Table 2 MS analysis of identified proteins in cells reprogrammed with c-MYC.

From: MYCL promotes iPSC-like colony formation via MYC Box 0 and 2 domains

(i) Proteins enriched more than two-fold in c-MYC-WT compared with MYCL-WT (SeV)

ATXN7L3B

TIMM21

SLC2A3

CA14

CRLF3

SYT6

TMEM161A

MTM1

METTL15

NKAP

CDS2

MRS2

MARS2

ERCC2

TDP1

MFAP4

ANAPC16

CARS2

NOLC1

IGHMBP2

MRPL34

FECH

PARP2

ING1

ADNP2

STEAP3

AK6

PDZD8

EPB41L5

PEX16

ZER1

CKS1B

GGPS1

DBNDD1

MIEF1

FUCA1

ADSSL1

POTEJ

TMEM209

CCNL2

TOP3A

ULK1

MGA

FAM162A

AMMECR1

ISG20L2

CEP78

NOM1

PAPD4

PROCR

IFRD2

LRRC41

UBR3

PHF3

RIN1

SPPL2B

ARAF

DNM2

HPS5

PSEN1

PARD3

ARHGEF16

RHPN2

PRPF18

SEMA4C

RPUSD3

NYNRIN

ARHGEF7

VRTN

PHF10

DMD

RPL26L1

RANBP6

CNOT4

TSPYL5

CDC25C

REEP4

FADD

INPP5F

ZBTB7A

GPN3

RBPMS2

BRAF

ORC6

CACNA2D2

AP1B1

NCAPD3

RRP8

MASTL

POLR2M

CASC3

NCL

C1orf174

LRRC14

SLC27A3

ACSF3

DHRS11

RBM23

WDR55

CAMK4

NDRG3

ALS2

NOVA1

SOX3

CLCN7

EHMT1

C7orf26

NSUN5

NMRAL1

STK25

NFKB2

OSBPL1A

VPS37B

RAD23A

HS2ST1

LYAR

PHKA1

SDC4

MGST2

SNTB1

MEN1

WDR4

DDX28

C1orf198

AKAP9

COQ9

STYX

PHF5A

PCDH1

TMSB4X

AP1G2

MYO1G

UCKL1

APC

TBC1D15

FASTKD1

APCDD1L

MARH5

ULK3

LONP2

SETD1A

ETFDH

ANKS1A

LRP8

PALD1

ANAPC5

CARMIL1

GATM

PANX1

NME3

UBA52

ZNF806

NCOR2

DVL2

CTDP1

PHKB

GINS3

DNPH1

CDCA5

BCKDK

TTF1

TGFBRAP1

HAUS2

HMGCR

SNCA

KLHDC4

TBP

AP1M2

E2F4

AFAP1L1

ZMYM6NB

N4BP2

TRIT1

CCDC134

ATL1

INTS6

CHD8

SPINT2

RASA2

NCK2

MAL2

ATAD3A

SLC25A32

LSAMP

ACOT8

KIFAP3

JARID2

CLSTN1

USP36

PTGIS

PIAS4

TMEM41B

SEC14L1

TUBGCP4

GEMIN8

VWA9

RPP25L

NRBP2

DOLPP1

WARS2

PLEKHA6

MRGBP

ZCCHC6

ZFP36L1

SLC4A7

SCARB1

ARID1B

PMF1

XXYLT1

ANKRD50

MT-CO1

MET

RBM47

LIN28B

EXD2

GORAB

GCSH

PLTP

PRKAB1

CUTC

SDSL

FARS2

LRRC8E

ARHGAP12

FBXW9

PMS2

NAA30

STRA13

FASTKD5

ZCCHC10

TTK

BNC2

COX16

BCS1L

NDE1

STX3

LARP1B

PTCD1

TPD52

SMG1

ACBD7

TRIP12

PTPMT1

ASB3

MTG1

ANKRD12

STK33

HEXIM1

RBM45

ATG9A

ANKIB1

B3GALNT2

C12orf43

SLC25A15

NDUFAF5

BAG4

NOA1

SFRP2

VPRBP

FOXK1

GPM6B

POLE

TRADD

AMFR

RPS6KA1

PLA2G4A

SELO

PROM1

CHTF18

BOD1

SPC24

KAT7

RAB17

IGFBP6

PNPLA4

AGTRAP

UBE2Q1

HIGD2A

RAPH1

SDF2

ARHGAP4

ODR4

MRPS18C

QSOX1

COX17

CHUK

RAPGEF2

GINS1

DFFA

CENPV

PTPN9

FUT11

ERMP1

SOGA1

DHX32

GEMIN6

HDHD2

GLE1

PTPRZ1

CREG1

GATC

PDXP

MID1

WRAP53

POU2F1

CA2

APPL1

TMEM14C

TXNIP

SLC7A3

FABP6

ITGA2

CWC22

MPDZ

PIGG

ACTB

INCENP

CARNMT1

RHBDD2

MRPL38

PUM1

HPDL

NME4

CDKN2A

TRIM27

ARHGEF10L

BDH1

CDC26

CTU1

ATF7

HMGXB4

L3MBTL3

MAP1LC3A

ISLR

URB1

MRPL21

CAMK1

RILPL1

WDR37

IGF2BP1

NAPEPLD

DPH6

FCF1

ANKRD29

ANAPC13

CD3EAP

WDR89

SLC25A17

DNA2

CENPM

CEP170B

GCA

CSTF2T

NKRF

SLC35A2

PMS1

SLC5A6

COQ5

SPR

RBM15B

USP19

LAMA4

DNM1L

INTS2

BCAS3

KIF22

NHEJ1

RPP40

TNC

SPNS1

RPRD1A

DDB2

IFIT5

ARMCX1

FAT1

DAP

BMPR1A

NPHP3

ARID3A

MRPL13

ZBED1

GTF2H1

PATZ1

DPH2

C11orf98

RRP7A

AKAP1

ANAPC1

NUDT16

CD74

DCAKD

ASB6

DNMBP

UTP11L

TUBG1

HAUS7

GAA

PDK1

DOHH

ISYNA1

BRMS1

EXOC6

ARAP3

CHKB

NOL8

DDX52

ORC5

COA7

NAA40

IQSEC1

TRIM24

DNTTIP1

HEATR6

SH3BP4

ZMYM3

MED30

CLASP2

PRPF38B

TMEM256

GTF3C2

MRPL10

NDUFAF7

VCPIP1

HSPB11

CASP7

TOR1B

