Supplementary Heatmaps: This Supplementary Document Contains

Supplementary Heatmaps:

This supplementary document contains heatmaps for each of the 41 genes whose mutation status was correlated with the drastic over- and under-expression of other genes. Each page of this document contains: a single heatmap (plotted expressed genes X samples) with a title indicating the hugo symbol for the mutated gene; the sample-dependent mutation status plotted along the top of the heatmap (black bar indicates that sample is mutated in said gene); the hugo symbol for each expressed gene; a color legend for the magnitude and direction of correlation. Note: some heatmaps contain many expressed genes and therefore the hugo symbols are illegible—for this reason the reader is encouraged to use the accompanying spreadsheet Supplementary Mutation-correlated expression available in the online supplement. Color Key

−2 0 2 4 Row Z−Score AKR1C3 Mutations

HMGN2

CDK4

KLHL7

HOXD13

RCL1

Samples Color Key

0510 Row Z−Score ANK1 Mutations

OTOR

C6ORF124

Samples Color Key

05 Row Z−Score ATM Mutations

PLK4KIFC1NCAPH MCM10TMPOBUB1B SNRPFBRCA2KIF22 TEX10EXOSC2CCT5 USP3DDX52DDX31 CCT3TAF5LTFDP2 BCS1LDET1GNPAT POLR2FACVR2ACENPC1 TRIM27UBXD6THOC5 ERCC3SFPQLOC90379 TP53C1ORF77SETDB1 ANKRD10GAS1LRP5 ZEB1ZNF22TPP2 AAASALDH8A1SACS THRAP3SAFBC17ORF85 PRR3AOF2BRD9 ZNF208ZNF493LIG3 SECISBP2ZNF510C11ORF30 ZSCAN16DLL3IKBKAP FAM77CZNF250CDC5L PDE10AKLRC4KLRC3 MAP3K4MTMR2SUSD5 UBE2IKIAA0922TMEM39B EDC3MCPH1TGS1 ATF7IPCCNJPDCD11 TFAMSUV39H2DHX8 RANBP17CBLN1ZNF239 PAPD1DCLRE1CZNF492 JMJD1CC10ORF18GTPBP4 CSTF2TPARGC10ORF137 IL13RA1FUCA1C10ORF68 MPP1CASP10PYCARD KCTD12TRIM22MAF MGST2PSMB10APOBEC3G ECHDC2ICAM3DOK1 SSPNDHX58FLJ11286 PAOXGJA1BHLHB3 FAHSTOMHEBP1 ACOX2RBKSBLVRB DYNLT3SLC25A24PSEN2 TMBIM1C3ORF14LGALS8 PHF11YIPF1PGCP FAM50BPNPLA4PPCS ACADSSLC25A20HDHD3 MT1ERBP1SLC22A5 RGNBDH1XKR8 TRIM68NUCB2MOSC2 ST5PRMT2SERGEF FBXO17KIAA0495PHKA2 EMP3F11RRAB36 EFEMP2TNFRSF1AMSN RAB11FIP5CYB561PHLDA3 SSH3SWAP70LBA1 DGKGC13ORF18KIAA0323 PH−4IDSNR3C2 Samples Color Key

−5 0 Row Z−Score CHL1 Mutations

SLC25A38

MLH3

Samples Color Key

−2 0 2 4 Row Z−Score ConsReg523 Mutations

CDK4

TSPAN31

TSFM

CYP27B1

METTL1

FAM119B

HOXA2

MDM2

GRB14

ZNF473

Samples Color Key

−2 0 2 Row Z−Score DST Mutations

UBE1L2

EIF2C4

SFRS16

SSR1

REST

LOC90379

TOMM40

NRF1

ZNF432

WRN

RIF1

GTF3C3

SF3B1

THRAP3

Samples Color Key

−4 0 2 4 6 Row Z−Score EP300 Mutations

TFDP2

CDH7

PRPS2

ACADS

SLC25A20

CBR1

SSH3

HEBP1

Samples Color Key

−2 0 2 4 Row Z−Score EP400 Mutations

ZNF239

SEPHS1

GTPBP4

ZNF22

C10ORF68

SFRS6

Samples Color Key

05 Row Z−Score EPHB4 Mutations

DEF6 PIK3CDPRKCD SLC24A6UNC93B1 FUCA1MKNK1 IL13RA1FES F11RLY75 ECHDC2PARP12 PHKA2FLJ11286 PYCARDRGS10 CASP10ACSL5 CADPS2PAOX RAB33BRRAS2 DHRS3C3ORF14 BLVRBSTOM SSPNC4ORF18 HEBP1BHLHB3 GJA1SLC7A11 TMEM47PPP1R3D TMBIM1SLC22A5 YIPF1PGCP NQO2PSEN2 RGNFAM50B HDHD3PNPLA4 SLC25A20ACADS EPHX2CBR1 TTC12RBKS MT1ERBP1 BDH1XKR8 MOSC2TMEM22 COBLTRIM68 PSMB10MGST2 APOBEC3DOK1 G FAHAPOBEC3F RAB32HFE ICAM3VAMP5 PPCSPHF11 SLC25A24PRPS2 RARRES2H2AFJ DYNLT3HPS1 IFITM2LGALS8 FAM129AC1S EMP3LEPREL1 EFEMP2MSN KIAA0323SWAP70 RAB3DHSPB1 FLJ21963TRIP6 KIAA0495C13ORF18 PICK1FBXO17 CYB561EML2 SDC4RAB11FIP5 RAB36C20ORF23 SSH3KLHL26 SUV39H2OPLAH TEX10EXOSC2 NCAPHPRR3 PLK4KIFC1 POLQMCM10 C10ORF13TFDP2 7 SKIV2L2TAF5 TAF5LTCERG1 SNRPFGNPAT CCT5UCK2 ALDH18A1GTPBP4 BMS1PDCD11 SETDB1GTF3C2 SMARCD1BRD9 GAS1LRP5 RANBP17SFRS6 TIAL1ZNF492 SUSD5TPTE C6ORF124DET1 MTMR2CDH7 PROX1DPYSL4 TPP2IKBKAP JMJD1CARHGEF7 Samples Color Key

