Supplementary Table S1: Amplification Scores and Average Expression Scores for All Paired Samples Based on the TCGA Copy Number Data and Gene Expression Data

Supplementary Table S1: Amplification scores and average expression scores for all paired samples based on the TCGA copy number data and gene expression data

Sample Amplification Scores Average expression scores TCGA-46-3768-01A-01D-1519-02 2.045246981 0.672389419 TCGA-60-2722-01A-01D-0847-02 1.916644908 0.785999602 TCGA-60-2711-01A-01D-0847-02 1.523310153 0.766122929 TCGA-18-3412-01A-01D-1519-02 1.472280991 0.349112684 TCGA-34-2600-01A-01D-0847-02 1.370236474 0.343048213 TCGA-43-3394-01A-01D-1519-02 1.34788017 0.466472433 TCGA-18-3408-01A-01D-1519-02 1.334968882 0.16463217 TCGA-66-2800-01A-01D-1197-02 1.333906029 0.529406238 TCGA-34-5240-01A-01D-1438-02 1.327530436 0.48692157 TCGA-66-2795-01A-02D-1519-02 1.294191556 0.276733412 TCGA-22-4601-01A-01D-1438-02 1.293028928 0.611597034 TCGA-66-2742-01A-01D-1519-02 1.283898207 0.684409253 TCGA-33-4533-01A-01D-1197-02 1.26161948 0.671151814 TCGA-66-2794-01A-01D-1197-02 1.260307276 0.602141435 TCGA-66-2766-01A-01D-0847-02 1.253831174 0.39553029 TCGA-66-2792-01A-01D-1519-02 1.211086939 0.484442252 TCGA-18-3416-01A-01D-1519-02 1.204938576 0.267573392 TCGA-39-5037-01A-01D-1438-02 1.190998509 0.807937473 TCGA-21-1077-01A-01D-0688-02 1.187561162 0.825188811 TCGA-60-2710-01A-01D-0847-02 1.180211422 0.209100556 TCGA-60-2719-01A-01D-0847-02 1.177541443 0.491699962 TCGA-66-2759-01A-01D-0847-02 1.177429217 0.368721757 TCGA-34-2605-01A-01D-0847-02 1.151803931 0.309992646 TCGA-37-4133-01A-01D-1095-02 1.124043658 0.227949298 TCGA-22-4613-01A-01D-1438-02 1.117028447 0.535916581 TCGA-66-2737-01A-01D-1519-02 1.08618485 0.435342819 TCGA-21-1082-01A-01D-0688-02 1.021712611 0.339142166 TCGA-39-5021-01A-01D-1438-02 1.014333233 0.789466366 TCGA-33-4538-01A-01D-1197-02 1.013761423 0.455192731 TCGA-66-2783-01A-01D-1197-02 0.989721647 0.334903399 TCGA-51-4080-01A-01D-1095-02 0.981245697 0.314741489 TCGA-60-2713-01A-01D-0847-02 0.970758043 0.150807621 TCGA-21-1075-01A-01D-0688-02 0.963846495 0.271133341 TCGA-21-1072-01A-01D-0688-02 0.957732985 0.231759062 TCGA-66-2777-01A-01D-1197-02 0.957292967 0.513311125 TCGA-37-4135-01A-01D-1095-02 0.954508329 -0.088024955 TCGA-33-4532-01A-01D-1197-02 0.951439743 0.357429891 TCGA-63-5131-01A-01D-1438-02 0.941558074 0.611089828 TCGA-56-1622-01A-01D-0688-02 0.928625438 0.16117661 TCGA-66-2781-01A-01D-0847-02 0.908899352 0.220157914 TCGA-18-4083-01A-01D-1095-02 0.900456141 0.51774666 TCGA-34-2596-01A-01D-0847-02 0.899849349 0.350543557 TCGA-66-2727-01A-01D-1519-02 0.896139235 0.227232653 TCGA-21-1080-01A-01D-0688-02 0.883820488 0.12757737 TCGA-66-2770-01A-01D-0847-02 0.864222689 0.188760299 TCGA-39-5016-01A-01D-1438-02 0.856049676 0.40902012 TCGA-22-4591-01A-01D-1197-02 0.845532752 0.167368579 TCGA-66-2789-01A-01D-1519-02 0.844945836 0.219508016 TCGA-60-2712-01A-01D-0847-02 0.831263395 -0.100175624 TCGA-66-2791-01A-01D-1519-02 0.822695404 0.270957936 TCGA-63-5128-01A-01D-1438-02 0.813518713 0.24313238 TCGA-22-0944-01A-01D-0688-02 0.813077581 0.188181666 TCGA-22-4599-01A-01D-1438-02 0.809785019 0.203255081 TCGA-60-2698-01A-01D-0847-02 0.8006377 0.145971104 TCGA-46-3765-01A-01D-1519-02 0.76387353 0.19256726 TCGA-66-2758-01A-02D-0847-02 0.763650483 0.002371962 TCGA-21-1081-01A-01D-0688-02 0.762418572 -0.12127097 TCGA-33-4547-01A-01D-1197-02 0.762356628 0.485111894 TCGA-18-4086-01A-01D-1095-02 0.755390399 0.254487814 TCGA-51-4079-01A-01D-1095-02 0.727600537 0.205422245 TCGA-18-3411-01A-01D-1519-02 0.727341166 0.066148262 TCGA-60-2721-01A-01D-0847-02 0.722285959 0.168808612 TCGA-60-2723-01A-01D-0847-02 0.706051674 0.027250343 TCGA-66-2787-01A-01D-1519-02 0.70061763 0.089671013 TCGA-21-1071-01A-01D-0688-02 0.698736726 0.293609389 TCGA-39-5036-01A-01D-1438-02 0.696261172 0.193697305 TCGA-37-3789-01A-01D-1519-02 0.695183514 0.051141565 TCGA-22-4604-01A-01D-1197-02 0.69395205 0.416585747 TCGA-60-2695-01A-01D-0847-02 0.693301615 -0.082173186 TCGA-51-4081-01A-01D-1095-02 0.682521902 0.292386625 TCGA-18-3415-01A-01D-1519-02 0.676499109 0.1055001 TCGA-34-2604-01A-01D-0847-02 0.660094251 0.075599253 TCGA-60-2726-01A-01D-0847-02 0.65348341 0.08292669 TCGA-18-3417-01A-01D-1438-02 0.653276996 -0.044195948 TCGA-43-2578-01A-01D-0847-02 0.652882532 -0.040322814 TCGA-22-4595-01A-01D-1197-02 0.644311222 0.27166572 TCGA-60-2706-01A-01D-0847-02 0.638017605 0.050706174 TCGA-66-2768-01A-01D-0847-02 0.632335379 0.112001139 TCGA-66-2773-01A-01D-1197-02 0.62471198 0.114567332 TCGA-21-1070-01A-01D-0688-02 0.623159974 -0.078337898 TCGA-66-2780-01A-01D-0847-02 0.618105442 0.088393188 TCGA-66-2790-01A-01D-1519-02 0.615031352 0.018449061 TCGA-66-2757-01A-01D-0847-02 0.59263251 -0.118010071 TCGA-43-3920-01A-01D-1519-02 0.582182292 -0.150822369 TCGA-37-4141-01A-02D-1095-02 0.568361359 -0.100575403 TCGA-18-3421-01A-01D-1519-02 0.544960941 -0.212413743 TCGA-21-1079-01A-01D-0688-02 0.531020135 -0.276817077 TCGA-66-2763-01A-01D-0847-02 0.530164153 -0.183602116 TCGA-33-4582-01A-01D-1438-02 0.530046227 0.040314668 TCGA-66-2767-01A-01D-0847-02 0.511023324 0.009755971 TCGA-60-2707-01A-01D-0847-02 0.505327485 -0.163844431 TCGA-21-1076-01A-02D-0688-02 0.496927998 -0.141670876 TCGA-66-2793-01A-01D-1197-02 0.492870413 -0.021887857 TCGA-66-2755-01A-01D-0847-02 0.489218749 -0.21952555 TCGA-21-1076-01A-01D-0688-02 0.488223519 -0.071967552 TCGA-18-3406-01A-01D-1519-02 0.480044094 -0.11149447 TCGA-21-1083-01A-01D-0688-02 0.471358341 -0.184273661 TCGA-22-4607-01A-01D-1197-02 0.470017602 -0.113135269 TCGA-66-2778-01A-02D-0847-02 0.441110914 -0.077639426 TCGA-18-3407-01A-01D-1519-02 0.433642805 -0.064666393 TCGA-39-5035-01A-01D-1438-02 0.418977148 -0.089540098 TCGA-66-2769-01A-02D-0847-02 0.410076533 -0.263637078 TCGA-22-0940-01A-01D-0688-02 0.401604886 -0.11319591 TCGA-37-4132-01A-01D-1095-02 0.388484606 -0.248949888 TCGA-66-2753-01A-01D-1519-02 0.386893799 -0.238185387 TCGA-39-5029-01A-01D-1438-02 0.38395871 -0.244222889 TCGA-37-3792-01A-01D-1519-02 0.370885108 -0.182761258 TCGA-60-2708-01A-01D-0847-02 0.368570112 -0.293652411 TCGA-60-2724-01A-01D-0847-02 0.361855341 -0.066770906 TCGA-18-3414-01A-01D-1519-02 0.360809144 -0.219476071 TCGA-66-2771-01A-01D-1519-02 0.347546946 -0.392850213 TCGA-34-5241-01A-01D-1438-02 0.344685081 -0.187682163 TCGA-46-3766-01A-01D-1519-02 0.343810953 -0.367907727 TCGA-37-3783-01A-01D-1197-02 0.330931739 -0.177123657 TCGA-34-2608-01A-02D-0847-02 0.325608614 -0.31618433 TCGA-60-2725-01A-01D-1197-02 0.321996306 -0.192376957 TCGA-66-2734-01A-01D-1519-02 0.306615869 -0.09399024 TCGA-22-1016-01A-01D-0688-02 0.305048453 -0.391465614 TCGA-22-1002-01A-01D-0688-02 0.303128897 -0.167591967 TCGA-66-2765-01A-01D-0847-02 0.296506385 -0.401217722 TCGA-66-2782-01A-01D-0847-02 0.295203831 -0.288543689 TCGA-66-2756-01A-01D-0847-02 0.281245322 -0.421346359 TCGA-18-3409-01A-01D-1519-02 0.2728122 -0.472839803 TCGA-46-3767-01A-01D-1519-02 0.265199606 -0.318685504 TCGA-18-3410-01A-01D-1519-02 0.2342138 -0.609012511 TCGA-37-4130-01A-01D-1095-02 0.219969359 -0.422997986 TCGA-66-2786-01A-01D-0847-02 0.217717758 -0.372524144 TCGA-39-5030-01A-01D-1438-02 0.208782891 -0.4064781 TCGA-33-4589-01A-01D-1438-02 0.205278309 -0.391176383 TCGA-60-2715-01A-01D-0847-02 0.197450813 -0.302316205 TCGA-66-2744-01A-01D-1519-02 0.171956199 -0.5270376 TCGA-66-2788-01A-01D-1519-02 0.161902479 -0.428088046 TCGA-34-2609-01A-01D-0847-02 0.148441051 -0.490158688 TCGA-60-2714-01A-01D-0847-02 0.12853145 -0.588466681 TCGA-22-1012-01A-01D-0688-02 0.127978327 -0.434537312 TCGA-43-2576-01A-01D-0847-02 0.120382746 -0.592647747 TCGA-22-1011-01A-01D-0688-02 0.116915628 -0.419392048 TCGA-22-1000-01A-01D-0688-02 0.111993679 -0.446323769 TCGA-33-4566-01A-01D-1438-02 0.106779156 -0.546673177 TCGA-60-2720-01A-01D-0847-02 0.073534212 -0.511118337 TCGA-66-2785-01A-01D-0847-02 0.066517276 -0.703912485 TCGA-60-2696-01A-01D-0847-02 0.063369377 -0.479589145 TCGA-22-1005-01A-01D-0688-02 0.047210817 -0.600239724 TCGA-22-4596-01A-01D-1197-02 0.023670756 -0.685480118 TCGA-43-2581-01A-01D-0847-02 0.008924457 -0.58745021 TCGA-39-5034-01A-01D-1438-02 0.005981774 -0.52587251 TCGA-22-1017-01A-01D-0688-02 -0.001155049 -0.736919214 TCGA-39-5011-01A-01D-1438-02 -0.001772498 -0.806844988 TCGA-60-2716-01A-01D-0847-02 -0.027085933 -0.559398488 TCGA-22-4594-01A-01D-1197-02 -0.045296013 -0.749968704 TCGA-21-1078-01A-01D-0688-02 -0.053945928 -0.652716608 TCGA-37-4129-01A-01D-1095-02 -0.317700509 -0.993853911 Table S2: The corr_exp_amp and corr_exp_ave for 164 genes in the 3q26-39 regions corr_exp_amp: correlation between gene expression and amplification score corr_exp_ave: correlation between gene expression and average expression score