ITPR2

PRPF39

GCFC2

KIF21A

DPPA4

TIMM8B

GTF2H4

MRPL16

BAZ1A

EXOC6B

MRPL41

POLR3B

USP9Y

SYNE2

MID1IP1

MOCS2

METTL5

PRUNE

UBE2V2

CDH1

GJA1

CHMP6

RCC1

RAPGEF6

COMMD9

HMBS

SQLE

IGFBP2

DIAPH2

EPB41

HIST1H1E

MAP3K4

CDK18

ARL15

UQCC1

HTATIP2

PTDSS2

TATDN2

MTA1

SNX18

EIF1B

MAEA

SCAF1

UBE2J2

NUP37

BAG1

TSSC4

RCOR2

FAM213A

MFF

TTLL12

UBXN6

EFEMP2

ZZEF1

NFYB

PDS5B

FXN

AGPAT5

ARFGEF2

TCOF1

SCAF11

RAPGEF1

PARG

PRIM1

USF1

L1TD1

SEPHS1

BRD8

POP7

EXT2

TSEN34

CAMKV

SLC29A1

MBD3

PPIF

MTX3

COG1

FASTKD2

ARL14EP

MRPL40

CD320

MBD1

VARS2

BRD3

MRPS18B

ACY1

PPIE

RIF1

VPS8

POGZ

RSL1D1

PAK1

STRBP

TERF2

TOP2A

SLC39A10

QRICH1

CISD1

POLB

DHX37

TRMT5

TIMMDC1

TRABD

SON

SET

LYST

RNASEH2B

MVK

ZC3HC1

NDUFC1

HSPA4L

EXOSC1

TCEANC2

NASP

CYP2S1

NSMCE3

HPRT1

HUS1

PRRC2A

RDH13

KANK1

PHF14

RBM7

SIRT5

QPCTL

CROCC

LIMK2

CWF19L1

KIF1B

VPS39

CHD7

YPEL5

SLC7A5

VPS25

LRWD1

FPGS

NT5C3A

NCKIPSD

PSIP1

CELF2

MDC1

ANP32A

ACADSB

GPC4

TUBB4A

BOP1

NT5C

CTSC

ANKLE2

ORC4

UTP18

CHST14

NUS1

PLK1

GPKOW

SIKE1

ADAM15

NUDCD2

SSU72

NFYC

LIG1

MSH2

HNRNPR

MSI2

STK26

EBP

ITPK1

STAU2

URI1

SLC7A8

MANBAL

RNGTT

PRIM2

SEC24B

MRPS34

RMND5A

F11R

SCAF8

RPAP1

SPATA5L1

RCC2

POLRMT

SERF2

TMEM115

PARP1

C2CD5

BEND3

BRAT1

TERF2IP

MT-ND2

FAM136A

NOP2

ARL5B

GFM2

WDR3

AARSD1

PPID

HRSP12

CHD2

MRPL45

YTHDF1

THEMIS

INTS4

PLEKHA1

CBX3

SIRT7

CENPF

CAMSAP2

MCC

PTPN2

NANOG

SLBP

MCAT

MRPL24

MZT1

ANAPC4

HIST1H1A

KPNA2

MED14

NDUFB9

NEFL

DUS3L

HSP90AA4P

CMSS1

ZNF706

PTRHD1

PBRM1

ABI3BP

MED10

PFAS

BRIX1

QRSL1

THNSL1

ADRM1

CECR2

NCOA5

ABRACL

WIPF2

USP28

GEMIN4

CHD1

SBNO1

LSM12

COG2

TARS2

KIF11

CHD1L

MLH1

MNAT1

DDX47

SRPK1

NACAP1

XPC

NELFCD

MPP6

HAUS6

TANC1

PPAN

MRPL33

PUM2

MRPL15

FAM65A

ERI3

TOM1L2

TIMM13

SPRYD4

MICU1

HMGN5

XPO4

WDR43

DDX20

YTHDC2

SLC25A22

CACUL1

PCF11

PRC1

DNAAF2

ACAT1

RWDD4

DHPS

PFKM

NUDT16L1

MTMR2

GPN1

SMARCA4

EI24

SCFD2

PPP3CB

RNASEH2A

GTF2E2

SMARCD1

ADCK3

TRMT1

RABEP1

CD97

GLT8D1

UBR5

HLTF

TXNRD2

TDP2

CCNY

NCAPD2

USP48

LRCH2

UBQLN1

TRIP10

MCM3

HSPA14

ZBTB8OS

MAP2K7

APOBEC3C

TTC27

DYSF

MINA

BAK1

HERC2

POLG2

TRAP1

EXOSC7

RCL1

C17orf62

PUS7

CASP6

ISOC1

THYN1

MYL6

CBR4

RFC3

SRSF10

LCLAT1

HIBADH

UHRF1

DHX57

MCM6

UBL4A

MRPS17

TFRC

GALK2

MKI67

CEBPZ

CHRAC1

TTC4

METTL3

GSTZ1

UBE2O

LRSAM1

NSA2

AGPAT4

MRPS5

MAP3K7

ZNF330

MLLT11

HK2

BLMH

PCCA

LYPLAL1

CPSF2

PEX3

INPP4A

SORD

SLC35F2

MRPL23

GNL3

WBP11

SAP30

INPPL1

TBC1D9B

MRPS31

GMPS

IMPDH2

SSRP1

LBR

TRIM28

NELFB

LDAH

DDX21

TWSG1

RBMX

NDUFAF1

PHF6

TFB2M

EBNA1BP2

ZMYM2

MLYCD

UROD

PKP3

NUBP2

FANCI

ARIH2

ZNF22

USP11

ARFRP1

PKN1

FAR1

MYBBP1A

PDS5A

CHMP7

COASY

SAP18

GTF3C4

SMARCAD1

DNAAF5

CTAGE5

GART

UBE2I

MRPL27

ENY2

PDK3

RUVBL1

PEAK1

WDR6

MYEF2

PWP2

RPA2

EXOSC4

FRA10AC1

ADAD2

NARS2

FAM64A

XRCC4

GTF2E1

DDX51

BMS1

OGFR

MRPL3

CHAC2

PES1

IGF2BP3

LDHB

ORC3

MSH6

DPYSL5

HEATR1

KATNA1

PTMA

SLC52A2

NLE1

MCM7

POLD1

MCM2

CXorf56

SMAD5

GPATCH4

STOML2

FLVCR1

MYH14

DAXX

ZCCHC8

TAMM41

TOMM34

LGALS3BP

PARN

KIF1BP

C5orf22

TP53RK

NACC1

MRPS30

TKT

ELAC2

PRKCI

PDCD11

DNAJB4

MTMR12