05 Row Z−Score FBXW7 Mutations

RGS10PYCARDCORO1A PRKCDCASP10IRF5TPK1 IL13RA1SLC24A6UNC93B1HLA−DRB6 HLA−ERARRES3NINJ1LY75 IRF7GLRXIFITM2IFITM3 PAOXPPP1R3DABHD8MARCH2 ADCK2EFHD2HPS1PAK1 FAHSQRDLNPC2C14ORF169 PSMB10DOK1APOBEC3FAPOBEC3G CD58YIPF1CD302MGST2 PPCSPHF11PGCPTMBIM1 HFEASLICAM3RAB32 ARSDHSPB1SH2D4ASLC25A24 HDHD3PNPLA4NQO2TRIP6 RAB3DRBP1ACADSSLC25A20 BLVRBSTOMXKR8MT1E PICK1LGALS8DYNLT3HEBP1 KIAA0323SSH3GALCEML2 SLC27A5MESTPRUNE2RRAGC MTHFSKHKSLC37A4ETV2 RAB33BFAM50BPDE6BS100A13 SSPNCOBLTDRD7C3ORF14 GJA1TMEM47ADRA1ABHLHB3 IQCGSLC22A5EPHX2CHRD KLHL26MOSC2RGNBDH1 MGC2752CAPNS1C13ORF18FLJ20699 EFEMP2MSNEMP3SLC43A3 PHKA2ECHDC2DDB2PLP2 RAB11FIP5CYB561FBXO17KIAA0495 PRPF4BSFRS2RAB36PSEN2 TAF5LEXOD1GTF3C3ERCC3 BRD9TRAF4SETDB1GTF3C2 THUMPD2NR2C1SFRS6CCT5 PLK4KIFC1NCAPHPOLA2 CNOT6MYBL1KIF14MKI67 MTMR2SR140SKIV2L2CCDC99 SCML2INTS7ZNF239EYA1 PRR3PHF16ZNF695TFDP2 TTC13GNPATDET1TEX10 DUSP10MLLT4C6ORF124AKAP7 TUBGCP4EDC3UBR5GAS1 FXYD7SUSD5GFRA1RANBP17 PCDHGA3TPTENEUROD4NEUROD1 ATXN2LPOLR3EEEF1DRPL23 LIMD1AMHEDG4UBFD1 POLQPOLENCAPD3MSH5 MTA2BOP1VARSCEP152 ZNF384CDK5RAP2NUP188PDCD11 DBN1PFASSMARCD1LRP5 EHMT2PROX1GSK3BJARID1B LBRRAF1ZNF318MDC1 DHX8KIAA0133NUP153TOPBP1 LRCH1WRNIP1CNNM3CDK10 HNRPA3HNRPH3SFRS1DNAJC7 ZC3H7ATPP2BRD1DDX46 JMJD1CARID4BMGEA5STX6 TCERG1PRDM10AGPAT4GNE C10ORF18GTPBP4IKBKAPSECISBP2 TAF5MPHOSPHPARGC10ORF1317 ZNF589ZNF37ABMS1ARHGEF11 QRICH1RNF123RAD54L2FLJ10213 CEP63RBM15BUSP19DHX30 ZNF167TSEN2PBRM1SMARCC1 LARSC4ORF15ANAPC1GNL3 KIAA0947DNAJC13C1ORF107NUCKS1 Samples Color Key