GeneSymbol corr_exp_amp corr_exp_ave ZNF639 0.866144975 0.857065482 ACTL6A 0.819469789 0.8188957 DCUN1D1 0.788696586 0.817472827 TBL1XR1 0.773925464 0.801221988 ATP11B 0.769411355 0.807543791 ABCC5 0.759481646 0.792085095 DNAJC19 0.759117715 0.780099287 PIK3CA 0.757790135 0.827591451 POLR2H 0.75478813 0.761675484 ECT2 0.753015249 0.752324975 SENP2 0.748075052 0.837060495 B3GNT5 0.735574483 0.768855134 MAGEF1 0.732929421 0.776221817 ALG3 0.727718205 0.73327114 PARL 0.727687606 0.738720036 SOX2 0.723977764 0.778379681 MRPL47 0.721611684 0.751153302 RFC4 0.721109357 0.705868684 FXR1 0.718918937 0.780988798 MFN1 0.703526801 0.744270006 C3orf21 0.698033065 0.734070763 EIF2B5 0.690662183 0.720118372 PIGX 0.686059227 0.757813408 YEATS2 0.682279813 0.731070469 DLG1 0.675627119 0.743846274 CLCN2 0.673323355 0.689811303 NDUFB5 0.672933795 0.688813483 NCBP2 0.672847232 0.731920267 PSMD2 0.669983623 0.732325204 KLHL24 0.669637358 0.671017909 DVL3 0.669091735 0.698233567 LSG1 0.667620633 0.747446288 FAM131A 0.66332522 0.691146306 WDR53 0.659015576 0.691868452 OPA1 0.656203227 0.750524539 MYNN 0.649755499 0.605014062 RPL35A 0.644342157 0.655383101 TMEM41A 0.641136218 0.6972876 MCCC1 0.636814084 0.649765239 PDCD10 0.634686259 0.64615608 ABCF3 0.634391296 0.699840759 SENP5 0.625239952 0.66480771 PRKCI 0.623067789 0.667236769 PAK2 0.61987218 0.62951721 TFRC 0.609507309 0.63819463 PPP1R2 0.605855367 0.611039255 EIF5A2 0.604706156 0.591498712 FYTTD1 0.60095801 0.690758455 RPL22L1 0.595249588 0.589715442 PHC3 0.58542978 0.629070729 DNAJB11 0.585308261 0.671510548 KCNMB3 0.57663393 0.575195292 PLD1 0.567054319 0.610808072 TP63 0.565766613 0.575298675 KPNA4 0.563651011 0.56597642 EPHB3 0.554305427 0.539621681 SMC4 0.548455771 0.532682017 FGF12 0.5450698 0.571930655 ECE2 0.544375645 0.558580909 FETUB 0.540459544 0.572717829 EHHADH 0.537423829 0.57058428 RNF168 0.536738223 0.54949118 EIF4A2 0.531677362 0.595650599 LRCH3 0.520075998 0.539810278 TRIM59 0.519737696 0.515367109 BDH1 0.519324216 0.537595938 FAM43A 0.51917386 0.530204553 VPS8 0.513214278 0.50935627 TMEM44 0.50058434 0.533690088 PCYT1A 0.495772934 0.529671471 HRG 0.487277797 0.485357336 TTC14 0.48707489 0.501302378 MFI2 0.482801277 0.488169684 C3orf34 0.481055092 0.549781641 RPL39L 0.480296476 0.521975957 MAP6D1 0.477313268 0.441056869 IFT80 0.468746369 0.426831102 NLGN1 0.462872091 0.444829259 EIF4G1 0.462040921 0.524811413 IGF2BP2 0.460944922 0.531397153 TNK2 0.448848065 0.408590135 AP2M1 0.447524286 0.460612139 USP13 0.446415025 0.46342922 LPP 0.435301726 0.509805228 BCL6 0.428743999 0.541657696 NMD3 0.426632905 0.4255189 TBCCD1 0.42093303 0.478557125 HRASLS 0.404060993 0.442323316 GOLIM4 0.397863572 0.446394522 ATP13A3 0.394853027 0.446507289 CRYGS 0.381300446 0.393120511 ATP13A5 0.344804844 0.42466802 B3GALNT1 0.336137426 0.333641166 ZMAT3 0.33442712 0.359464902 CCDC50 0.318641392 0.334649238 C3orf59 0.315929848 0.365134027 LEPREL1 0.298351802 0.365672235 PIGZ 0.294327101 0.334933723 GPR160 0.292962636 0.276368756 AHSG 0.281828701 0.212055693 MDS1 0.280580923 0.30223741 TNFSF10 0.278667013 0.262604396 SERPINI1 0.273772158 0.293304857 SKIL 0.251203281 0.272027679 BCHE 0.247208769 0.307931119 DGKG 0.245207808 0.316996284 KIAA0226 0.244920764 0.326914698 PPM1L 0.242190009 0.217907449 CLDN1 0.241122077 0.317044041 C3orf57 0.209501405 0.218747633 AADACL1 0.177615347 0.185225432 ETV5 0.17248956 0.201860319 MUC20 0.170533947 0.18675884 RTP1 0.17045506 0.211422162 ADIPOQ 0.135409734 0.174572488 SLITRK3 0.119837683 0.165267609 SLC7A14 0.11929083 0.161983545 FNDC3B 0.116522803 0.128042154 SPATA16 0.113877897 0.095626679 LIPH 0.106533464 0.146984775 SST 0.097603607 0.138765419 LAMP3 0.092717484 0.103764026 HTR3D 0.088952904 0.104566051 CLDN16 0.087364209 0.072707826 HTR3E 0.086313198 0.056532351 SI 0.076251205 0.088676112 HES1 0.07505177 0.067930344 IQCG 0.071031566 0.092465935 ZDHHC19 0.070025142 0.047358893 IL1RAP 0.068685719 0.103817952 EVI1 0.061865094 0.104153016 LRRC34 0.058850867 0.096692842 ATP13A4 0.047430735 0.078100105 GHSR 0.046398622 0.053349189 CLDN11 0.044474744 0.066064558 GNB4 0.039084158 0.117279811 SLC2A2 0.021779673 0.093519151 KNG1 0.021721487 0.057732033 THPO 0.014828939 0.042460418 WDR49 0.014642664 0.00456195 CAMK2N2 0.013010978 -0.037370467 TNIK -0.004100629 0.030078117 MAP3K13 -0.00566912 0.023940842 MCF2L2 -0.011163964 -0.009800504 SAMD7 -0.013795201 -0.018654447 KCNMB2 -0.018095782 -0.019589099 OSTN -0.019025245 -0.051039255 SERPINI2 -0.02462428 -0.030826482 PEX5L -0.035716482 0.02916231 RTP4 -0.037688395 -0.029517849 MUC4 -0.058734783 -0.041037119 CPN2 -0.065082171 0.009868857 HTR3C -0.066693378 -0.020487787 CHRD -0.08877016 -0.068853044 APOD -0.091201494 -0.092371883 GP5 -0.101753703 -0.017977843 MASP1 -0.117271368 -0.095295374 LRRC33 -0.127567165 -0.107921733 TM4SF19 -0.144140665 -0.093234725 KLHL6 -0.179730589 -0.142903519 ST6GAL1 -0.245091205 -0.191379793 LRRC15 -0.245662086 -0.210135227 LRRC31 -0.272076996 -0.324778673 ARL14 -0.352290803 -0.303819572 TableS3Descriptionofsixdatasetsusingtoidentifycandidatedrivergenes