SUPV3L1

DARS2

RAVER1

SIGMAR1

DHODH

SLC3A2

BTAF1

HSDL1

EIF3C

TBPL1

NOC2L

MRPS28

CADM1

MRPL37

SRI

BZW2

NDUFC2

PCCB

DNTTIP2

PCBD2

TRIM2

CPSF1

RABGGTB

RFC5

ECT2

AGTPBP1

TRIM22

ECM29

PANK4

C11orf73

MCAM

THUMPD1

WDR18

RNPS1

SCO1

TIMM17B

INTS8

TUSC3

DCAF16

GTF2A1

SIRT1

UTP6

MRPL11

XRN1

DCTPP1

HSPBP1

TUFM

WDR92

PIR

ACAA2

DNAJC2

NPM3

ADNP

CERS6

NUDT12

APTX

DSG2

NTHL1

BOLA3

DDX24

NUP35

ATL2

NOL11

DDX31

ATPAF1

GCDH

RCHY1

C12orf10

HIP1R

PRPS2

MCM5

WDR75

RHOT1

KIAA1211

DDX54

RSPRY1

CDC123

NOP16

TACO1

GLMN

HOOK1

WNK1

NUP155

POLR1A

TBL3

GNAI1

KIAA2013

C7orf50

GUSB

GUF1

TIMM17A

GRWD1

LBH

CCNK

ILKAP

SMYD5

AGL

POR

LIG3

CMTR1

LRBA

WDR5

TOMM5

ARL8A

PCK2

PDCD4

NAT10

ACO1

TSC2

GNL3L

MTFP1

ABT1

KEAP1

ANKRD28

UBTF

STK3

SCAP

PPAT

PSAT1

APOA1BP

WDR54

SYT1

SCRIB

PTBP3

RNASEH2C

APOO

ASF1A

GSPT2

SDHB

SUPT16H

DBR1

PSME3

PPWD1

UBQLN4

CHAF1A

TRMT10C

SACS

BYSL

CDH13

USP24

ARID1A

GJB2

TEX10

UBA2

CLUH

ARL2

AS3MT

ABCC1

MRPL57

DDX56

EIF2D

ATP1B3

DCAF8

AGK

AIF1L

RBM42

FEN1

CCDC12

ELOVL6

EFNB1

NCAPG2

SARS2

OSBPL2

CDCA8

GNA13

ATF7IP

CCDC50

ADI1

HAUS8

C1orf131

GOLM1

DEK

DTD1

MCL1

INTS1

AHCY

GYS1

PAICS

DTWD1

CCDC59

MAK16

RUVBL2

ISY1

ECT2L

GTPBP10

ZNF593

RBM26

FDXR

MRI1

HS1BP3

LSM6

DNAJC8

SALL4

AATF

LETM1

LAS1L

MRPS11

SMARCA5

TMPO

LTA4H

MYCBP

MRPL19

NEPRO

PCBP2

WBSCR22

CCNH

DLGAP5

NDUFS7

NOP58

HDAC2

WDR48

GLTSCR2

PELP1

HARS2

NT5DC1

HIST1H1B

TOX4

TPI1

LUC7L

ATP11C

NXF1

HNRNPC

VRK1

KDM2A

COMMD8

CACNA2D1

RAD21

HNRNPU

WIPI1

USP39

SSB

CDCA7L

SNF8

LARS

ASH2L

VPS36

ZNF346

CRNKL1

TELO2

LRRC57

AASDHPPT

CNPY3

GLUL

CWC27

TNPO3

CHORDC1

CKAP2

CXADR

ILF2

PEG10

TTI2

MANBA

DCAF13

PLS1

LVRN

C1QBP

UBE2A

MEMO1

EIF4A3

EXTL2

MED24

GLYR1

UBXN1

MRPS18A

EIF5B

NIFK

POLR2H

HMOX2

ABCB6

NDUFB4

FNBP1L

NOL10

KIF5C

EXOSC9

ATP2B1

TOMM40

RBM28

GSTP1

TATDN1

FTSJ3

DAGLB

PLCG1

IFI16

HSPA4

TMEM192

MPI

SMPD4

POLE4

KDM1A

NUP188

TSFM

DLAT

FAM210A

POLR2D

NOL6

PRPF40A

UBAP2

MSTO1

GTF2I

SHPK

NUP133

RBM12B

DAB2IP

SAFB

LARP1

SPCS1

PDHA1

STX18

PPFIA1

NUP50

METTL13

SAAL1

QTRTD1

SUPT6H

ADSL

QSER1

POLR3C

TRMT1L

ASUN

BMP1

AFG3L2

GEMIN5

NEU1

PEX6

HDAC3

NDC80

MRRF

HMGN1

TIMM44

REEP6

OTX2

LPCAT1

MTPAP

SNU13

UMPS

TRIAP1

TUT1

GRSF1

NAA20

ACSS3

NCK1

ERBB2

CCDC28B

XRN2

NDUFAF4

MIF

PPP2R5A

SGSH

CRADD

MT-ND4

GATAD2A

MRPL9

RAD50

OSGEPL1

ADGRL2

MTUS2

NRBF2

FAM192A

DNPEP

THAP11

HEATR5B

RABGEF1

POP1

HEATR3

SRRM2

CACTIN

PRKD1

MRPL50

PRMT1

NIPBL

STK4

SLC25A35

ECE2

RPL13A

SDCBP

NTMT1

TBRG4

ZFAND6

DSEL

SDAD1

RPL21

PDCD5

PPIG

RALGAPB

MYO5C

TRMT6

RBM39

GULP1

DCP1A

IGSF1

POLG

UBE3A

SLC30A1

RFC4

TUBAL3

MGRN1

TPK1

KCTD10

SMAP

ACIN1

UBXN7

TMEM41A

DNAL1

F8A1,F8A2,F8A3

TKFC

BSG

ARHGEF40

FBP1

FBXL6

DFFB

TRIM33

EHBP1

ATP5S

CDC20

PLEKHA7

WDR73

CD70

EMC3

SLC9A3R1

COBLL1

TRIM9

SP1

YARS2

RBM19

CKMT1A,CKMT1B

HSP90AB3P

MRPL35

CCNA2

HDDC2

KDM3B

PPA1

SMARCAL1

MALSU1

AURKB

PPM1G

EARS2

HSP90AA1

SH3GL3

MPHOSPH6

NACC2

HMGB2

GTPBP4

ABCB10

CYP2U1

BSDC1

TLK1

LEO1

MFAP1

GIT1

FLCN

TYRO3

SH3PXD2A

EMC4

CPS1

INTS9

IRS2

SIRT3

FUT8

CDK2

TNFAIP6

SDHAF4

KITLG