024 Row Z−Score FGFR1 Mutations

ALDH1A3

ABCB4

Samples Color Key

−4 0 2 4 6 Row Z−Score FGFR4 Mutations

TFDP2

CDH7

PRPS2

ACADS

SLC25A20

CBR1

SSH3

HEBP1

Samples Color Key

−2 0 2 4 Row Z−Score FN1 Mutations

ZNF239

SEPHS1

GTPBP4

ZNF22

C10ORF68

SFRS6

Samples Color Key

05 Row Z−Score FURIN Mutations

−3 −1 1 Row Z−Score HPN Mutations

GALR1

NSMAF

HGSNAT

Samples Color Key

−5 0 5 10 Row Z−Score IDH1 Mutations

TRIT1SUPT3HZNF239WDR70VRK1C14ORF10HIST1H2AC16ORF68DUS2LCENPTRXRBRP5−1077HTRA2 BK4 PRR3RBMXRBM4TRMT12ARMC1CNOT8CHCHD8NDUFC2STX8RNF5NDUFB11PQBP1ZNF124 TUBD1ZNF187ZSCAN16SPASTRBM4BNARS2CEP57PRKRIRLOC40050TRAP1NIP30RRN3HIRIP3 6 ARL3CUEDC2ADKASCC1VPS26ATMLHEANGEL2TOMM70ARBM34PCCBTTC13COG2ZNF22 BCCIPMRPS16ECDRPP30GLRX3C10ORF68COMMD3PDSS1ATP5C1HSPA14COX15CUTCABI1 RPL10LRPL10RPL37ARPL39RPS10RPL18ARPS3SLC25A16TIAL1NOC3LCWF19L1TFAMMARCH5 ZNF695UPK2CHRNA4SLC25A21POLLPCCAKBTBD4ATP5G2PHB2RPS11RPL30RPL29RPL7A SKIV2L2CNOT6NAB1WDR67MYBL1MAPK8HSF2BPNHLH2LHX1ITGB1BP2DOK4TFAP4ZSCAN2 PALB2EXOD1THUMPD1FBXO38SF3B1CENPC1PRPF4BCCNT2GTF3C3ERCC3TCERG1DDX46SR140 PRKYHCRP1C16ORF67GSDMLEDG4UCNLRP2BPTRPC3PRDM10TERF1NPATNR2C1CSTF3 KIAA0528WDR42APOU6F1CALCOCO1LETMD1ANKZF1SEC31BC8ORF44CYP2E1ANGEL1ZNF409KIAA0913COL7A1 MSTNC2ORF33GADD45GUSTC20ORF42LUZP2C13ORF15TMEM100PDE8BRASSF4CRYABSUHW4ZNF518 BCL7ATOX3MYCNPHF16DLL3SLC22A14DNASE1L2AGERNUDT13SIGLEC6TNFBMPR1ANUDT4 LGR5ALCAMRBPJAMOTL2EYA1CDC5LLRRC1DNAJB5MARCKSMYCL1SLCO5A1VIPR2RPRM PCDH11XZFPM2SORCS3GFRA1ELAVL2CRTAC1FGF12C2ORF27ZNF804AFLRT1FCHSD2RAP2AEVL SPSB3LOC51035PELI2TUT1COL11A2DLGAP1DRP2SPTBN2PAX4LGALS4PRYFGF17TNR ZIC3REM1ASB13TPTEPTCH1PARD3DHTKD1CUGBP2PRKXSEMA4GPCDH21GRIK4SEMA6C SCD5DSCAMOLIG2ACCN4FXR2FASNPIK3R2ADD2DPYSL4DBN1CRMP1CPS1TRIM48 RFXAPTTC28HPS4GTPBP1EIF4ENIF1CSNK1ESAMM50AKT3MAPTRALGPS1C20ORF19ARHGEF9PID1 DCLRE1CFRMD4AZNF208ZNF257H2AFY2RANBP17CBLN1ADAMTS6NBR2ERCC5TPP2TUBGCP3FAM48A NACAP1RPL37RPL31RPL4EIF3EIPRPL3RPL23JOSD3PARGZNF248PAPD1WACMLLT10 MPSTPOLR2FKIAA0974CBARA1C10ORF22CSTF2TKIAA1279SIRT1SUSD5C10ORF76MMS19TUBGCP2TNKS2 H1F0CROCCMEF2DMTMR8CBLBBMP2EEF1GEIF3FIMPDH2VAX2CORO1CCECR5BID DET1XRCC4APAF1ERCC6KIAA0182BCOREPB41TLE3UPF2C10ORF18GTPBP4LARP5EIF4EBP2 KLHL20CDKAL1TUBGCP4EDC3TAF5C10ORF13MPHOSPHSUPV3L1DDX50NOLC1PDCD11MTA2PEO1 17 DHFRPOLA2ATAD2BRIP1TMPORACGAP1CDC2FBXO5KIF11PLK4EXO1KIFC1NCAPH E2F2CDC25CMXD3KIF22INTS7XRCC5TMEM97CKAP2RFC5HMGB3CDC25AKIF15CCDC99 SFRS2BYSLSRPK1TFDP2SCML2DNA2LZNF492ZNF286AAOF2ZNF643MCM10SUV39H2HIST1H4A USP3FAM60ANUP88C12ORF48TEX10EXOSC2DDX52SMARCE1UTP6NUP160ZNF207TAF11TIA1 ILF3SFRS1SFPQHNRNPRDHX9HNRPH1TAF5LBAT2EWSR1BRD1DCCNEUROD1INSM1 POLR3EMSH5CREBZFIKBKAPCAMSAP1TTF1SECISBP2NUP188MDC1SMPD4SUZ12ZNF131HNRPA3 NONORFWD3TCF3PFASLRP5SMARCD1CSNK2A1SETDB1GTF3C2INCENPFANCEBOP1VARS XRCC2POLQATAD5POLEKIF14MKI67SPAG5ESPL1TROAPCEP152LIMD1PRPF40ALBR NFX1PLCB4FHOD3KIAA1166C14ORF93HIC2ZNF74CENPJDBF4BDDX11WHSC1TOPBP1NCAPD3 RBM5CHD9TAF1CBTAF1CXORF45TROSIAH1UBAP2RNF38ZBTB5NFIBWDR32GNE RFX5ZNF589PHF8MED12PCNTSFRS15ZNF674GNL3LNFATC2IPUBE2G2CROPSFRS18NKTR