DataID Platform NumberofSCCsample Numberofgenesin3q2629 Reference GSE2109 AffymetrixHumanGenomeU133Plus2.0Array 38 173 https://expo.intgen.org/geo/ GSE3141 AffymetrixHumanGenomeU133Plus2.0Array 52 173 16273092 GSE4573 AffymetrixHumanGenomeU133AArray 128 124 16885343 GSE8894 AffymetrixHumanGenomeU133Plus2.0Array 75 173 19080156 GSE17710 AgilentUNCcustom4X44K 56 160 20643781 Roepmanetal. Agilent44Kwholegenomelowdensityarray 92 114 19118056 Table S4 Predicted information based on GSE2109

Average expression scores for 38 samples Sample name Average expression score GSM46976 0.928340991 GSM102507 0.73491362 GSM301680 0.734705879 GSM138003 0.692035651 GSM277696 0.622875688 GSM117763 0.607327425 GSM88949 0.595169675 GSM231897 0.567738146 GSM152609 0.445081779 GSM117610 0.442339347 GSM231952 0.316163393 GSM46973 0.187330524 GSM353933 0.162841049 GSM277678 0.144524085 GSM53167 0.099021129 GSM152670 0.06714512 GSM102451 0.064518766 GSM203641 -0.043430186 GSM203699 -0.089810549 GSM152624 -0.152251961 GSM117629 -0.184262473 GSM231899 -0.206406469 GSM231907 -0.322553254 GSM38100 -0.329300171 GSM46936 -0.334888674 GSM46850 -0.338345904 GSM46817 -0.356785382 GSM102455 -0.35967223 GSM46884 -0.367874981 GSM102449 -0.394909532 GSM46833 -0.422447344 GSM102553 -0.433674529 GSM46868 -0.438103567 GSM152757 -0.457148408 GSM231950 -0.488119889 GSM38103 -0.524034174 GSM231885 -0.57473774 GSM203732 -0.593314848

Correlation between gene expression data and average expression scores for 173 genes in 3q26-29 GeneSymbol Correlation ABCC5 0.90961812 YEATS2 0.880730933 PSMD2 0.833023307 ECE2 0.832804464 PARL 0.827771091 MRPL47 0.817704344 MFN1 0.81354634 CLCN2 0.811795601 ALG3 0.808731809 ECT2 0.808294124 EIF2B5 0.807856439 FXR1 0.80698107 MAGEF1 0.804573805 POLR2H 0.800853485 TMEM41A 0.798665062 DVL3 0.794507058 PDCD10 0.794069373 MYNN 0.791224423 SENP5 0.790349054 FAM131A 0.789473684 ACAP2 0.784002626 RFC4 0.782251888 NCBP2 0.780938834 TFRC 0.779406937 PIGX 0.773279352 PLD1 0.767151767 SOX2 0.765619871 PCYT1A 0.75424007 AP2M1 0.751613962 LSG1 0.751613962 IGF2BP2 0.748112485 SENP2 0.744392165 NDUFB5 0.736294999 ZNF639 0.734106576 ABCF3 0.733012365 PRKCI 0.725134041 EIF4G1 0.724477514 TRA2B 0.719225298 UBXN7 0.715942663 TBCCD1 0.714191925 PIK3CA 0.711346975 KLHL24 0.711346975 ACTL6A 0.710471605 DLG1 0.709158551 PAK2 0.704562862 PHC3 0.703249809 VPS8 0.701280228 ATP11B 0.694277273 TP63 0.693620746 BDH1 0.691213481 C3orf21 0.690338111 FGF12 0.678082941 DCUN1D1 0.676551045 DNAJC19 0.675456833 B3GNT5 0.661450925 DGKG 0.655104497 TMEM44 0.644600066 FBXO45 0.644381223 WDR53 0.639785535 EHHADH 0.636065215 EIF5A2 0.630594157 MAP6D1 0.628624576 PPP1R2 0.62337236 DNAJB11 0.622715833 TBL1XR1 0.622059306 RPL39L 0.621840464 FYTTD1 0.621621622 ATP13A3 0.608928767 RPL22L1 0.606083817 SKIL 0.597330124 KCNMB3 0.590764854 HRASLS 0.581354634 EIF4A2 0.58004158 KPNA4 0.559032717 SMC4 0.550716709 C3orf34 0.548090601 EPHB3 0.545245651 OPA1 0.541087646 NMD3 0.534741219 LPP 0.533647007 CAMK2N2 0.52730058 HES1 0.519422256 PPM1L 0.512638144 ETV5 0.508698982 FAM43A 0.508042455 SERPINI1 0.499507605 PIGZ 0.482656746 MAP3K13 0.480030638 TTC14 0.471058103 USP13 0.448298501 TPRG1 0.448079659 LRRC34 0.447860816 TNK2 0.431447642 HRG 0.425757742 LRCH3 0.422256264 LIPH 0.420505526 GPR160 0.416785206 CLDN1 0.411095306 MUC20 0.400809717 TRIM59 0.385053069 FETUB 0.371266003 RPL35A 0.367107999 TNFSF10 0.35966736 RNF168 0.359448517 MFI2 0.333843965 MCCC1 0.329685961 BCL6 0.328154065 ZDHHC19 0.325527957 IL1RAP 0.31546121 SLC2A2 0.311740891 ATP13A5 0.307582887 GOLIM4 0.30692636 MUC4 0.30605099 ZMAT3 0.305613306 AHSG 0.303862567 C3orf65 0.293139293 NLGN1 0.279789911 PEX5L 0.276726119 SEC62 0.273662326 LMLN 0.267972426 KNG1 0.253966517 LEPREL1 0.253091148 CLDN16 0.240617135 SPATA16 0.233176496 GNB4 0.227048911 SLC7A14 0.218732903 TNIK 0.210198052 C3orf70 0.202538571 VWA5B2 0.195097932 KCNMB2 0.192252982 GP5 0.190283401 THPO 0.189626874 KIAA0226 0.183061604 HTR3C 0.178465915 B3GALNT1 0.1732137 ATP13A4 0.17233833 WDR49 0.170149907 LRRC31 0.169931065 MCF2L2 0.167742641 UTS2D 0.148484517 FNDC3B 0.146733778 SLITRK3 0.117627749 TMEM207 0.115336215 CRYGS 0.11018711 RTP1 0.102527629 C3orf59 0.10077689 CPN2 0.093992778 ZBBX 0.090491301 C3orf43 0.069044753 APOD 0.066199803 SST 0.046285152 LAMP3 0.042127147 ADIPOQ 0.041908305 IFT80 0.024838604 ARL14 0.017179122 BCHE 0.00755006 LRRC15 0.007112376 TMEM212 0.006237006 SI 0.004923952 LRRC33 0.003610898 GHSR -0.003392056 MASP1 -0.012802276 CCDC39 -0.034029981 RTP4 -0.040157566 SERPINI2 -0.060075505 C3orf57 -0.062260641 KLHL6 -0.072765073 NAALADL2 -0.083488347 IQCG -0.085895612 ST6GAL1 -0.127913338 CLDN11 -0.148484517 CHRD -0.177152861 CCDC50 -0.278476857 Table S5 Predicted information based on GSE3141

Average expression scores for 52 samples Sample name Averagre expression score GSM70231 0.966977272 GSM70165 0.722732673 GSM70232 0.500514393 GSM70158 0.493009113 GSM70126 0.464757206 GSM70128 0.440347145 GSM70133 0.417197224 GSM70217 0.363813158 GSM70143 0.363034343 GSM70149 0.334727435 GSM70160 0.312641046 GSM70187 0.292722165 GSM70139 0.281688722 GSM70166 0.246176607 GSM70176 0.244258852 GSM70189 0.244204078 GSM70137 0.243004036 GSM70180 0.223600054 GSM70213 0.192591852 GSM70135 0.172129202 GSM70188 0.161366534 GSM70157 0.13885334 GSM70132 0.138476674 GSM70152 0.134259103 GSM70198 0.125755766 GSM70185 0.114879911 GSM70221 0.091947285 GSM70192 0.085958138 GSM70207 0.038014305 GSM70186 0.006117904 GSM70162 -0.071650482 GSM70147 -0.099298114 GSM70215 -0.111041789 GSM70168 -0.146905962 GSM70142 -0.149060471 GSM70182 -0.212634004 GSM70134 -0.229565438 GSM70206 -0.247780645 GSM70210 -0.305230206 GSM70200 -0.321233234 GSM70125 -0.381458699 GSM70167 -0.419532118 GSM70216 -0.440635416 GSM70178 -0.471086442 GSM70212 -0.518735323 GSM70202 -0.527870335 GSM70205 -0.546195278 GSM70230 -0.581786161 GSM70191 -0.591593269 GSM70228 -0.710578958 GSM70211 -0.724252503 GSM70141 -0.747630694