ALDH3A1

GPR180

CFAP36

ANK3

CBX2

RBBP9

EML2

POLR3GL

FN3K

VWA5A

RAVER2

ATXN7L3B

TIMM21

SLC2A3

CA14

CRLF3

SYT6

TMEM161A

MTM1

METTL15

NKAP

CDS2

MRS2

MARS2

ERCC2

TDP1

MFAP4

ANAPC16

CARS2

NOLC1

IGHMBP2

MRPL34

FECH

PARP2

ING1

ADNP2

STEAP3

AK6

PDZD8

EPB41L5

PEX16

ZER1

CKS1B

GGPS1

DBNDD1

MIEF1

FUCA1

ADSSL1

POTEJ

TMEM209

CCNL2

TOP3A

ULK1

MGA

FAM162A

AMMECR1

ISG20L2

CEP78

NOM1

PAPD4

PROCR

IFRD2

LRRC41

UBR3

PHF3

RIN1

SPPL2B

ARAF

DNM2

HPS5

PSEN1

PARD3

ARHGEF16

RHPN2

PRPF18

SEMA4C

RPUSD3

NYNRIN

ARHGEF7

VRTN

PHF10

DMD

RPL26L1

RANBP6

CNOT4

TSPYL5

CDC25C

REEP4

FADD

INPP5F

ZBTB7A

GPN3

RBPMS2

BRAF

ORC6

CACNA2D2

AP1B1

NCAPD3

RRP8

MASTL

POLR2M

CASC3

NCL

C1orf174

LRRC14

SLC27A3

ACSF3

DHRS11

RBM23

WDR55

CAMK4

NDRG3

ALS2

NOVA1

SOX3

CLCN7

EHMT1

C7orf26

NSUN5

NMRAL1

STK25

NFKB2

OSBPL1A

VPS37B

RAD23A

HS2ST1

LYAR

PHKA1

SDC4

MGST2

SNTB1

MEN1

WDR4

DDX28

C1orf198

AKAP9

COQ9

STYX

PHF5A

PCDH1

TMSB4X

AP1G2

MYO1G

UCKL1

APC

TBC1D15

FASTKD1

APCDD1L

MARH5

ULK3

LONP2

SETD1A

ETFDH

ANKS1A

LRP8

PALD1

ANAPC5

CARMIL1

GATM

PANX1

NME3

UBA52

ZNF806

NCOR2

DVL2

CTDP1

PHKB

GINS3

DNPH1

CDCA5

BCKDK

TTF1

TGFBRAP1

HAUS2

HMGCR

SNCA

KLHDC4

TBP

AP1M2

E2F4

AFAP1L1

ZMYM6NB

N4BP2

TRIT1

CCDC134

ATL1

INTS6

CHD8

SPINT2

RASA2

NCK2

MAL2

ATAD3A

SLC25A32

LSAMP

ACOT8

KIFAP3

JARID2

CLSTN1

USP36

PTGIS

PIAS4

TMEM41B

SEC14L1

TUBGCP4

GEMIN8

VWA9

RPP25L

NRBP2

DOLPP1

WARS2

PLEKHA6

MRGBP

ZCCHC6

ZFP36L1

SLC4A7

SCARB1

ARID1B

PMF1

XXYLT1

ANKRD50

MT-CO1

MET

RBM47

LIN28B

EXD2

GORAB

GCSH

PLTP

PRKAB1

CUTC

SDSL

FARS2

LRRC8E

ARHGAP12

FBXW9

PMS2

NAA30

STRA13

FASTKD5

ZCCHC10

TTK

BNC2

COX16

BCS1L

NDE1

STX3

LARP1B

PTCD1

TPD52

SMG1

ACBD7

TRIP12

PTPMT1

ASB3

MTG1

ANKRD12

STK33

HEXIM1

RBM45

ATG9A

ANKIB1

B3GALNT2

C12orf43

SLC25A15

NDUFAF5

BAG4

NOA1

SFRP2

VPRBP

FOXK1

GPM6B

POLE

TRADD

AMFR

RPS6KA1

PLA2G4A

SELO

PROM1

CHTF18

BOD1

SPC24

KAT7

RAB17

IGFBP6

PNPLA4

AGTRAP

UBE2Q1

HIGD2A

RAPH1

SDF2

ARHGAP4

ODR4

MRPS18C

QSOX1

COX17

CHUK

RAPGEF2

GINS1

DFFA

CENPV

PTPN9

FUT11

ERMP1

SOGA1

DHX32

GEMIN6

HDHD2

GLE1

PTPRZ1

CREG1

GATC

PDXP

MID1

WRAP53

POU2F1

CA2

APPL1

TMEM14C

TXNIP

SLC7A3

FABP6

ITGA2

CWC22

MPDZ

PIGG

ACTB

INCENP

CARNMT1

RHBDD2

MRPL38

PUM1

HPDL

NME4

CDKN2A

TRIM27

ARHGEF10L

BDH1

CDC26

CTU1

ATF7

HMGXB4

L3MBTL3

MAP1LC3A

ISLR

URB1

MRPL21

CAMK1

RILPL1

WDR37

IGF2BP1

NAPEPLD

DPH6

FCF1

ANKRD29

ANAPC13

CD3EAP

WDR89

SLC25A17

DNA2

CENPM

CEP170B

GCA

CSTF2T

NKRF

SLC35A2

PMS1

SLC5A6

COQ5

SPR

RBM15B

USP19

LAMA4

DNM1L

INTS2

BCAS3

KIF22

NHEJ1

RPP40

TNC

SPNS1

RPRD1A

DDB2

IFIT5

ARMCX1

FAT1

DAP

BMPR1A

NPHP3

ARID3A

MRPL13

ZBED1

GTF2H1

PATZ1

DPH2

C11orf98

RRP7A

AKAP1

ANAPC1

NUDT16

CD74

DCAKD

ASB6

DNMBP

UTP11L

TUBG1

HAUS7

GAA

PDK1

DOHH

ISYNA1

BRMS1

EXOC6

ARAP3

CHKB

NOL8

DDX52

ORC5

COA7

NAA40

IQSEC1

TRIM24

DNTTIP1

HEATR6

SH3BP4

ZMYM3

MED30

CLASP2

PRPF38B

TMEM256

GTF3C2

MRPL10

NDUFAF7

VCPIP1

HSPB11

CASP7

TOR1B

ITPR2

PRPF39

GCFC2

KIF21A

DPPA4

TIMM8B

GTF2H4

MRPL16

BAZ1A

EXOC6B

MRPL41

POLR3B

USP9Y

SYNE2

MID1IP1

MOCS2

METTL5

PRUNE

UBE2V2

CDH1

GJA1

CHMP6

