LCAT NRN1L


NOB1 CTRL ZDHHC1 ELMO3 DPEP2


SLC12A4 ACD EXOC3L FAM65A


TPPP3 CDH8 CA7 LRRC29 VPS35 LOC388272 ORC6L MLCK SHCBP1


STARD3 NEUROD2 TCAP

transmembrane and coiled-coil domains 7 dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae) cadherin 11, type 2, OB-cadherin (osteoblast) nuclear import 7 homolog (S. cerevisiae) hypothetical gene supported by BC032064; BC041612 pyruvate dehydrogenase phosphatase regulatory subunit nuclear transport factor 2 translin-associated factor X interacting protein 1 cadherin 16, KSP-cadherin hypothetical protein FLJ37464 chromosome transmission fidelity factor 8 homolog (S. cerevisiae) hyaluronan synthase 3 transmembrane emp24 protein transport domain containing 6 par-6 partitioning defective 6 homolog alpha (C. elegans) lecithin-cholesterol acyltransferase neuritin 1-like NIN1/RPN12 binding protein 1 homolog (S. cerevisiae) chymotrypsin-like zinc finger, DHHC-type containing 1 engulfment and cell motility 3 dipeptidase 2 solute carrier family 12 (potassium/chloride transporters), member 4 adrenocortical dysplasia homolog (mouse) exocyst complex component 3-like family with sequence similarity 65, member A tubulin polymerization-promoting protein family member 3 cadherin 8, type 2 carbonic anhydrase VII leucine rich repeat containing 29 vacuolar protein sorting 35 homolog (S. cerevisiae) similar to RIKEN cDNA 4921524J17 origin recognition complex, subunit 6 like (yeast) MLCK protein SHC SH2-domain binding protein 1 StAR-related lipid transfer (START) domain containing 3 neurogenic differentiation 2 titin-cap (telethonin)

16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 17 17 17

SUM225

C17orf37


ERBB2 PNMT PERLD1 GRB7 IKZF3


PPP1R1B CRKRS ZPBP2 SLC35B1 MYST2 SPOP FAM117A PHB


NGFR ZNF652 NXPH3 PHOSPHO1


ALG12 CRELD2 ZBED4 TRABD


MOV10L1 PIM3 PANX2 BRD1

SUM225

FAM19A5

SUM225

MLC1


EIF4ENIF1 MORC2 RNF185


YWHAH PIK3IP1 SFI1 C22orf30 LIMK2 DEPDC5

chromosome 17 open reading frame 37 v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) phenylethanolamine N-methyltransferase per1-like domain containing 1 growth factor receptor-bound protein 7 IKAROS family zinc finger 3 (Aiolos) protein phosphatase 1, regulatory (inhibitor) subunit 1B (dopamine and cAMP regulated phosphoprotein, DARPP-32) Cdc2-related kinase, arginine/serine-rich zona pellucida binding protein 2 solute carrier family 35, member B1 MYST histone acetyltransferase 2 speckle-type POZ protein family with sequence similarity 117, member A prohibitin nerve growth factor receptor (TNFR superfamily, member 16) zinc finger protein 652 neurexophilin 3 phosphatase, orphan 1 asparagine-linked glycosylation 12 homolog (S. cerevisiae, alpha-1,6-mannosyltransferase) cysteine-rich with EGF-like domains 2 zinc finger, BED-type containing 4 TraB domain containing Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse) pim-3 oncogene pannexin 2 bromodomain containing 1 family with sequence similarity 19 (chemokine (C-C motif)-like), member A5 megalencephalic leukoencephalopathy with subcortical cysts 1 eukaryotic translation initiation factor 4E nuclear import factor 1 MORC family CW-type zinc finger 2 ring finger protein 185 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide phosphoinositide-3-kinase interacting protein 1 Sfi1 homolog, spindle assembly associated (yeast) chromosome 22 open reading frame 30 LIM domain kinase 2 DEP domain containing 5

17

17 17 17 17 17

17 17 17 17 17 17 17 17 17 17 17 17 22 22 22 22 22 22 22 22 22 22 22 22 22

22 22 22 22 22 22


SLC5A1 SMTN PATZ1 SELM DRG1 PISD PLA2G3 C22orf24 OSBP2

solute carrier family 5 (sodium/glucose cotransporter), member 1 smoothelin POZ (BTB) and AT hook containing zinc finger 1 selenoprotein M developmentally regulated GTP binding protein 1 phosphatidylserine decarboxylase phospholipase A2, group III chromosome 22 open reading frame 24 oxysterol binding protein 2

Supplementary Table S5: SUM-52 cell line shRNA screen results




22 22 22 22 22 22 22 22 22