Correlation between gene expression data and average expression scores for 173 genes in 3q26-29 GeneSymbol Correlation DCUN1D1 0.87057116 NDUFB5 0.86025912 SENP2 0.85913088 NCBP2 0.846580722 DNAJC19 0.826090668 PRKCI 0.825236916 PCYT1A 0.816187142 UBXN7 0.815504141 PAK2 0.81140613 MFN1 0.810893879 RFC4 0.806112866 ALG3 0.804319986 DLG1 0.802868608 PIGX 0.798087595 ABCC5 0.796123965 C3orf21 0.791342952 B3GNT5 0.788867071 TMEM41A 0.78459831 ATP11B 0.783915308 TP63 0.783744557 EIF4G1 0.778365918 ACTL6A 0.777597541 TRA2B 0.777512166 SENP5 0.774267907 PIK3CA 0.770169897 TBL1XR1 0.764620507 DVL3 0.76205925 ABCF3 0.76009562 POLR2H 0.755997609 OPA1 0.75437548 DNAJB11 0.75242791 EIF2B5 0.7522411 PSMD2 0.751488762 LSG1 0.749338342 FYTTD1 0.748826091 IGF2BP2 0.743874328 FXR1 0.741739947 ZNF639 0.74097157 SOX2 0.736361308 PDCD10 0.733800051 MYNN 0.72773841 ECT2 0.725689405 MRPL47 0.722872023 FBXO45 0.709211987 MAGEF1 0.706053103 PLD1 0.702638094 SMC4 0.69896696 VPS8 0.694698199 TBCCD1 0.688892683 RPL35A 0.683428669 WDR53 0.678135405 ATP13A3 0.676854777 RPL22L1 0.672842141 TMEM44 0.670451635 ACAP2 0.67036626 TFRC 0.667634253 AP2M1 0.664902245 MCCC1 0.651839836 BDH1 0.638350551 PPP1R2 0.625032016 PARL 0.623751387 C3orf34 0.605139588 YEATS2 0.600956203 FAM131A 0.58669854 HRASLS 0.581576027 ECE2 0.578417143 KLHL24 0.577734142 EIF5A2 0.574831384 CLCN2 0.572440878 PHC3 0.571587125 EPHB3 0.566379237 KPNA4 0.562451976 EHHADH 0.531631521 MAP6D1 0.526167506 RPL39L 0.48749253 MFI2 0.483309144 CLDN1 0.482113891 ZMAT3 0.470758986 TPRG1 0.469307607 KCNMB3 0.456928199 TRIM59 0.452317937 GPR160 0.444036541 TNK2 0.427132246 BCL6 0.420046103 IL1RAP 0.411679331 ETV5 0.407922821 NMD3 0.403910185 LRCH3 0.403141808 DGKG 0.402629557 MAP3K13 0.389908649 FGF12 0.380090498 MUC20 0.373601981 C3orf59 0.365491334 NLGN1 0.362759327 EIF4A2 0.346879536 LMLN 0.345001281 SKIL 0.337232135 TTC14 0.334329378 LPP 0.333646376 SEC62 0.316400581 CRYGS 0.310082814 USP13 0.302911295 HES1 0.299923162 SERPINI2 0.294032272 HRG 0.285580125 CLDN16 0.270212584 ZDHHC19 0.265516947 LEPREL1 0.239306753 GOLIM4 0.236062495 ATP13A5 0.228976351 TNFSF10 0.225817468 SLITRK3 0.223426961 SERPINI1 0.216255443 ATP13A4 0.210279177 RNF168 0.209596175 MUC4 0.208657048 BCHE 0.195850764 CCDC39 0.177238965 KIAA0226 0.169128319 C3orf65 0.161529924 UTS2D 0.154956032 FAM43A 0.152565525 SPATA16 0.143345001 FETUB 0.135405105 SLC2A2 0.133526851 LRRC34 0.13139247 TMEM207 0.129684965 PIGZ 0.123281824 PPM1L 0.119781439 CAMK2N2 0.117647059 GHSR 0.105011526 TNIK 0.099803637 NAALADL2 0.096388628 C3orf57 0.094597767 VWA5B2 0.088704858 GP5 0.073849569 GNB4 0.072910441 FNDC3B 0.062153163 LRRC31 0.061299411 RTP1 0.060616409 IFT80 0.052847264 TMEM212 0.051566635 KNG1 0.03432084 WDR49 0.028259199 ADIPOQ 0.02663707 KCNMB2 0.019977802 LRRC15 0.013147785 ZBBX -0.000939127 B3GALNT1 -0.008366772 C3orf70 -0.031076582 SI -0.037394348 PEX5L -0.041577734 RTP4 -0.046614872 ARL14 -0.050115257 AHSG -0.056518398 CHRD -0.065226671 C3orf43 -0.077179203 LIPH -0.091095364 SST -0.097413131 MCF2L2 -0.112996521 CCDC50 -0.11423205 HTR3C -0.114234488 APOD -0.123452574 THPO -0.164603432 IQCG -0.186203364 SLC7A14 -0.24938103 LRRC33 -0.26654145 LAMP3 -0.268590455 MASP1 -0.273969094 CLDN11 -0.275420473 ST6GAL1 -0.33142662 CPN2 -0.383590882 KLHL6 -0.474600871 Table S6 Predicted information based on GSE4573

Average expression scores for 128 samples Sample name Averagre expression score GSM102193 1.024331939 GSM102142 0.986727848 GSM102202 0.921927801 GSM102209 0.882503038 GSM102125 0.853004239 GSM102224 0.75669378 GSM102199 0.732718177 GSM102128 0.72193853 GSM102204 0.6693539 GSM102194 0.643289783 GSM102212 0.624653147 GSM102170 0.601977852 GSM102124 0.58508955 GSM102138 0.584555633 GSM102129 0.568923737 GSM102210 0.562179391 GSM102139 0.555648539 GSM102144 0.555074257 GSM102218 0.546339844 GSM102147 0.526429967 GSM102162 0.52109197 GSM102152 0.501082602 GSM102140 0.492276987 GSM102158 0.433350924 GSM102195 0.42957841 GSM102180 0.411533813 GSM102151 0.400959532 GSM102135 0.375109118 GSM102119 0.351262658 GSM102197 0.339446703 GSM102231 0.334078805 GSM102243 0.327532069 GSM102228 0.318658616 GSM102160 0.30183353 GSM102155 0.241302597 GSM102130 0.237719931 GSM102169 0.22010777 GSM102164 0.216054838 GSM102165 0.2159547 GSM102121 0.201453425 GSM102154 0.201196633 GSM102183 0.198545942 GSM102189 0.174839784 GSM102136 0.16769413 GSM102223 0.147363472 GSM102198 0.140165684 GSM102179 0.134964717 GSM102133 0.121256545 GSM102222 0.108870575 GSM102117 0.095655964 GSM102229 0.090563052 GSM102167 0.07856542 GSM102227 0.066124735 GSM102178 0.064710281 GSM102190 0.06143203 GSM102208 0.0552928 GSM102214 0.04229787 GSM102184 0.030459775 GSM102157 0.017958404 GSM102187 0.005553326 GSM102145 -0.002468845 GSM102177 -0.003803891 GSM102242 -0.023835921 GSM102205 -0.027660612 GSM102203 -0.036080178 GSM102156 -0.049572802 GSM102201 -0.057863703 GSM102161 -0.064827131 GSM102226 -0.08234158 GSM102153 -0.084203348 GSM102220 -0.100144722 GSM102131 -0.102072285 GSM102120 -0.120173812 GSM102230 -0.121951098 GSM102191 -0.12863783 GSM102225 -0.149694502 GSM102148 -0.150370093 GSM102116 -0.161408485 GSM102137 -0.184122106 GSM102126 -0.19225457 GSM102127 -0.203311818 GSM102200 -0.232797487 GSM102159 -0.250137665 GSM102149 -0.251312574 GSM102115 -0.251686336 GSM102173 -0.251757581 GSM102186 -0.253004234 GSM102207 -0.258216628 GSM102213 -0.265144348 GSM102150 -0.271664215 GSM102143 -0.29399743 GSM102175 -0.295592584 GSM102181 -0.301130895 GSM102240 -0.303288116 GSM102132 -0.311507715 GSM102188 -0.319630193 GSM102234 -0.32729987 GSM102118 -0.344339657 GSM102236 -0.34439664 GSM102172 -0.352233109 GSM102123 -0.353923965 GSM102122 -0.354469219 GSM102141 -0.359242619 GSM102166 -0.383018477 GSM102232 -0.395194577 GSM102134 -0.398260223 GSM102239 -0.412911114 GSM102192 -0.424542148 GSM102146 -0.431113704 GSM102221 -0.476013905 GSM102211 -0.525605958 GSM102237 -0.542528043 GSM102241 -0.546690206 GSM102206 -0.557760818 GSM102233 -0.564815708 GSM102174 -0.601765607 GSM102238 -0.607167459 GSM102114 -0.610817214 GSM102235 -0.613370437 GSM102196 -0.614070767 GSM102216 -0.616198986 GSM102182 -0.650302583 GSM102171 -0.653862905 GSM102185 -0.660488659 GSM102163 -0.685131918 GSM102168 -0.70410791 GSM102176 -0.711367003 GSM102219 -0.796582344

Correlation between gene expression data and average expression scores for 124 genes in 3q26-29

GeneSymbol Correlation EIF4G1 0.892430416 DCUN1D1 0.883017076 PIK3CA 0.868443378 PSMD2 0.866200286 SENP2 0.860237451 PARL 0.841636779 POLR2H 0.835521196 NDUFB5 0.832964713 FXR1 0.831498352 ALG3 0.826617149 FAM131A 0.816911967 ABCC5 0.812211644 PRKCI 0.800448636 MFN1 0.797644662 NCBP2 0.796666133 EIF2B5 0.79471021 YEATS2 0.785078282 RFC4 0.78114798 MCCC1 0.779148134 EIF4A2 0.776227409 ATP11B 0.774739023 UBXN7 0.772202893 SENP5 0.765570637 ACTL6A 0.764329971 MAGEF1 0.763064642 PDCD10 0.756327647 DVL3 0.756145852 AP2M1 0.753953846 TBCCD1 0.74619102 DLG1 0.710647088 TRA2B 0.707087759 TBL1XR1 0.699449362 MYNN 0.69896768 IGF2BP2 0.695586739 SOX2 0.690607261 TP63 0.676387109 PLD1 0.668352866 LSG1 0.6680038 ACAP2 0.666613258 ABCF3 0.663402994 CLCN2 0.649743637 KLHL24 0.646104193 BDH1 0.644421809 ECT2 0.643511948 EPHB3 0.641217268 OPA1 0.63061367 SEC62 0.629841146 TFRC 0.628165383 PAK2 0.618184627 VPS8 0.606048294 NMD3 0.568342565 SMC4 0.554362754 PPP1R2 0.553647455 PCYT1A 0.547656107 RPL39L 0.546774858 RPL35A 0.543713377 HRASLS 0.532714933 KPNA4 0.530515431 TNK2 0.513436184 ATP13A3 0.492715391 FETUB 0.48482993 MAP6D1 0.473568934 LRCH3 0.46917918 EIF5A2 0.459288677 EHHADH 0.456642065 KCNMB3 0.453562763 LPP 0.438037905 PHC3 0.416842153 CLDN1 0.410541796 BCL6 0.409986724 FGF12 0.403417414 NLGN1 0.388094506 LEPREL1 0.385317478 USP13 0.382822514 DGKG 0.374954221 GOLIM4 0.374181697 SKIL 0.344196347 KIAA0226 0.325507004 ETV5 0.324848929 MFI2 0.286176982 HES1 0.262743774 SERPINI1 0.260375075 KCNMB2 0.258149429 BCHE 0.253602611 ZMAT3 0.252025728 HRG 0.251773943 ECE2 0.247170629 AHSG 0.222057862 KNG1 0.221925929 PIGZ 0.215726023 TNFSF10 0.21330228 B3GALNT1 0.209908899 APOD 0.177577367 CLDN11 0.169735067 ZNF639 0.154167048 THPO 0.136547793 LRRC31 0.131964721 MASP1 0.130871177 ADIPOQ 0.128819883 MCF2L2 0.121371571 IL1RAP 0.117755448 LAMP3 0.108107644 SERPINI2 0.106614097 IQCG 0.106247711 TNIK 0.103375069 SLC2A2 0.086978292 SLITRK3 0.077395395 GP5 0.060319767 RTP4 0.042111106 CLDN16 0.003095816 CHRD -0.005642282 FNDC3B -0.007052872 SST -0.025819484 MAP3K13 -0.028606253 MUC4 -0.036491714 SI -0.036631965 TMEM212 -0.047041017 CPN2 -0.080657391 GHSR -0.080720106 LRRC15 -0.142361747 ZBBX -0.142725732 PEX5L -0.143231551 ARL14 -0.176450055 ST6GAL1 -0.192484206 Table S7 Predicted information based on GSE8894