RCC1

RAPGEF6

COMMD9

HMBS

SQLE

IGFBP2

DIAPH2

EPB41

HIST1H1E

MAP3K4

CDK18

ARL15

UQCC1

HTATIP2

PTDSS2

TATDN2

MTA1

SNX18

EIF1B

MAEA

SCAF1

UBE2J2

NUP37

BAG1

TSSC4

RCOR2

FAM213A

MFF

TTLL12

UBXN6

EFEMP2

ZZEF1

NFYB

PDS5B

FXN

AGPAT5

ARFGEF2

TCOF1

SCAF11

RAPGEF1

PARG

PRIM1

USF1

L1TD1

SEPHS1

BRD8

POP7

EXT2

TSEN34

CAMKV

SLC29A1

MBD3

PPIF

MTX3

COG1

FASTKD2

ARL14EP

MRPL40

CD320

MBD1

VARS2

BRD3

MRPS18B

ACY1

PPIE

RIF1

VPS8

POGZ

RSL1D1

PAK1

STRBP

TERF2

TOP2A

SLC39A10

QRICH1

CISD1

POLB

DHX37

TRMT5

TIMMDC1

TRABD

SON

SET

LYST

RNASEH2B

MVK

ZC3HC1

NDUFC1

HSPA4L

EXOSC1

TCEANC2

NASP

CYP2S1

NSMCE3

HPRT1

HUS1

PRRC2A

RDH13

KANK1

PHF14

RBM7

SIRT5

QPCTL

CROCC

LIMK2

CWF19L1

KIF1B

VPS39

CHD7

YPEL5

SLC7A5

VPS25

LRWD1

FPGS

NT5C3A

NCKIPSD

PSIP1

CELF2

MDC1

ANP32A

ACADSB

GPC4

TUBB4A

BOP1

NT5C

CTSC

ANKLE2

ORC4

UTP18

CHST14

NUS1

PLK1

GPKOW

SIKE1

ADAM15

NUDCD2

SSU72

NFYC

LIG1

MSH2

HNRNPR

MSI2

STK26

EBP

ITPK1

STAU2

URI1

SLC7A8

MANBAL

RNGTT

PRIM2

SEC24B

MRPS34

RMND5A

F11R

SCAF8

RPAP1

SPATA5L1

RCC2

POLRMT

SERF2

TMEM115

PARP1

C2CD5

BEND3

BRAT1

TERF2IP

MT-ND2

FAM136A

NOP2

ARL5B

GFM2

WDR3

AARSD1

PPID

HRSP12

CHD2

MRPL45

YTHDF1

THEMIS

INTS4

PLEKHA1

CBX3

SIRT7

CENPF

CAMSAP2

MCC

PTPN2

NANOG

SLBP

MCAT

MRPL24

MZT1

ANAPC4

HIST1H1A

KPNA2

MED14

NDUFB9

NEFL

DUS3L

HSP90AA4P

CMSS1

ZNF706

PTRHD1

PBRM1

ABI3BP

MED10

PFAS

BRIX1

QRSL1

THNSL1

ADRM1

CECR2

NCOA5

ABRACL

WIPF2

USP28

GEMIN4

CHD1

SBNO1

LSM12

COG2

TARS2

KIF11

CHD1L

MLH1

MNAT1

DDX47

SRPK1

NACAP1

XPC

NELFCD

MPP6

HAUS6

TANC1

PPAN

MRPL33

PUM2

MRPL15

FAM65A

ERI3

TOM1L2

TIMM13

SPRYD4

MICU1

HMGN5

XPO4

WDR43

DDX20

YTHDC2

SLC25A22

CACUL1

PCF11

PRC1

DNAAF2

ACAT1

RWDD4

DHPS

PFKM

NUDT16L1

MTMR2

GPN1

SMARCA4

EI24

SCFD2

PPP3CB

RNASEH2A

GTF2E2

SMARCD1

ADCK3

TRMT1

RABEP1

CD97

GLT8D1

UBR5

HLTF

TXNRD2

TDP2

CCNY

NCAPD2

USP48

LRCH2

UBQLN1

TRIP10

MCM3

HSPA14

ZBTB8OS

MAP2K7

APOBEC3C

TTC27

DYSF

MINA

BAK1

HERC2

POLG2

TRAP1

EXOSC7

RCL1

C17orf62

PUS7

CASP6

ISOC1

THYN1

MYL6

CBR4

RFC3

SRSF10

LCLAT1

HIBADH

UHRF1

DHX57

MCM6

UBL4A

MRPS17

TFRC

GALK2

MKI67

CEBPZ

CHRAC1

TTC4

METTL3

GSTZ1

UBE2O

LRSAM1

NSA2

AGPAT4

MRPS5

MAP3K7

ZNF330

MLLT11

HK2

BLMH

PCCA

LYPLAL1

CPSF2

PEX3

INPP4A

SORD

SLC35F2

MRPL23

GNL3

WBP11

SAP30

INPPL1

TBC1D9B

MRPS31

GMPS

IMPDH2

SSRP1

LBR

TRIM28

NELFB

LDAH

DDX21

TWSG1

RBMX

NDUFAF1

PHF6

TFB2M

EBNA1BP2

ZMYM2

MLYCD

UROD

PKP3

NUBP2

FANCI

ARIH2

ZNF22

USP11

ARFRP1

PKN1

FAR1

MYBBP1A

PDS5A

CHMP7

COASY

SAP18

GTF3C4

SMARCAD1

DNAAF5

CTAGE5

GART

UBE2I

MRPL27

ENY2

PDK3

RUVBL1

PEAK1

WDR6

MYEF2

PWP2

RPA2

EXOSC4

FRA10AC1

ADAD2

NARS2

FAM64A

XRCC4

GTF2E1

DDX51

BMS1

OGFR

MRPL3

CHAC2

PES1

IGF2BP3

LDHB

ORC3

MSH6

DPYSL5

HEATR1

KATNA1

PTMA

SLC52A2

NLE1

MCM7

POLD1

MCM2

CXorf56

SMAD5

GPATCH4

STOML2

FLVCR1

MYH14

DAXX

ZCCHC8

TAMM41

TOMM34

LGALS3BP

PARN

KIF1BP

C5orf22

TP53RK

NACC1

MRPS30

TKT

ELAC2

PRKCI

PDCD11

DNAJB4

MTMR12

SUPV3L1

DARS2

RAVER1

SIGMAR1

DHODH

SLC3A2

BTAF1

HSDL1

EIF3C

TBPL1

NOC2L

MRPS28

CADM1

MRPL37

SRI

BZW2

NDUFC2

PCCB

DNTTIP2

PCBD2

TRIM2

CPSF1