JMJD1CARID4BMGEA5ANKRD26ZNF37AZNF236SLC12A6ZNF609VPS53MDN1BMS1ARHGEF11ATF7IP LRFN4TCF4NOVA1ZEB1ZNF254ZNF85ZNF682ZNF675ZNF253KLF12ARHGEF7CCDC88AMYST4 MSL2L1DVL2TBCDRBM12BPOU2F1ALMS1ZNF318POGZPBRM1SMARCC1CHD7BAHCC1AZI1 SAPS3JRKLGSK3BJARID1BJMJD3HCG_4073TMCC1HNRNPA1SLC39A6CTCFRAF1SMC3HNRPH3 8 MTA1PNNTCF12RFXDC2ZNF384CNNM3C4ORF30MCM3APAC20ORF11CKAP5RSF1C11ORF30EHMT2 S7 TOP2BTTC3SMAD9BCRMUM1NFIXNFRKBNUMA1C17ORF85SAFBTSC2CHD8PABPN1 PHF21ATLK2ZNF292CLASP1BRWD1DYRK1AARID4AYTHDC1FBXO11ZNF510ZNF711MTMR1JMJD1B HLA−DMBAIF1CD53TLR1LYRNASE6CD86CTSSSLC7A7IAPPGPATCH8MLLSETD2 N NCF2ALOX5ALOX5APFGL2HLA−DPB1HLA−DRACD74HLA−DMACASP10RPS6KA1SERPINB1NPC2PYCARD ASAHLLY75IL13RA1FLJ22662CASP4CASP1S100A4S100A11SQRDLCAPGSP140UNC93B1LHFPL2 OSTF1MAFP2RY5SLC2A9CD302MGST2KCTD12TMEM176BMKNK1CARD9NLRP3PRKCDSERPINB9 CXCL10PLSCR1NMIGCH1GLRXAPOBEC3PSMB8TRIM21NINJ1CCDC69TPK1TNFSF12RHOG G APOL3APOL2ISG20LOC93349SP100HLA−EIFITM2IFITM3TRIM14MYD88TAPBPLBST2IRF7 OGFRL1BLVRBSTOMCOPZ2DHRS3RARRES3FPGTZMPSTE24HERC5PARP12HERC6FLJ20035OAS1 DCTDYIPF1PGCPTMBIM1PIRACAA2PRDX1HEBP1BHLHB3SSPNTMEM47FLJ20920EPHX2 CST3XKR8MT1ERBP1CBR1SLC25A20ACADSHDHD3PNPLA4RGNNQO2PPCSPHF11 ELOVL1CSRP1HRASLS3CYP27A1INADLABCA5WDR78SPAG1IQCGC14ORF45MOSC2TMEM22GJA1 PLEKHF1PPP1R3DMARCH2EFHD2PAOXSEPP1PDE6BGCAFLJ11151CYB5R2PICK1GPR37EML2 SOX18LILRP2FOXP3SEC14L4CEBPEC20ORF23SDC4PTP4A2SYTL2GLULC1ORF34NUPR1BAG3 FAHRRASICAM3VAMP5RAB32ORAI3PSMB10DOK1TFR2GPR157RGS14SARDHMAGEA12 TSPOMED8RER1MRLC2SERPINB8TMSB10IFNGR2DAPUBTD1BET1LPSEN2BCAP31HFE CYB5R1S100A6LEPROTRP11−217CD58S100A13MTHFSBCAP29ASLGSTK1ETHE1ILKC1ORF78 H HPS1DUSP3CXCL14RCAN3UPP1SLC25A24SH2D4APRPS2SDC2TAF13URODTMEM53CYBRD1 C10ORF59DYNLL1IQWD1PAK1SNX10PTPRHGALNT12MFI2NPAL2C9ORF95A4GALTLGALS8DYNLT3 ACTN1MAN1C1C1RLSERPING1SH3BP2FLJ20699SLC24A6PLTPSNFTCLDN1EMID1TNFRSF11DDB2 B TCAG7.131PIGBSWAP70LOC26010KLF3CD164SPP1LITAFGALCNUMBTGFB2MAOBHRH1 4 EFEMP2MSNEMP3SLC43A3TWISTNBOLFML2AACVRL1FUT4NSUN5TMEM185BATP10DRNASELTBC1D1 RIC8ASMPD1RNH1PFKLMGC2752IRF3TMEM147CAPNS1TRIP4DRG2FBXO17KIAA0495AEBP1 TRIP6ANXA5SLC2A10ARSDLGALS1CD63CD151TAGLN2NUCB2SCG2SLC9A1STIM1PARVA PMP22SERPINB6M6PRBP1CASTPTRFPLP2LGALS3CHI3L1PYGLLDHASTBD1ANGRNASE4 CASP8HEXBCUL7MXRA8COL1A2HSPB1MAP3K6ACOX2FZD7IL17RCMOXD1FLJ21963RAB3D ANKRD25RELBCLEC5ADPYDFAM129AANXA1ANXA2PDPNCCDC109BCLIC1SH3GLB1LIMS1RBMS1 UTRNOSBPL10HLCSARL4COSMRLMAN1PLOD2ADMBHLHB2NDRG1PTPN14PLOD3SLC2A4RG NUP210FSCN1AYTL2KIAA0323SSH3LBA1SLC12A7RAB11FIP5CYB561CCDC46RAB36C14ORF16FAM50B 9 COBLTLE4ITGA6TRIM68SPRY1SPRY4DUSP6LAMC1IGFBP2PLATCCL27AQP5MEST GALNT11USP4MAN2B2CTR9CENTD1KIAA0494ITPKBMAP4TRPS1DMNITGB4KIAA0562WWC3 MID1DHDDSSEPT11RTCD1RRAGCC7ORF24FTSJ2CEBPGTFRCLPIN2ATXN1SIRT3AP2A2 PKD2ATP1A1APLP2MACF1KIF13BCES2PHKA2FLJ11286ECHDC2C13ORF18FKBP5CLCC1C1ORF108 NR2E1FEM1CSNAPC2FZD8AK3L1SLC27A3CDH6ZNF334HSP90AA1MLC1BBOX1ALDH7A1EYA2 TMEM50ARAP1AIMPACTUBBMINAVAV3ELOVL2ARNTLPDGFAFABP7MCCGNA12F3 OSBPL1AKLHL26BDH1SLC26A4INPP4BADRA1ADKK3TUFT1BCAS4TRIM36C9ORF40RAB33BTMED5 Samples Color Key