Average expression scores for 75 samples

Sample name Averagre expression score GSM225765 0.924438265 GSM225780 0.84838216 GSM225901 0.724895745 GSM225851 0.666298676 GSM225824 0.660171507 GSM225820 0.639850412 GSM225819 0.619609876 GSM225852 0.51302979 GSM225825 0.490376833 GSM225821 0.38433856 GSM225565 0.381089734 GSM225778 0.371827408 GSM225846 0.310300703 GSM225772 0.308840138 GSM225844 0.305309891 GSM225771 0.298361761 GSM225801 0.283047297 GSM225604 0.265200265 GSM225848 0.261896654 GSM225788 0.246078246 GSM225831 0.245159271 GSM225575 0.23504182 GSM225790 0.223773723 GSM225787 0.221003723 GSM225902 0.214695597 GSM225832 0.207389727 GSM225795 0.165210997 GSM225876 0.134862268 GSM225783 0.124042346 GSM225886 0.123014204 GSM225890 0.120824 GSM225800 0.116767692 GSM225859 0.116346659 GSM225584 0.107532914 GSM225591 0.084123438 GSM225854 0.072938651 GSM225836 0.063823838 GSM225789 0.055940503 GSM225590 0.050924228 GSM225792 0.013960561 GSM225568 0.00937703 GSM225791 0.002057701 GSM225829 -0.020430424 GSM225578 -0.026390513 GSM225809 -0.02784292 GSM225828 -0.062952594 GSM225781 -0.071128574 GSM225889 -0.075982941 GSM225563 -0.081413967 GSM225552 -0.111135412 GSM225861 -0.123289104 GSM225593 -0.136387665 GSM225594 -0.137744073 GSM225603 -0.165304588 GSM225835 -0.261517385 GSM225833 -0.268061492 GSM225794 -0.273094167 GSM225879 -0.301398508 GSM225598 -0.347406431 GSM225553 -0.380870051 GSM225777 -0.458249282 GSM225596 -0.480360919 GSM225775 -0.492084781 GSM225895 -0.498297938 GSM225799 -0.515301044 GSM225807 -0.519785193 GSM225857 -0.60980528 GSM225779 -0.611302665 GSM225827 -0.663161335 GSM225900 -0.690084061 GSM225818 -0.720684407 GSM225558 -0.758978322 GSM225595 -0.77170464 GSM225823 -0.774869058 GSM225808 -0.775135081

Correlation between gene expression data and average expression scores for 173 genes in 3q26-29

GeneSymbol Correlation SENP5 0.855049787 WDR53 0.84628734 PRKCI 0.832204836 FAM131A 0.829985775 PSMD2 0.822475107 ACAP2 0.817809388 SENP2 0.817012802 FXR1 0.812432432 ATP11B 0.811493599 PAK2 0.806571835 DLG1 0.80512091 DCUN1D1 0.80344239 PCYT1A 0.79883357 EIF2B5 0.798321479 MYNN 0.795960171 PDCD10 0.794765292 CLCN2 0.787254623 UBXN7 0.785035562 DNAJC19 0.784694168 POLR2H 0.784295875 ZNF639 0.783100996 C3orf21 0.772944523 NCBP2 0.770981508 PIGX 0.767482219 YEATS2 0.765661451 ABCC5 0.76512091 PLD1 0.762219061 TMEM41A 0.755135135 ABCF3 0.752944523 PHC3 0.75083926 TBCCD1 0.748677098 DVL3 0.747368421 FBXO45 0.746571835 PIK3CA 0.742219061 ACTL6A 0.739231863 RFC4 0.738065434 TBL1XR1 0.735305832 VPS8 0.734708393 IGF2BP2 0.734366999 PPP1R2 0.73200569 MAGEF1 0.73027027 KPNA4 0.72742532 LSG1 0.727083926 MFN1 0.72625889 ECE2 0.723157895 MCCC1 0.719943101 DNAJB11 0.718890469 MAP6D1 0.715647226 ALG3 0.713883357 B3GNT5 0.710128023 TPRG1 0.709416785 AP2M1 0.7085633 EIF4G1 0.707795164 BDH1 0.706031294 TRA2B 0.702816501 EIF5A2 0.694480797 OPA1 0.692773826 ECT2 0.688477952 EHHADH 0.682759602 MRPL47 0.680483642 NDUFB5 0.675846373 FYTTD1 0.675277383 PARL 0.666770982 SOX2 0.662901849 ATP13A3 0.662532006 C3orf34 0.653570413 KLHL24 0.64799431 TFRC 0.642076814 SMC4 0.640853485 EIF4A2 0.640256046 RPL39L 0.631891892 TP63 0.631465149 LRCH3 0.62002845 SKIL 0.607140825 KCNMB3 0.607140825 TMEM44 0.605547653 EPHB3 0.58059744 RPL35A 0.56 NMD3 0.556756757 FGF12 0.547254623 RPL22L1 0.547027027 MFI2 0.543840683 TNK2 0.536472262 LMLN 0.536187767 PIGZ 0.521223329 FAM43A 0.510640114 TTC14 0.505974395 IL1RAP 0.497268848 HES1 0.488847795 IFT80 0.449644381 BCL6 0.444295875 DGKG 0.444267425 LPP 0.43940256 CLDN1 0.432062589 KIAA0226 0.419658606 C3orf59 0.410753912 HRASLS 0.402219061 FETUB 0.40002845 TNFSF10 0.376244666 ETV5 0.370896159 NLGN1 0.361991465 LEPREL1 0.357098151 ZMAT3 0.355533428 TRIM59 0.344409673 GPR160 0.341194879 USP13 0.29374111 SEC62 0.273997155 IQCG 0.273172119 MUC20 0.267937411 RNF168 0.265007112 C3orf57 0.259260313 RTP4 0.250668563 HRG 0.24458037 NAALADL2 0.236813656 GOLIM4 0.232489331 BCHE 0.226714083 LRRC34 0.222219061 SERPINI1 0.215817923 MAP3K13 0.204722617 B3GALNT1 0.173570413 CAMK2N2 0.170725462 CRYGS 0.138549075 ATP13A5 0.133314367 SERPINI2 0.122930299 MUC4 0.116728307 FNDC3B 0.110384068 PEX5L 0.105291607 PPM1L 0.104950213 WDR49 0.071578947 TMEM207 0.0673689 TMEM212 0.06688478 AHSG 0.059516358 CLDN16 0.054110953 C3orf70 0.03200569 CPN2 0.024665718 C3orf43 0.022816501 RTP1 0.020341394 SLITRK3 0.019004267 KCNMB2 0.004694168 C3orf65 -0.006657183 SST -0.011891892 GHSR -0.016699858 KNG1 -0.018093883 SLC7A14 -0.018662873 ADIPOQ -0.019118065 CHRD -0.02059744 MCF2L2 -0.02170697 APOD -0.02341394 ARL14 -0.02398293 SLC2A2 -0.037297297 GNB4 -0.044039829 VWA5B2 -0.048051209 SI -0.050128023 CLDN11 -0.052147937 HTR3C -0.052631579 LIPH -0.055561878 SPATA16 -0.058008535 ATP13A4 -0.059772404 THPO -0.063527738 GP5 -0.100113798 CCDC39 -0.108990043 UTS2D -0.127567568 ZDHHC19 -0.153456615 LAMP3 -0.158719772 LRRC31 -0.164238976 LRRC15 -0.167169275 ZBBX -0.201678521 TNIK -0.215305832 MASP1 -0.239630156 CCDC50 -0.264495021 LRRC33 -0.274566145 KLHL6 -0.331123755 ST6GAL1 -0.447283073 Table S8 Predicted information based on GSE17710

Average expression scores for 56 samples

Sample name Averagre expression score GSM442103 0.778184543 GSM442075 0.753094524 GSM442124 0.675916144 GSM442099 0.629599968 GSM442093 0.532771395 GSM442088 0.522165182 GSM442098 0.513325369 GSM442120 0.434335264 GSM442125 0.4177698 GSM442074 0.402980535 GSM442078 0.354561617 GSM442095 0.341817422 GSM442077 0.326589042 GSM442114 0.316248475 GSM442118 0.288015848 GSM442112 0.279898426 GSM442107 0.270517922 GSM442101 0.268726362 GSM442108 0.245854705 GSM442081 0.198436069 GSM442109 0.197061652 GSM442111 0.160039154 GSM442087 0.114173878 GSM442123 0.073652626 GSM442083 0.012632458 GSM442090 -0.057740304 GSM442122 -0.058211427 GSM442121 -0.063916806 GSM442079 -0.075308033 GSM442089 -0.114211815 GSM442070 -0.127147547 GSM442105 -0.136726117 GSM442094 -0.169360987 GSM442110 -0.174589154 GSM442097 -0.192041822 GSM442084 -0.193924705 GSM442085 -0.195238926 GSM442119 -0.201936822 GSM442100 -0.221468275 GSM442086 -0.270310467 GSM442102 -0.279887342 GSM442106 -0.283275819 GSM442092 -0.295981207 GSM442080 -0.296698476 GSM442082 -0.301270638 GSM442115 -0.383709866 GSM442091 -0.427618124 GSM442113 -0.456362043 GSM442073 -0.46225973 GSM442116 -0.464107394 GSM442096 -0.473405039 GSM442117 -0.487418259 GSM442076 -0.502031883 GSM442104 -0.539627898 GSM442072 -0.559865026 GSM442071 -0.642716427