RABGGTB

RFC5

ECT2

AGTPBP1

TRIM22

ECM29

PANK4

C11orf73

MCAM

THUMPD1

WDR18

RNPS1

SCO1

TIMM17B

INTS8

TUSC3

DCAF16

GTF2A1

SIRT1

UTP6

MRPL11

XRN1

DCTPP1

HSPBP1

TUFM

WDR92

PIR

ACAA2

DNAJC2

NPM3

ADNP

CERS6

NUDT12

APTX

DSG2

NTHL1

BOLA3

DDX24

NUP35

ATL2

NOL11

DDX31

ATPAF1

GCDH

RCHY1

C12orf10

HIP1R

PRPS2

MCM5

WDR75

RHOT1

KIAA1211

DDX54

RSPRY1

CDC123

NOP16

TACO1

GLMN

HOOK1

WNK1

NUP155

POLR1A

TBL3

GNAI1

KIAA2013

C7orf50

GUSB

GUF1

TIMM17A

GRWD1

LBH

CCNK

ILKAP

SMYD5

AGL

POR

LIG3

CMTR1

LRBA

WDR5

TOMM5

ARL8A

PCK2

PDCD4

NAT10

ACO1

TSC2

GNL3L

MTFP1

ABT1

KEAP1

ANKRD28

UBTF

STK3

SCAP

PPAT

PSAT1

APOA1BP

WDR54

SYT1

SCRIB

PTBP3

RNASEH2C

APOO

ASF1A

GSPT2

SDHB

SUPT16H

DBR1

PSME3

PPWD1

UBQLN4

CHAF1A

TRMT10C

SACS

BYSL

CDH13

USP24

ARID1A

GJB2

TEX10

UBA2

CLUH

ARL2

AS3MT

ABCC1

MRPL57

DDX56

EIF2D

ATP1B3

DCAF8

AGK

AIF1L

RBM42

FEN1

CCDC12

ELOVL6

EFNB1

NCAPG2

SARS2

OSBPL2

CDCA8

GNA13

ATF7IP

CCDC50

ADI1

HAUS8

C1orf131

GOLM1

DEK

DTD1

MCL1

INTS1

AHCY

GYS1

PAICS

DTWD1

CCDC59

MAK16

RUVBL2

ISY1

ECT2L

GTPBP10

ZNF593

RBM26

FDXR

MRI1

HS1BP3

LSM6

DNAJC8

SALL4

AATF

LETM1

LAS1L

MRPS11

SMARCA5

TMPO

LTA4H

MYCBP

MRPL19

NEPRO

PCBP2

WBSCR22

CCNH

DLGAP5

NDUFS7

NOP58

HDAC2

WDR48

GLTSCR2

PELP1

HARS2

NT5DC1

HIST1H1B

TOX4

TPI1

LUC7L

ATP11C

NXF1

HNRNPC

VRK1

KDM2A

COMMD8

CACNA2D1

RAD21

HNRNPU

WIPI1

USP39

SSB

CDCA7L

SNF8

LARS

ASH2L

VPS36

ZNF346

CRNKL1

TELO2

LRRC57

AASDHPPT

CNPY3

GLUL

CWC27

TNPO3

CHORDC1

CKAP2

CXADR

ILF2

PEG10

TTI2

MANBA

DCAF13

PLS1

LVRN

C1QBP

UBE2A

MEMO1

EIF4A3

EXTL2

MED24

GLYR1

UBXN1

MRPS18A

EIF5B

NIFK

POLR2H

HMOX2

ABCB6

NDUFB4

FNBP1L

NOL10

KIF5C

EXOSC9

ATP2B1

TOMM40

RBM28

GSTP1

TATDN1

FTSJ3

DAGLB

PLCG1

IFI16

HSPA4

TMEM192

MPI

SMPD4

POLE4

KDM1A

NUP188

TSFM

DLAT

FAM210A

POLR2D

NOL6

PRPF40A

UBAP2

MSTO1

GTF2I

SHPK

NUP133

RBM12B

DAB2IP

SAFB

LARP1

SPCS1

PDHA1

STX18

PPFIA1

NUP50

METTL13

SAAL1

QTRTD1

SUPT6H

ADSL

QSER1

POLR3C

TRMT1L

ASUN

BMP1

AFG3L2

GEMIN5

NEU1

PEX6

HDAC3

NDC80

MRRF

HMGN1

TIMM44

REEP6

OTX2

LPCAT1

MTPAP

SNU13

UMPS

TRIAP1

TUT1

GRSF1

NAA20

ACSS3

NCK1

ERBB2

CCDC28B

XRN2

NDUFAF4

MIF

PPP2R5A

SGSH

CRADD

MT-ND4

GATAD2A

MRPL9

RAD50

OSGEPL1

ADGRL2

MTUS2

NRBF2

FAM192A

DNPEP

THAP11

HEATR5B

RABGEF1

POP1

HEATR3

SRRM2

CACTIN

PRKD1

MRPL50

PRMT1

NIPBL

STK4

SLC25A35

ECE2

RPL13A

SDCBP

NTMT1

TBRG4

ZFAND6

DSEL

SDAD1

RPL21

PDCD5

PPIG

RALGAPB

MYO5C

TRMT6

RBM39

GULP1

DCP1A

IGSF1

POLG

UBE3A

SLC30A1

RFC4

TUBAL3

MGRN1

TPK1

KCTD10

SMAP

ACIN1

UBXN7

TMEM41A

DNAL1

F8A1,F8A2,F8A3

TKFC

BSG

ARHGEF40

FBP1

FBXL6

DFFB

TRIM33

EHBP1

ATP5S

CDC20

PLEKHA7

WDR73

CD70

EMC3

SLC9A3R1

COBLL1

TRIM9

SP1

YARS2

RBM19

CKMT1A,CKMT1B

HSP90AB3P

MRPL35

CCNA2

HDDC2

KDM3B

PPA1

SMARCAL1

MALSU1

AURKB

PPM1G

EARS2

HSP90AA1

SH3GL3

MPHOSPH6

NACC2

HMGB2

GTPBP4

ABCB10

CYP2U1

BSDC1

TLK1

LEO1

MFAP1

GIT1

FLCN

TYRO3

SH3PXD2A

EMC4

CPS1

INTS9

IRS2

SIRT3

FUT8

CDK2

TNFAIP6

SDHAF4

KITLG

ALDH3A1

GPR180

CFAP36

ANK3

CBX2

RBBP9

EML2

POLR3GL

FN3K

VWA5A

RAVER2

(ii) Proteins enriched more than two-fold in c-MYC-WT compared with MYCL-WT (EpiP)