024 Row Z−Score INHBC Mutations

TSFM

CENTG1

Samples Color Key

−2 0 2 4 Row Z−Score KCNG1 Mutations

EHBP1

LEPR

PIGK

DNAJB4

PLD3

NAPA

NUDT9

SDAD1

Samples Color Key

05 Row Z−Score KLF6 Mutations

05 Row Z−Score LEMD3 Mutations

−3 −1 1 Row Z−Score LGALS3BP Mutations

IFI44L

PKN2

BHLHB3

PIGK

Samples Color Key

−4 0 4 Row Z−Score LUM Mutations

ADAM2

CR2

PLAC4

TMEM40

LMAN1L

OR2H2

OR7A17

PRDM8

Samples Color Key

−20246 Row Z−Score MADD Mutations

CXCL12

GZMK

KLF4

ITGBL1

MCTP2

ISLR

OGN

EML4

FLJ22662

LNPEP

CTGF

COL15A1

EGFL6

OLFML1

Samples Color Key

05 Row Z−Score MAPK9 Mutations

CD53 LCP2PTPN6TLR1LYAIF1 N FGL2CD74HLA−DRAPYCARDGMFG PSMB10CASP1APOBEC3CD302P2RY5 G GIMAP4HCLS1RGS10CASP10RPS6KA1 MKNK1SERPINB9PRKCDNLRP3DEF6 UNC93B1STAT5AAXLPIK3CDRHBDF2 FAHSQRDLNPC2GAS6SLC24A6 DHRS3C4ORF18LY75IL13RA1SLC2A9 RARRES3GBP1HLA−EBLVRBSTOM APOL3APOL2IRF7BST2IFITM3 CSF1LOC93349SP100SECTM1FES PAOXBAG3GALNAC4SBHLHB3SSPN EML2PDE6BGCARAB11FIP5SYTL2 PSEN2PPP1R3DMARCH2TNFSF12EFHD2 LITAFHPS1PAK1C9ORF95NPAL2 DCTDYIPF1PGCPTMBIM1RCAN3 DYNLT3NQO2SH2D4ASLC25A24PRPS2 SLC25A20ACADSH2AFJPIRLGALS8 GNG12RHOCCNN3HEBP1CBR1 RP11−217CD58ORAI3C1ORF54MGST2 H C1ORF78HFEVAMP5RAB32LEPROT PDPNF3CSRP2C13ORF18PLEKHF1 C1RLCSDAFAM129AFLJ21963TRIP6 EFEMP2MSNEMP3SLC43A3PTRF HSPB1ANXA1ANXA2LEPREL1LDHA SAMD9PARP12KIAA0323CUL7MXRA8 MAN1C1SH3BP2TPST1GDPD2HERC5 CLUWDR78SPAG1IQCGTGFB2 TIMP3GPR177KAL1VCAM1RNF19A APOEPRUNE2DMNITGB4PLEC1 PPAP2BCHRDROM1TDRD7PEA15 TMEM47FLJ20920EPHX2BMPR1BGJA1 KIAA0495RBP1TRIM36C3ORF14ADRA1A MOSC2TMEM22BDH1RAB36FBXO17 RGNTTC12PHF11MT1EFAM50B NCAPHOPLAHSSH3ECHDC2PNPLA4 CDC2KIF11PLK4EXO1KIFC1 HMG4LHMGB3DHFRCCDC99ARHGAP11A QSER1FANCEMCM4FEN1POLA2 MKI67POLQPOLECEP152MPHOSPH9 TMEM97RAD1TUBG1MYBL1KIF14 RBM4CCT7XRCC5NUP88ZNF207 DNA2LVRK1INTS7TEX10PRR3 CHMLTTC13NAB1TFDP2SCML2 WDR32DNAJB5TAF5C10ORF13MPHOSPH17 SIAH2GRK6C12ORF11POLR3DVARS AGBL5SFXN1UIMC1KTELC1UMPS MRPS30CCT8NUP155UCK2SLC25A15 NDUFS2ATICKLHL12UCHL5RBM34 SKIV2L2CNOT6FAM48AARMCX5ASB1 TCERG1FBXO38EXOD1GTF3C3SFRS2 TUBGCP4EDC3RPL4CLK3DCP2 ZBTB11TOMM70AANGEL2DET1EYA1 NUCKS1ELK4CHD1LEIF4EBP2KIAA0913 VASH1POLR3ECREBZFCLK2NFATC2IP RCOR1KIAA0586ARID4APABPN1MTA1 PRPF19USP21HNRPH3SFRS1TAF5L FXR2FASNPIK3R2BMS1ARHGEF11 PA2G4HDGFDVL2RNF126CSNK2A1 NUP188GLE1LKIAA0133HNRPABRFWD3 EHMT2MDC1RBM14SETDB1GTF3C2 ALMS1TOPBP1CEP63BRPF1RAF1 PSMD11KIAA0692DDX21STX6BRD2 PPP4R2CNOT1UBN1MAML1DHX8 DBN1JMJD3NUP153CFDP1ADD2 SMARCD1LRP5SOX12GSK3BJARID1B JRKLMTA2TCF3HNRNPUPFAS BRD1H1F0JOSD3TUT1SAPS3 PRKXSNRPD3HMG2L1EIF3EIPGTPBP1 DZIP1ARHGEF7TPP2APPL1PHF16 IKBKAPSECISBP2CXORF45ARHGEF9RNF44 ZNF236MYST4JMJD1CHCRP1NR2C2 TRAP1PCCBCNOT8ANKRD26ZNF37A TPTEC14ORF13TTC19RMND5B 13 GTPBP4LARP5DIP2CRANBP17H2AFY2 ECDVDAC2UPF2C10ORF18KIF5B DDX50SIRT1SUPT3HZNF239SLC25A16 ZSCAN2ZNF695PARGKIAA0974SUPV3L1 ST3GAL5NUDT13PRKYATP5G2TLX1 Samples Color Key