Correlation between gene expression data and average expression scores for 160 genes in 3q26-29

GeneSymbol Correlation ACTL6A 0.888516746 LSG1 0.887969925 SENP2 0.861107314 OPA1 0.849692413 MRPL47 0.839712919 TBCCD1 0.827067669 ABCC5 0.823991798 PDCD10 0.822624744 DLG1 0.816473001 DCUN1D1 0.813328776 ZNF639 0.813260424 SENP5 0.811619959 TBL1XR1 0.810799727 NDUFB5 0.802187286 NCBP2 0.801435407 FYTTD1 0.796172249 MYNN 0.794531784 DVL3 0.788653452 KPNA4 0.788311688 PRKCI 0.786466165 B3GNT5 0.781818182 MFN1 0.777648667 EIF2B5 0.776418319 PIGX 0.772043746 C3orf21 0.767053999 ATP11B 0.766917293 PIK3CA 0.763568011 RFC4 0.76151743 PARL 0.754613807 WDR53 0.748051948 TMEM41A 0.747163363 DNAJC19 0.745864662 ATP13A3 0.745112782 TP63 0.74203691 PSMD2 0.740533151 ALG3 0.732330827 PCYT1A 0.730690362 FXR1 0.729323308 CLCN2 0.728844839 MCCC1 0.713533835 ECT2 0.712440191 KLHL24 0.710594668 PAK2 0.709911141 DNAJB11 0.70683527 PHC3 0.699111415 RPL35A 0.680519481 ABCF3 0.677853725 POLR2H 0.671565277 FAM131A 0.669788107 EHHADH 0.668489405 MAGEF1 0.653725222 VPS8 0.649965824 PPP1R2 0.649213944 EIF4G1 0.646411483 SOX2 0.632057416 IGF2BP2 0.630143541 NMD3 0.623581681 RPL39L 0.595967191 RNF168 0.584688995 ECE2 0.578673958 C3orf34 0.577238551 PLD1 0.57265892 AP2M1 0.569036227 TFRC 0.567874231 YEATS2 0.565686945 HRASLS 0.55796309 IL1RAP 0.553861928 EIF4A2 0.546001367 SMC4 0.543472317 SKIL 0.542515379 IFT80 0.533561176 GOLIM4 0.529254956 CLDN1 0.520847573 EIF5A2 0.51722488 TRIM59 0.504032809 FGF12 0.501435407 LPP 0.498086124 EPHB3 0.491182502 TTC14 0.483868763 TNFSF10 0.476008202 HRG 0.453588517 ZMAT3 0.45140123 TMEM44 0.428913192 RPL22L1 0.423581681 PPM1L 0.419412167 BCL6 0.400956938 KCNMB3 0.39391661 MAP3K13 0.377580314 IQCG 0.365892003 BCHE 0.360560492 DGKG 0.356732741 RTP4 0.354066986 SERPINI1 0.340601504 MUC20 0.337525632 FAM43A 0.330280246 HES1 0.326384142 MAP6D1 0.305673274 FETUB 0.300546822 MFI2 0.299111415 GPR160 0.289268626 USP13 0.276760082 AADACL1 0.274777854 LRCH3 0.262952837 NLGN1 0.262679426 KIAA0226 0.254203691 LEPREL1 0.248940533 EVI1 0.248803828 LIPH 0.232740943 MDS1 0.2316473 CLDN16 0.228434723 ZDHHC19 0.227409433 TNK2 0.227067669 C3orf59 0.225632262 CRYGS 0.216062884 SERPINI2 0.195215311 FNDC3B 0.160082023 PIGZ 0.146684894 C3orf57 0.130690362 RTP1 0.126452495 MCF2L2 0.119822283 OSTN 0.114969241 HTR3E 0.058851675 ATP13A4 0.055228982 GP5 0.048188653 ETV5 0.039302802 SAMD7 0.034723172 CCDC50 0.027819549 B3GALNT1 0.026794258 MUC4 0.026520848 LRRC31 0.020437457 PEX5L -0.009501025 TM4SF19 -0.019958988 SPATA16 -0.027887902 LRRC34 -0.043267259 SI -0.054818865 CLDN11 -0.055297334 ARL14 -0.057484621 LAMP3 -0.067327409 GNB4 -0.07593985 SLC2A2 -0.077990431 SLC7A14 -0.082296651 KNG1 -0.092754614 KCNMB2 -0.134859877 APOD -0.137320574 AHSG -0.141285031 SLITRK3 -0.159466849 CAMK2N2 -0.162200957 TNIK -0.173820916 MASP1 -0.203349282 ADIPOQ -0.227956254 HTR3C -0.233151059 CPN2 -0.250717703 GHSR -0.258851675 SST -0.270334928 THPO -0.292276145 LRRC33 -0.336090226 LRRC15 -0.369651401 KLHL6 -0.393301435 ST6GAL1 -0.417293233 CHRD -0.52228298 Table S9 Predicted information based on Roepman et al. dataset

Average expression scores for 92 samples

Sample name Averagre expression score 5001013 0.82295231 6000415 0.747935998 5000500 0.742692625 5000996 0.738853672 6000452 0.738226747 6000440 0.731058848 6000456 0.628190069 5000975 0.618458623 5000353 0.561779198 5001224 0.541300279 6000425 0.521044619 6001484 0.471415345 5000997 0.450685273 5001232 0.39766826 5000417 0.366696928 5001008 0.336425071 5001010 0.322549229 6000445 0.305063954 5000481 0.285569307 5001234 0.28033674 6000404 0.277506024 5000431 0.273283728 5001229 0.266068593 5000454 0.253348449 5000422 0.239943962 6000708 0.184741467 5000407 0.169911427 5000403 0.169507355 5000507 0.157937093 6000463 0.156549012 6000451 0.153209034 6000707 0.150620021 5001238 0.146295784 5000493 0.129517615 5000510 0.122047346 6000738 0.11399297 5000450 0.11069229 5000970 0.10911829 5000429 0.066374002 5000443 0.06105649 6000716 0.054239229 5000463 0.046567418 6000730 0.032868284 5000437 0.032743406 5000452 0.020836123 6000444 0.015720675 5000404 -0.021456531 5000459 -0.024364708 6000416 -0.030179662 6000421 -0.047999273 5000440 -0.056308749 6000702 -0.063585252 6000401 -0.066257767 6000442 -0.07887468 5000506 -0.087503086 6000043 -0.105160751 5000579 -0.109394249 6000447 -0.140880877 6000420 -0.145822756 5000496 -0.156309439 5000482 -0.1782195 6000464 -0.195087584 6000726 -0.205301724 5000457 -0.21614333 6000417 -0.219601659 6000459 -0.262882422 6000736 -0.270610532 6000721 -0.275291268 5000458 -0.276492877 5000503 -0.283826909 5000494 -0.307282547 5000424 -0.319063619 5000406 -0.322016052 5000425 -0.330311571 6000460 -0.334036651 5000415 -0.357793474 6001485 -0.359326249 5000352 -0.376467085 6001488 -0.402349498 5000495 -0.427887323 5000451 -0.448185911 5000492 -0.453564193 5001219 -0.491752821 6000428 -0.49584051 6000729 -0.508332856 6000743 -0.51224341 5000442 -0.553109113 6000723 -0.605170002 5000479 -0.665687645 6000418 -0.703488396 5000432 -0.791523323 5000586 -0.840611347

Correlation between gene expression data and average expression scores for 114 genes in 3q26-29