FIGNL2

MCEE

NDUFB7

BCCIP

CCDC86

HSPA4L

URB1

INTS14

MRPS10

PDHX

SNCA

RPL26L1

NBN

DNAJC2

NDUFAF2

WDR36

UBE2G1

INTS3

NDUFB1

EIF3C

WARS2

SUPV3L1

TOP2A

ANKZF1

PCCA

AKAP9

NOP16

EHMT2

MRPL3

KAT7

POLR3D

MAPKAP1

PAIP1

GK

INTS13

MT-ATP6

NF1

NABP2

OSBPL11

IMPDH2

DIEXF

WDR73

BRD2

MCM7

SFXN4

HSPD1

REXO4

GEMIN4

NCAPD3

NDFIP1

BOP1

PM20D2

TRMT5

STEAP3

SSR2

MTA3

TOMM40

PDS5A

SLC25A17

RIDA

GTF2A2

DCUN1D5

ORC5

CDKN2AIPNL

SET

TFAM

CORO7

THTPA

POLR1B

HSPE1

APOO

NDUFS7

UBE2G2

WRAP53

HARS2

POLRMT

IRF9

RBM19

PPP4R3B

DPCD

FBXO22

CLUH

TSR1

ZNF740

ATP7A

HIGD2A

TIMM17A

COA7

ALKBH5

TTI1

ATR

ITPA

PABPN1

TYMS

RARS2

PHC2

MBTPS1

FAM234A

LPCAT3

BMS1

INTS11

UBE2S

VAMP3

TTC12

TNPO2

NOC3L

TBL3

POLR1A

PFKFB3

CARS2

FBL

LSAMP

ABHD11

ORC2

SH3PXD2A

INCENP

SMN1,SMN2

GNL3

MRPS15

MRPL17

ZNF318

ITM2C

NIP7

SYF2

UCK2

MARS2

CWF19L1

INTS9

CDK1

STK26

IRF2BP2

PTCD1

RBX1

POLR3B

SLC4A7

DNPH1

DIMT1

DUS3L

ULK3

IFT57

NDUFAF4

NGDN

PCBP2

CEPT1

TTC33

ARMCX1

HDDC3

PPIF

MDC1

PES1

CWC27

TRAP1

BRIX1

TOMM6

NCAPG

PWP2

NOL11

DDX41

GCA

DDX20

HEATR1

NT5DC2

KDM3B

TASOR

NCL

MGST1

GTF2H4

SSNA1

ZC3HC1

PALD1

EEF1E1

TRMT10C

NUDT3

COIL

VRK2

SYNPO2

PSMF1

PTBP3

TGS1

NOL10

DDX60

HIGD1A

RAB11FIP5

C1QBP

BCS1L

POLD3

PHACTR4

SIK3

TRIM65

DNMT1

LYAR

YY1

ASPM

CABIN1

WDR43

POLD2

WDR3

DCAF1

GPD1L

MAP3K4

MYC

FAM162A

DDX18

WDHD1

GTF3C2

MYBBP1A

URB2

HMGN5

BAZ1A

MDP1

STAG1

DDX21

VRK1

GUCY1B2

SLC1A3

MTMR6

COX6A1

TMEM33

UBE2D3

RFC5

RRP1

NEDD4

SAAL1

NPM3

TEX10

CDK2AP1

POLR2F

RSL1D1

EDC3

PLA2G4A

HMGA1

DDX24

TRRAP

SELENOO

DTD2

MED23

PBX1

UTP4

H1-4

FANCI

SLC35E1

PEG10

GRPEL1

DPH2

DNAJA3

HAUS1

CCDC115

NOLC1

GNL2

POLD1

MRPS2

ZNF565

PVR

AKAP1

PRRX1

NDUFAF3

PARP12

STRIP1

ZCCHC3

NELFCD

PODXL2

PRR35

KDM1B

BMI1

TRAPPC8

SPNS1

BLOC1S4

UMODL1

KIF21B

C8orf33

NFIX

AFP

TTN

RAVER2

NFATC2IP

CHD1

UBE2D1

DHX38

CDK5RAP1

IDUA

IRAK1

ORMDL3

GPAA1

B3GALT6

XPC

LIN7C

VWA1

MET

METTL1

COA4

CTIF

SHPK

PNKP

 

(iii) Proteins enriched more than two-fold in c-MYC-WT compared with c-MYC-ΔMB0 (EpiP)

FAM83G

IFT20

DOP1B

NOC3L

POLR2F

EXOC8

STK25

ASPM

WIPI2

LSAMP

KHNYN

S100A3

BTAF1

GPD1L

OARD1

ARF1

HACD2

VWA1

URB1

STAG2

SLC25A15

SYF2

RIDA

METTL1

PCDHGA12

CCNYL1

IKBKG

GXYLT1

CEP250

SMARCA4

TGFB1

NECAP1

MAP3K4

NLE1

RBM19

PRIM2

SERPINE2

PPHLN1

UTP3

PTBP3

LMF2

SHPK

SP1

STAG1

CD320