−4 024 Row Z−Score MARK1 Mutations

DSCR2 MED8 ACAA2 C7ORF24 REXO2 PRDX6 TIPARP MINA TSPO CTBS ELOVL1 PHF11 PPCS CHI3L1 LGALS3 DYNLT3 SPATA6 C1ORF63 ATR ZNF783

Samples Color Key

−4 024 Row Z−Score MET Mutations

MCM10

TRIM68

DHX58

PHKA2

SSPN

BHLHB3

ACAA1

LZTFL1

NR3C2

PH−4

Samples Color Key

−3 −1 1 3 Row Z−Score MKI67 Mutations

RAMP2

UNC84A

Samples Color Key

−2 0 2 Row Z−Score MSH6 Mutations

CASP10

PRKCH

PDXK

Samples Color Key

−2 0 2 Row Z−Score MYST4 Mutations

CPE

PDXK

Samples Color Key

−2 0 2 Row Z−Score NF1 Mutations

EGR2

ATG7

TCN2

BCKDK

CAMK1

ZNF659

LONRF3

ACP6

MREG

DNMBP

Samples Color Key

−4 0 2 4 Row Z−Score NOS3 Mutations

TSN SUMO1 PRKRA RY1 C2ORF47 UTP11L DDX18 MRPS10 LYRM2 C9ORF156 GGPS1 C11ORF51 COX8A TMEM177 CINP ZNF410 MED6 SIP1 CEP27 CDC42 C2ORF3 PRKAG1 PRNPIP TXNDC14 HSDL2 PRRG2 MPPE1 MED18 COMMD3 HSPA14 FOXN2 TADA2L C15ORF29 ZNF22 C14ORF133 ZMAT5 TOMM22 BNIP1 CHCHD8 MRTO4 STX5 SSSCA1 LSM12 MAPK12 TRMU TFPI RHBG ZNF444 QARS RNF123 USP19 WDR6 DCP1A RAD54L2 ATXN7 ANKRD11 KLHL18 FYCO1 GOLGA4 Samples Color Key

−4 0 2 Row Z−Score PI15 Mutations

TRIM21 PSMB8 MTHFS ASL RAB32 MRLC2 S100A13 CYB5R1 CYBRD1 CYP27A1 ELOVL1 TMBIM1 PGCP PPCS YIPF1 SLC25A24 DYNLT3 LGALS8 S100A11 CAPG IL13RA1 DPYD HSPB1 SLC43A3 EMP3 MSN TNFRSF1A EFEMP2 RNASE4 ANG CLIC1 CCDC109B LGALS3 HDHD3 ACADS RAB33B ALDH7A1 PHKA2 RBP1 KIAA0495 RAB36 GALC FLJ11286 XKR8 SWAP70 SSH3 KIAA0323 Samples Color Key

−4 0 2 4 Row Z−Score PTK2B Mutations

SDHC MRPL15 EIF3I SCYE1 MAP2K1IP1 RY1 UBE2V2 ZC3H15 EBAG9 PTRH2 HIP2 PRDX3 VPS26A PEX11B RABGGTB HMGN3 ECHDC1 FIG4 FRG1 CDKN2AIP CCNC MOBKL3 SLC35A1 COMMD3 DCTN3 ACR C19ORF60 RABAC1 PLD3 ACAT1 SPOP FAM8A1 RAD17 USP14 KIAA1012 C4ORF20 FLJ12716 UTP6 DPH4 TNKS2 AP2B1 KRAS GPS2 RSAD1 SLC25A36 SMURF2 FKBP2 NUDT9 PAK4 HARS MAEA COASY ABCF1 TCL1B PSG1 Samples Color Key