GeneSymbol Correlation ATP11B 0.833993496 SENP2 0.794769046 PIGX 0.793736418 UBXN7 0.778771019 SENP5 0.771542623 ZNF639 0.762788404 ABCC5 0.754727741 PDCD10 0.754558205 PLD1 0.75073594 DVL3 0.743569194 VPS8 0.731378019 MYNN 0.730175855 FXR1 0.724010912 MCCC1 0.714347364 FYTTD1 0.710817934 NCBP2 0.694727432 WDR53 0.692446404 PRKCI 0.686173574 PHC3 0.679762033 PSMD2 0.674074873 TFRC 0.672872709 DLG1 0.671208175 KLHL24 0.670237196 IGF2BP2 0.663733181 MFN1 0.662638904 ACTL6A 0.646779588 PPP1R2 0.644221137 TP63 0.643727941 YEATS2 0.643142271 DNAJB11 0.639951913 EIF5A2 0.637686297 TBCCD1 0.636900267 FAM131A 0.622566774 KPNA4 0.621040951 TPRG1 0.618374613 SOX2 0.614983894 BDH1 0.612934051 ECE2 0.607770911 EHHADH 0.600804525 ECT2 0.593684016 BCL6 0.583820107 RFC4 0.581169181 TMEM44 0.567960791 RPL22L1 0.562119507 GOLIM4 0.552887505 MAGEF1 0.548402509 POLR2H 0.534130666 PAK2 0.533313811 ZMAT3 0.531972936 ATP13A3 0.526609435 EIF4G1 0.524759953 C3orf59 0.4993758 SMC4 0.476349737 FETUB 0.474330718 AHSG 0.468612734 CLDN1 0.465761448 IFT80 0.452738005 AP2M1 0.441610283 PARL 0.435414515 FGF12 0.434443537 TNFSF10 0.434227764 LEPREL1 0.430960344 EPHB3 0.430143489 MRPL47 0.411109227 MFI2 0.40680918 LPP 0.366459627 IL1RAP 0.341969391 MAP6D1 0.313379468 HRASLS 0.305195506 PIGZ 0.298136646 NLGN1 0.296965307 SERPINI1 0.283217484 GPR160 0.279379807 KIAA0226 0.276482283 LAMP3 0.24246721 ETV5 0.232880724 CLDN16 0.223818257 KCNMB3 0.211026001 FNDC3B 0.205184717 SLC2A2 0.196399673 AADACL1 0.193425088 PEX5L 0.176132423 HES1 0.168040935 C3orf70 0.161151611 SERPINI2 0.160427231 PPM1L 0.154863369 LIPH 0.154847957 B3GALNT1 0.153352958 GHSR 0.137277869 GP5 0.091056209 UTS2D 0.090532189 KCNMB2 0.082733536 CCDC50 0.066935869 MUC4 0.034986052 SI -0.005024429 LRRC15 -0.025322504 SLITRK3 -0.029345129 ZBBX -0.059692061 WDR49 -0.060894225 VWA5B2 -0.067521539 LRRC31 -0.083796988 KNG1 -0.089684509 CPN2 -0.1096281 RTP1 -0.110922738 HTR3C -0.112371499 ADIPOQ -0.126273446 HTR3D -0.128831897 CAMK2N2 -0.157514295 SLC7A14 -0.197863847 SAMD7 -0.223016815 SPATA16 -0.224296041 ST6GAL1 -0.233235208 ARL14 -0.270671825 THPO -0.281275527 TableS10Orderstatisticresultfor181genesin3q2629 genesymbol Band TCGA GSE2109 GSE17710 GSE3141 GSE4573 GSE8894 Roepman QStatistic pvalue FDR ABCC5 q27.1 6 1 7 15 12 26 7 8.35E08 0 0 ACTL6A q26.33 2 43 1 22 24 35 26 3.54E06 0 0 DCUN1D1 q26.33 3 53 10 1 2 12 NA 3.66E07 0 0 DLG1 q29 25 44 9 13 30 11 22 1.78E05 0 0 MFN1 q26.32 20 7 22 10 14 44 25 1.28E05 0 0 NCBP2 q29 28 23 15 4 15 23 16 1.38E06 0 0 PRKCI q26.2 43 36 20 6 13 3 18 6.17E06 0 0 PSMD2 q27.1 29 3 35 33 4 5 20 1.34E06 0 0 SENP2 q27.2 11 32 335721.27E09 0 0 SENP5 q29 42 19 12 24 23 1 5 2.12E06 0 0 UBXN7 q29 NA 39 NA 8 22 18 4 0.00010516 0 0 ZNF639 q26.32 1 34 11 38 95 21 6 2.68E05 0 0 ATP11B q26.33 5 48 26 19 21 9 1 2.46E06 0.001 0.00905 DVL3 q27.1 31 16 18 27 27 32 10 1.45E05 0.001 0.00905 EIF2B5 q27.1 22 11 23 32 16 14 NA 2.83E05 0.001 0.00905 FXR1 q26.33 19 12 38 37 9 8 13 3.60E06 0.001 0.00905 LSG1 q29 32 30 2 34 38 43 NA 0.00011126 0.001 0.00905 NDUFB5 q26.33 27 33 14 2 8 61 NA 6.47E05 0.001 0.00905 PIGX q29 23 25 24 14 NA 24 3 6.86E06 0.001 0.00905 PIK3CA q26.32 8 41 27 25 3 34 NA 1.61E05 0.001 0.00905 ALG3 q27.1 14 9 36 12 10 49 NA 7.66E05 0.002 0.01645455 PDCD10 q26.1 40 17 8 40 26 16 8 1.85E05 0.002 0.01645455 MYNN q26.2 36 18 17 41 33 15 12 4.38E05 0.004 0.02896 POLR2H q27.1 9 14 48 29 7 20 47 7.46E05 0.004 0.02896 RFC4 q27.3 18 22 28 11 18 36 42 7.72E05 0.004 0.02896 DNAJC19 q26.33 7 54 32 5 NA 19 NA 0.00026852 0.006 0.04176923 TMEM41A q27.2 38 15 31 18 NA 28 NA 0.00023409 0.007 0.04525 WDR53 q29 34 59 30 51 NA 2 17 0.0001778 0.007 0.04525 C3orf21 q29 21 51 25 16 NA 22 NA 0.00047034 0.008 0.04670968 FAM131A q27.1 33 20 49 64 11 4 33 0.00013813 0.008 0.04670968 YEATS2 q27.1 24 2 65 63 17 25 29 0.00011958 0.008 0.04670968 TBL1XR1 q26.32 4 65 13 26 32 37 NA 0.00040543 0.009 0.05090625 MAGEF1 q27.1 13 13 51 45 25 41 46 0.00036601 0.011 0.06033333 TBCCD1 q27.3 87 40 6 49 29 31 32 0.00049218 0.012 0.06388235 EIF4G1 q27.1 79 37 54 21 1 53 51 0.00029366 0.013 0.06722857 MRPL47 q26.33 17 6 5 43 NA 60 64 0.00039454 0.014 0.07038889 ABCF3 q27.1 41 35 47 28 40 29 NA 0.00063422 0.015 0.0724 B3GNT5 q27.1 12 55 21 17 NA 50 NA 0.00093084 0.016 0.0724 PLD1 q26.31 53 26 62 46 37 27 9 0.00044132 0.016 0.0724 SOX2 q26.33 16 27 55 39 35 64 36 0.00059016 0.016 0.0724 ECT2 q26.31 10 10 41 42 44 58 40 0.00036878 0.017 0.0732619 PARL q27.1 15 5 29 61 6 63 59 0.00034783 0.017 0.0732619 OPA1 q29 35 78 4 30 46 57 NA 0.00111519 0.021 0.08638636 PAK2 q29 44 45 43 9 49 10 48 0.00041933 0.021 0.08638636 CLCN2 q27.1 26 8 39 69 41 17 NA 0.00096758 0.022 0.08848889 PCYT1A q29 70 28 37 7 54 13 NA 0.00091046 0.026 0.10230435 FYTTD1 q29 48 67 16 35 NA 62 15 0.00124851 0.028 0.10782979 ACAP2 q29 NA 21 NA 55 39 6 NA 0.00272631 0.031 0.11689583 TP63 q28 54 49 34 20 36 72 28 0.00098764 0.032 0.11820408 IGF2BP2 q27.2 80 31 56 36 34 39 24 0.00092759 0.035 0.1267 KLHL24 q27.1 30 42 42 67 42 67 23 0.0010712 0.037 0.13131373 DNAJB11 q27.3 51 64 44 31 NA 47 30 0.00131953 0.04 0.13923077 VPS8 q27.2 68 47 52 48 50 38 11 0.00215199 0.052 0.17441818 PPP1R2 q29 46 63 53 60 53 40 27 0.00180813 0.053 0.17441818 TFRC q29 45 24 64 56 48 68 21 0.00141262 0.053 0.17441818 ECE2 q27.1 59 4 60 66 87 45 38 0.00256018 0.062 0.19687719 MCCC1 q27.1 39 106 40 58 19 46 14 0.00195757 0.062 0.19687719 BDH1 q29 66 50 NA 59 43 54 37 0.00340494 0.066 0.20596552 KPNA4 q26.1 55 74 19 72 58 42 34 0.00360455 0.078 0.23144262 PHC3 q26.2 50 46 45 70 68 30 19 0.00290609 0.078 0.23144262 TRA2B q27.2 NA 38 NA 23 31 55 NA 0.00741312 0.078 0.23144262 SMC4 q26.1 57 75 69 47 52 69 53 0.00432825 0.088 0.25690323 AP2M1 q27.1 82 29 63 57 28 52 58 0.00594757 0.104 0.29879365 EIF5A2 q26.2 47 61 74 68 64 56 31 0.00671697 0.113 0.31957813 RPL39L q27.3 75 66 58 75 55 71 NA 0.00776895 0.118 0.32858462 EHHADH q27.2 61 60 50 73 65 59 39 0.0051839 0.121 0.33183333 ATP13A3 q29 90 68 33 52 60 65 50 0.00747691 0.134 0.362 FBXO45 q29 NA 58 NA 44 NA 33 NA 0.03091768 0.148 0.39394118 C3orf34 q29 74 76 61 62 NA 66 NA 0.01420328 0.156 0.40921739 EPHB3 q27.1 56 77 78 71 45 77 63 0.01198381 0.168 0.4344 TMEM44 q29 69 57 83 54 NA 76 43 0.01441985 0.184 0.46907042 RPL22L1 q26.2 49 69 84 53 NA 81 44 0.01629723 0.194 0.48769444 EIF4A2 q27.3 63 73 68 95 20 70 NA 0.01480562 0.2 0.49589041 RPL35A q29 37 102 46 50 56 78 NA 0.01902959 0.236 0.57724324 FGF12 q28 58 52 76 91 71 80 60 0.01771834 0.252 0.60492105 NMD3 q26.1 86 79 57 87 51 79 NA 0.02308186 0.254 0.60492105 LPP q28 84 80 77 99 67 93 66 0.02153972 0.267 0.62762338 HRASLS q29 88 72 66 65 57 97 69 0.02538998 0.297 0.68919231 TPRG1 q28 NA 91 NA 79 NA 51 35 0.05859701 0.311 0.7125443 MAP6D1 q27.1 76 62 97 74 62 48 68 0.0275705 0.329 0.7443625 BCL6 q27.3 85 107 86 84 70 91 41 0.02978111 0.345 0.77035366 CLDN1 q28 109 98 73 77 69 94 56 0.02861778 0.349 0.77035366 TTC14 q26.33 72 89 79 98 NA 87 NA 0.05419382 0.358 0.7806988 KCNMB3 q26.32 52 71 87 80 66 75 78 0.03780473 0.369 0.79510714 LRCH3 q29 64 95 103 88 63 73 NA 0.05396544 0.384 0.81769412 MFI2 q29 73 105 99 76 80 82 65 0.04437597 0.401 0.84396512 DGKG q27.3 106 56 91 89 75 92 NA 0.05327021 0.414 0.86131034 TRIM59 q26.1 65 100 75 81 NA 104 NA 0.07209889 0.435 0.89279775 GPR160 q26.2 99 97 100 82 NA 105 73 0.06889397 0.439 0.89279775 TNK2 q29 81 93 112 83 59 83 NA 0.07365325 0.455 0.90698901 SKIL q26.2 104 70 70 97 77 74 NA 0.06448891 0.456 0.90698901 GOLIM4 q26.2 89 112 72 109 76 115 45 0.0558385 0.469 0.92270652 USP13 q26.33 83 90 101 102 74 106 NA 0.06239333 0.475 0.92446237 ZMAT3 q26.32 94 114 82 78 85 103 49 0.065604 0.492 0.94501053 NLGN1 q26.31 78 117 104 94 72 101 71 0.06220878 0.496 0.94501053 FETUB q27.3 60 101 98 124 61 98 54 0.06870475 0.507 0.94605155 RNF168 q29 62 104 59 115 NA 110 NA 0.11345084 0.507 0.94605155 SERPINI1 q26.1 103 86 93 113 82 118 72 0.06741908 0.519 0.95856122 LEPREL1 q28 97 122 106 108 73 102 62 0.07951979 0.54 0.98727273 HRG q27.3 71 94 81 105 86 113 NA 0.10341571 0.555 1 FAM43A q29 67 85 95 122 NA 86 NA 0.13168323 0.562 1 TNFSF10 q26.31 102 103 80 111 91 99 61 0.09352491 0.575 1 MUC20 q29 113 99 94 92 NA 109 NA 0.14426857 0.588 1 SEC62 q26.2 NA 119 NA 100 47 107 NA 0.20426663 0.61 1 PIGZ q29 98 87 117 128 90 85 70 0.11830863 0.629 1 KIAA0226 q29 107 133 105 119 78 95 74 0.13093622 0.66 1 LMLN q29 NA 120 NA 96 NA 84 NA 0.29669292 0.667 1 ETV5 q27.2 112 84 125 86 79 100 76 0.13738072 0.672 1 ATP13A5 q29 92 111 NA 110 NA 123 NA 0.24245054 0.676 1 MDS1 q26.2 101 NA 109 NA NA NA NA 0.46127119 0.705 1 PPM1L q26.1 108 83 85 129 NA 128 86 0.18170012 0.707 1 AADACL1 q26.31 111 NA 102 NA NA NA 81 0.35786427 0.717 1 HES1 q29 127 82 96 103 81 89 83 0.17779037 0.727 1 IL1RAP q28 130 109 67 85 101 88 67 0.17731501 0.727 1 C3orf59 q29 96 146 113 93 NA 96 52 0.22319829 0.737 1 EVI1 q26.2 131 NA 107 NA NA NA NA 0.55589844 0.8 1 CRYGS q27.3 91 144 114 101 NA 122 NA 0.33398574 0.809 1 IFT80 q26.1 77 154 71 141 NA 90 57 0.26564245 0.814 1 C3orf65 q27.2 NA 116 NA 120 NA 140 NA 0.50040896 0.821 1 BCHE q26.1 105 156 90 117 84 116 NA 0.28856206 0.835 1 LRRC34 q26.2 132 92 134 126 NA 117 NA 0.38394554 0.851 1 TMEM207 q28 NA 143 NA 127 NA 130 NA 0.55154077 0.86 1 HTR3E q27.1 125 NA 122 NA NA NA NA 0.6832279 0.868 1 B3GALNT1 q26.1 93 135 128 149 92 120 88 0.32098894 0.887 1 CLDN16 q28 124 123 110 106 110 133 77 0.36697587 0.899 1 C3orf70 q27.2 NA 128 NA 150 NA 134 84 0.53072887 0.914 1 SLC2A2 q26.2 137 110 140 125 106 150 80 0.38997408 0.915 1 GNB4 q26.33 136 125 139 137 NA 151 NA 0.50234429 0.918 1 FNDC3B q26.31 118 141 116 138 112 126 79 0.41525022 0.919 1 MAP3K13 q27.2 143 88 88 90 114 119 NA 0.443823 0.925 1 VWA5B2 q27.1 NA 129 NA 135 NA 152 100 0.59277279 0.925 1 WDR49 q26.1 140 137 NA 144 NA 129 99 0.52053493 0.926 1 KNG1 q27.3 138 121 142 143 89 143 102 0.45292246 0.933 1 KCNMB2 q26.32 146 130 143 146 83 139 92 0.48212408 0.941 1 ATP13A4 q29 133 136 123 114 NA 158 NA 0.5576426 0.945 1 LIPH q27.2 120 96 108 158 NA 156 87 0.54095851 0.946 1 SLITRK3 q26.1 116 142 146 112 107 138 97 0.49858546 0.949 1 C3orf43 q29 NA 149 NA 157 NA 136 NA 0.74058123 0.95 1 AHSG q27.3 100 115 145 155 88 132 55 0.45131104 0.952 1 C3orf57 q26.1 110 166 118 134 NA 111 NA 0.60355188 0.954 1 OSTN q28 147 NA 121 NA NA NA NA 0.84836033 0.954 1 UTS2D q28 NA 140 NA 121 NA 162 91 0.69749647 0.954 1 RTP1 q27.3 114 145 119 140 NA 137 104 0.52810251 0.955 1 HTR3D q27.1 123 NA NA NA NA NA 107 0.8430576 0.956 1 ZDHHC19 q29 129 108 111 107 NA 163 NA 0.61468348 0.961 1 MCF2L2 q27.1 144 139 120 160 100 147 NA 0.6065504 0.962 1 CCDC39 q26.33 NA 163 NA 118 NA 161 NA 0.81854725 0.972 1 NAALADL2 q26.31 NA 168 NA 133 NA 114 NA 0.80445069 0.974 1 TM4SF19 q29 159 NA 132 NA NA NA NA 0.89894817 0.974 1 GP5 q29 156 131 124 136 108 160 90 0.55854081 0.975 1 ADIPOQ q27.3 115 153 150 145 99 145 106 0.63107185 0.979 1 MUC4 q29 151 113 129 116 115 125 94 0.58831661 0.98 1 SI q26.1 126 159 135 151 116 153 95 0.62081159 0.981 1 CAMK2N2 q27.1 141 81 147 130 NA 121 108 0.69474634 0.985 1 RTP4 q27.3 150 164 92 153 109 112 NA 0.70204312 0.985 1 SERPINI2 q26.1 148 165 115 104 103 124 85 0.65639162 0.986 1 TMEM212 q26.31 NA 158 NA 142 117 131 NA 0.78212131 0.989 1 HTR3C q27.1 153 134 151 162 NA 155 105 0.70575107 0.991 1 SST q27.3 121 151 154 159 113 141 NA 0.77295801 0.991 1 APOD q29 155 150 144 163 93 148 NA 0.7375856 0.992 1 SLC7A14 q26.2 117 126 141 166 NA 144 109 0.76997045 0.994 1 IQCG q29 128 169 89 165 104 108 NA 0.8113433 0.995 1 PEX5L q26.33 149 118 131 152 122 127 82 0.73633586 0.995 1 TNIK q26.31 142 127 148 132 105 168 NA 0.79869964 0.995 1 GHSR q26.31 134 161 153 131 119 142 89 0.74366998 0.996 1 LAMP3 q27.1 122 152 138 168 102 164 75 0.78932454 0.997 1 SAMD7 q26.2 145 NA 126 NA NA NA 110 0.88169464 0.997 1 SPATA16 q26.31 119 124 133 123 NA 157 111 0.77805289 0.997 1 ZBBX q26.1 NA 148 NA 148 121 167 98 0.87165507 0.997 1 CLDN11 q26.2 135 171 136 170 94 154 NA 0.9162254 0.998 1 MASP1 q27.3 157 162 149 169 98 169 NA 0.8689306 0.998 1 ARL14 q26.1 164 155 137 154 123 149 113 0.95553171 1 1 CCDC50 q28 95 173 127 161 NA 170 93 0.97722197 1 1 CHRD q27.1 154 172 160 156 111 146 NA 0.99598663 1 1 CPN2 q29 152 147 152 172 118 135 103 0.92737967 1 1 KLHL6 q27.1 160 167 158 173 NA 172 NA 0.99965804 1 1 LRRC15 q29 162 157 157 147 120 166 96 0.91658701 1 1 LRRC31 q26.2 163 138 130 139 97 165 101 0.92756438 1 1 LRRC33 q29 158 160 156 167 NA 171 NA 0.94180655 1 1 ST6GAL1 q27.3 161 170 159 171 124 173 112 0.99999122 1 1 THPO q27.1 139 132 155 164 96 159 114 0.97854478 1 1 Table S11 Correlation between gene expression and 3q26-29 amplification level for identified 20 genes in head and neck SCC