YTHDF2

ORC2

F8A1,F8A2,F8A3

GLUL

SREK1

ARMC9

C7orf50

MRPL17

BMI1

PHKG2

COX6A1

RPL36A

DNMT1

MARS2

C8orf33

NF1

BRI3BP

LAS1L

FAM162A

PTCD1

CCDC93

BRD2

LPIN2

PLA2G4A

HMGN5

CEPT1

MET

ATP6V0C

ZNF622

PEG10

CDK2AP1

LIMD2

COA4

NCAPD3

SNX21

CCDC58

NUP50

ORC4

TTC5

SSR2

NUDT16

LYRM7

SLC16A1

LAGE3

CCDC63

PRIM1

SAAL1

WARS2

ERCC4

RMC1

PODXL2

GTF2A2

DTD2

ZNF24

UTP4

NOL10

BLOC1S4

EPHB3

WASF2

NAA16

BUD23

POLD3

CDK5RAP1

UBE2G2

CCDC115

BOP1

SELENBP1

H2AC21

SPATA5L1

PLCB3

HAPLN3

TNFRSF10B

SNCA

CNBP

XPC

ATP7A

DNAJC2

ORC5

VPS33A

CAMLG

MPC1

PTK2

AKAP9

HARS2

CTSC

DOCK1

MIPEP

HSPA14

THTPA

TIMM17A

INTS13

SPR

PVR

ATR

CEP41

PABPN1

REXO4

CSNK2A1

AKAP1

VAMP3

XPO4

NOLC1

PDF

CCDC51

SRC

PFKFB3

CSTF2T

SMN1,SMN2

APOO

CLPB

AFP

DOCK11

QRSL1

WRNIP1

MSH3

YY1

RAVER2

ZFYVE27

TTC12

HDDC3

IGFBP5

HEATR5A

CRLF3

RNASEH2B

CARS2

STARD4

SMYD3

WDHD1

DDX60

SH3PXD2A

C17orf75

GCA

RPL10L

NSD2

HIGD1A

TNS2

CRLF2

TRIM65

INTS11

MDP1

EXOG

ATG16L1

TNFRSF12A

PBX1

IMP3

GLE1

POLRMT

TTI2

INCENP

UQCC1

AATF

MTMR6

MRPS30

ULK3

INTS9

NDUFAF1

MRPS15

THNSL1

RRP1

TTC33

MTRR

EHMT2

LIG1

RBFOX2

CDC16

KDM3B

TRAP1

HSPD1

POLA2

PKMYT1

KIF21B

TTC21B

PTBP2

UBR5

CCDC171

MAP3K7

NFATC2IP

HEATR3

PALD1

CDKN2AIPNL

TGS1

RSL1D1

TERF2

ZC3HC1

ISY1

NAF1

BAZ1A

FANCI

RIF1

VRK2

SYNPO2

PRORP

   

(iv) Commonly enriched proteins in (i) and (ii) and (iii)

KDM3B

     

HMGN5

     

URB1

     

PALD1

     

LSAMP

     

MET

     

DNAJC2

     

RBM19

     

AKAP1

     

INTS9

     

SNCA

     

MARS2

     

MAP3K4

     

INCENP

     

AKAP9

     

GCA

     

NCAPD3

     

FAM162A

     

ORC5

     

ULK3

     

POLRMT

     

ZC3HC1

     

PTCD1

     

NOL10

     

SHPK

     

XPC

     

SH3PXD2A

     

RAVER2

     

PTBP3

     

BOP1

     

PEG10

     

TIMM17A

     

SAAL1

     

CARS2

     

FANCI

     

HARS2

     

BAZ1A

     

PLA2G4A

     

APOO

     

WARS2

     

TRAP1

     

RSL1D1

     
  1. Four groups are described: (i) proteins whose peptide counts increased more than two-fold in c-MYC-WT/HDFs compared with MYCL-WT/HDFs using SeV on day 3, 5, or 7; (ii) proteins whose peptide counts increased more than two-fold in c-MYC-WT compared with MYCL-WT using EpiP; (iii) proteins whose peptide counts increased more than two-fold in c-MYC-WT compared with c-MYC-ΔMB0 using EpiP; and (iv) commonly identified proteins. n=3 for EpiP reprogramming.