−2024 Row Z−Score RB1 Mutations

HIST1H2BE

HIST1H2BI

HIST1H2BO

HIST1H2BL

HIST1H2BJ

HIST1H2AG

APEX2

ALDH3A1

XYLB

LAMA3

C9ORF40

CHAF1B

Samples Color Key

−4 −2 0 2 Row Z−Score SRGAP1 Mutations

TRIM68

RBP1

PMP22

ACADS

SLC25A20

Samples Color Key

−2 0 2 4 Row Z−Score STK36 Mutations

P2RX7

LPIN1

Samples Color Key

−5 0 5 Row Z−Score SYNE1 Mutations

MXD3KIF22HIST1H4APKMYT1 DDX39SNRPBC12ORF48CDC2CDCA3CASC5WDR76 ANAPC5DUS2LHIST1H2AC16ORF68NUP85POLE2RNASEH2AK UTP18ZNF207MAD2L1BPTAF11LOC40050BCS1LDFFB 6 NOL11RAD1DUSP12SMAD4CEP76SNRPD1NUP88 USP3ZNF22RAD54BTAF7WDR12EXOD1DDX18 GNPATRBM34XRCC5AGBL5CCT3DEDDPMF1 ZFP37EXOSC2MCM10SUV39H2INTS7PRIM1DET1 SCML2DNA2LZNF492SEPHS1ZNF239TFDP2TEX10 TOMM22ZNF764UBE2IPA2G4HDGFC18ORF22PTMS THOC5SNRPD3SMARCB1MPSTPOLR2FXRCC6ADSL PPP4CLRRC42PIGCEIF2B3POLR3CUTP11LMRPL9 NAT13G3BP1NHEJ1GABPB2UCK2THOC6DCTN5 WDR74ZFPL1CHCHD8HTRA2ABT1SNRPCDAP3 NME4PEMTC20ORF67IFT52GSTP1PSMB6SSSCA1 MRPS35UQCRC2PEX19SDHCPUF60CLNS1AATPAF2 GTPBP8UBXD6TIPRLDGUOKMAGMASMRPS27BTF3 GPS1ASPSCR1ARMCX5RMND5BPUS7LNIT2CCNH BNIP1MRPS7URM1SSNA1SURF2OBFC2BPQBP1 ZNF124PLEKHO1ATP5G2PHB2RPS3STX8PSMB3 ASCC1GDI2COMMD3TFAMPDSS1ATP5C1HSPA14 MTG1TRDMT1RPP38NMT2C10ORF68MRPS16SLC25A16 PCCBCIAPIN1MED27LSM4SCYL3ZNF364MED18 TRAPPC2CLGNTRMT12PRUNEFKBPLZNF232PPOX SUPT3HHOXA10TMLHEANGEL2SIRT4TTC13DCLRE1A APEX1C17ORF39SKIV2L2CFDP1TEX15ZSCAN2ZNF695 METT11D1DLSTCOQ6VRK1C14ORF10PSMB5HNRNPC 4 NXNZNF286AAOF2DBN1RAC3YY1C14ORF133 VAX2CCDC28BGADD45GMTSS1FAM77CPHF16DLL3 NUP153CDC5LZNF770TUBGCP4EDC3EYA1MTMR2 CDKAL1GMEB1MCPH1ZNF669TGS1ACVR2ATCP1 H1F0TPTEDIP2CSUSD5RANBP17H2AFY2KLHL20 SUPV3L1DDX50KIF5BYME1L1C10ORF18GTPBP4DDX21 JMJD1CZNF37ADCLRE1CTAF5MPHOSPHPARGC10ORF1317 CSTF1NOL5ATH1LCSNK2BLOC90379CDC34PRMT1 TRIM27POLR3ECDK10TP53CTPS2RBM38ACTR5 DDX31GTF3C4GLE1LNUP188NOL1KIAA0922VARS DNMT1ILF3TOP3ALIMD1LIG3GEMIN4PFAS GTF2H4DHX8PRPF40AKIAA0133NCAPD2SSRP1TCF3 HNRNPLRBM12DDX52SMARCE1PSMD11PSMD3TAF5L CCNT2GTF3C3ERCC3ORC2LTIA1SFRS2SNRPA SNRPFPWP1CENPC1ELF2FBXO38SF3B1PRPF4B KIFC1NCAPHTDP1TMEM48NUP155CCT5CCT7 POLA2CTPSCCDC99BRIP1TMPOCDC6PLK4 MCM2POLERAD54LFANCAHMG4LHMGB3FEN1 BUB1BUB1BBRCA2GINS4E2F8CDK2FANCC XRCC2POLQATAD5CEP152NCAPD3MPHOSPHMKI67 9 RNF126FARSAATG4BUSP21SFMBT1PASKMYBL1 RBM10RBM14THOP1DVL2PRPF19BRD9RANBP3 PPP1R10ALMS1TOPBP1CEP63SMPD4HNRPH3MDC1 THRAP3SAFBDHX16BRD2BAT3KIAA0692BRD1 IKBKAPSECISBP2ZNF510TCERG1PRDM10BMS1ARHGEF11 TLK2C11ORF30EHMT2CCNJSAPS3MTA2ATF7IP SETDB1SFPQHNRPH1DHX9SFRS1GSK3BJARID1B NRF1LIG1KIAA0406CSE1LGTF3C2RAF1C1ORF77 ZNF85ZNF675ZNF253LRP5SMARCD1MSH5CREBZF RBM4BTPP2ARHGEF7PGAP1FBXO11ZNF254ZNF43 C1ORF183TADA2LNARS2PRKRIRPRR3RBM4ZSCAN16 UGCGL2PCID2SFRS6TSEN2MLH1ROBO3KCNAB3 SP140LGALS9LCP2PTPN6GAS1NUFIP1SLC25A15 LY75IL13RA1FAHSQRDLNPC2STX11UNC93B1 LAT2PYCARDCD53KCTD12AXLTRIM22HLA−E HCLS1CD302FGL2CASP10RPS6KA1RGS10LILRA2 IL17RAPIK3CDPRKCDPLCG2DEF6DENND3RHBDF2 MAFPRKCHACSL5GIMAP6GIMAP4MKNK1SLC24A6 PARP12DHX58BST2APOETMEM176BTMEM176AGALNAC4S FLJ11151NPAL2EML2PICK1APOL3APOL2FLJ11286 CYB561TACC1IQSEC1CADPS2PAOXSPINT2HPS1 C4ORF18RBKSBLVRBSTOMC1ORF54MGST2RAB11FIP5 DYNLT3PPCSPHF11SLC25A20ACADSPPP1R3DMARCH2 RCAN3HSPB1ICAM3RAB3DMT1ETMBIM1LGALS8 EFEMP2MSNSWAP70F11RFAM129AIFITM3PLEKHF1 SERGEFCPT1ALMCD1LBA1FESMXRA8KIAA0323 GJA1SLC7A11MOSC2ACAA1PLCD1MAPK4BDH1 CYP2J2MTUS1SERINC1PRNPSMARCA2ITPK1CENTD1 FYCO1ZFHX3KIF1CPTPRBPDGFBPPARAADRA1A FKBP5DHCR7UTRNPHACTR2HEBP1BHLHB3SSPN OPLAHSSH3RAB36CCL27PHKA2KIAA0495C13ORF18 Samples Color Key

