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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 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 −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
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