GeneSymbol corr pvalue ABCC5 0.78298714 0 ACTL6A 0.83532132 0 DCUN1D1 0.73934278 0 DLG1 0.61813607 0 MFN1 0.63031672 0 NCBP2 0.69521358 0 PRKCI 0.73285807 0 PSMD2 0.59651276 0 SENP2 0.84590649 0 SENP5 0.71994344 0 UBXN7 0.54592922 1.27E-24 ZNF639 0.79940518 0 ATP11B 0.52563669 0 DVL3 0.86412067 0 EIF2B5 0.75438576 0 FXR1 0.76622657 0 LSG1 0.76289735 0 NDUFB5 0.71058607 0 PIGX 0.68222891 0 PIK3CA 0.68517744 0 Table S12 Correlation between gene expression and 3q26-29 amplification level for identified 20 genes in cervical SCC

GeneSymbol corr pvalue ABCC5 0.58434732 0 ACTL6A 0.82713523 0 DCUN1D1 0.62746433 0 DLG1 0.5604896 1.06E-10 MFN1 0.59459009 0 NCBP2 0.76167527 0 PRKCI 0.63245948 0 PSMD2 0.66749769 0 SENP2 0.6679395 0 SENP5 0.72089354 0 UBXN7 0.45642089 7.31E-07 ZNF639 0.76086378 0 ATP11B 0.47410229 2.40E-07 DVL3 0.71126389 0 EIF2B5 0.74170367 0 FXR1 0.7151951 0 LSG1 0.83177873 0 NDUFB5 0.70897369 0 PIGX 0.70757613 0 PIK3CA 0.59042445 0 Supplementary Table S13 Copy number alteration and mRNA expression of four genes in a panel of NSCLC cell lines (data from Cancer Cell Line Encyclopedia database)

Copy number (log2 ratio) mRNA expression Cell lines Subtype SENP2 DCUN1D1 DVL3 UBXN7 SENP2 DCUN1D1 DVL3 UBXN7 HCC95 SCC 1.2205 1.2205 1.2205 1.3284 9.478904 9.153986 9.008998 9.557272 NCIH1648 ADC 1.005 1.005 1.005 1.0545 9.133941 8.577067 9.248071 8.66825 NCIH520 SCC 0.8218 0.8056 0.8056 0.8889 9.190379 9.318588 9.285064 9.313435 SW900 SCC -0.0243 -0.0243 -0.0243 0.0166 7.961592 7.567277 8.113743 7.834931 A549 ADC -0.4399 -0.4399 -0.4399 -0.4312 7.514961 7.533205 7.204725 6.89983 HCC15 SCC -0.5992 -0.61 -0.61 -0.5494 7.47321 7.256136 7.280834 7.540116 NCIH23 ADC -1.0416 -1.0253 -1.0416 -0.1184 7.184188 7.001839 6.87608 7.273177