−4 0 2 4 Row Z−Score TCF12 Mutations

C3ORF63 TRIM68 HDHD3 SLC25A20 CBR1 RGN MOSC2 KIAA0495 FBXO17 RAB36 CSRP1 SDC4 HEBP1 HLCS OSBPL10 PRPS2 FKBP5 OSMR SLC2A10 FLJ21963 NEO1 TRIM44 UTRN LRRC16 C20ORF23 SWAP70 SSH3 KIAA0323

Samples Color Key

−2 0 2 4 Row Z−Score TP53 Mutations

BUB3 HSPA14 TFAM TIMM23 SAR1A SLC25A16 C18ORF22 HIST1H2BG GFPT1 GORASP2 PGRMC2 DERL1 SND1 ALDH1B1 OPRS1 RECK PRPF18 GTPBP4 SEPHS1 LRRC1 PQBP1 GADD45G PHF17 BAT2 C1ORF77 INTS9 DDX31 TMEM39B UGDH PLK1 DBF4 AOF2 TEX10 TCP1 TGS1 TAF2 CERK MDM2 Samples Color Key

−5 0 5 Row Z−Score TRPM3 Mutations

HLA−GHLA−B LOC93349HLA−EHLA−AHLA−F TMEM51RAB20LGALS3BPLAP3 DRAMCASP4TNFRSF1AMYD88 SLC43A3TGFBIHMOX1RELB NUPR1ATF3WDR1FAM129A ABCC3MANBAF11RCXCR4 CASTDPYDSTEAP3SRPX2 ACOX2CHPT1CSRP2CLEC5A SFRP4PALLDSLC2A4RGGNAI2 SH2D4ACD63CLIC1TAGLN2 STK17AUPP1ELK3LIMS1 B2MTRIM21IFI35NOX4 IRF7IFITM3TAP1PSMB8 DHX58SP110OAS1IRF9 NPC2ALOX5APSLC7A7RNASE6 DNASE2RARRES3CD302FCGRT S100A4CAPGS100A11ORAI3 FAHANXA4APOBEC3FAPOBEC3G CD300ASERPINA1RAB32HFE UNC93B1SERPINB1NCF2ALOX5 LILRA2PYCARDLAT2SP140 SPRASAHLLY75PRKCD ILKRBKSBLVRBMTCP1 PMP22TRIP6ANXA5M6PRBP1 B3GALT4HTRA1ABHD11IL17RC CYP27A1UBTD1TMEM53BET1L SREBF1SMPD1RNH1HRASLS3 AQP5ACBD4HS6ST1NLRX1 TDRD7EPHX2LRRC23WHDC1L1 CD9FEZ2ITGA6SSPN C14ORF45BBOX1HES1RHOC DCUN1D4CCDC46IQCGARNTL ZNF146SFPQHNRNPA0SGCB NOC2LCHMP7LAPTM4BSMARCA4 AARSD1TAF2TGS1PRKDC CNOT6SFRS6NUFIP1PPME1 CENPC1TPP2TCERG1DDX46 FBXO38CCNT2NUPL2PCGF3 HNRPH3BAT2EWSR1BRD1 STX6SEMA4CJHDM1DTAF5L RRS1JARID2MDN1ZNF281 MYBBP1AJRKSMG5GPATCH4 DAZAP1UBAP2NFX1RPAP1 SLC7A6ZNF37ABMS1BRPF1 PTGES2EIF4G3ARHGEF11ZBTB40 RNGTTPPP2R5DACTR5BRD9 ZBTB11FAM20BTTC13TCP1 KIAA0922E2F3AMMECR1TPTE RANGAP1MAP3K4ASB1GMEB1 CERKZBED4THOC5NUP50 HIST1H4EACVR2AARMC1TRMT12 ZNF536PLCL1ICA1ZNF702 MYO5AKLF13KLHL11TAF4B DCLRE1CZNF248PAPD1PITRM1 GOT2RPS6KC1C1ORF216SUHW4 SIRT1FGF12NET1SLC25A44 PTPN4CDK5R1SPTBN2C10ORF22 LOC55288ARHGEF9UBQLN2DLGAP1 9 CCT3SUV39H2PIP4K2BUBE2O CTPSZNF286AAOF2ZNF643 WDR67C1ORF135KIF14TROAP CLGNEPB41PRR3EXOSC2 RBPJAMOTL2CDC5LSRPK1 KIF21BDNM3RAB33AICK OLIG2RAP2AMTSS1DGKI RAD21CRB1DLL3DPF1 ACVR1BUSP46CBR4TERF1 ZNF667KRASCCDC88ACRKL GDAP1ZNF510ZNF675PTK2 IKBKAPCAMSAP1SECISBP2MTMR9 POGZC11ORF30EHMT2C20ORF117 SLC35E2RBM12BDGCR8PHF20L1 SOX5EDC4GFOD2DFFB MMP16CHD7CENPJKLF12 ZNF696GSK3BJARID1BDBN1 MED24SAFBTSC2XPO7 TTC3GRLF1MED1TAF15 CKAP5USP22CEP63MAP4K4 ZNF407ZNF623NUCKS1ANP32E Samples Color Key

−5 0 Row Z−Score WISP1 Mutations

SLC25A38

MLH3

Samples