Supplementary Figure 1.stg

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PAX3. ATF3. CREBP1CJUN. COUPTF. MTF1. CACCCBINDINGFACTOR. HMEF2 ..... POU3F2. PAX3. RUSH1A. HNF3B. TEL2. CACBINDINGPROTEIN. IK2ER.
a

b

6

6

AP4

5

FOXOCT NANOG HSF2 TFE IRF2 OTX OCT4OCT1

RORA1 ER USFMYCMAX CRX

5

ARNT

RBPJK ZTA MAZ FAC1 NKX3A SPZ1 OSF2 SREBP1 POU1F1 FOXO3 MAF AP2REP TFIII LRH1 CACBINDINGPROTEIN IK HAND1E47 SMAD3 NFKB ETS1 TEF FREAC3 ELK1 ICSBP ISRE HFH4

MYOD

ERR1

4

SP3 KAISO PIT1 FOX CMYB SOX CP2 CREB CART1 PBX HES1 CDPCR1 RORA MEIS1BHOXA9 CREL OTX AML NFKAPPAB65 MUSCLE MAF KROX HSF UF1H3BETA FREAC4 ALPHACP1 AML1 COREBINDINGFACTOR SMAD4 AP2REP POU3F2 TAL1BETAITF2 ZIC2 HNF4ALPHA EGR3 ER CDX2 DEC BACH2 NFKAPPABHNF1 VDR PADSCRX PTF1BETA CETS168 NKX22 E2F1DP2 TAL1 CLOCKBMAL XBP1 ISRETAL1ALPHAE47 CACD USF2 TAL1BETAE47 DMRT5 MYC NFE2 XPF1 MAXICSBP EBOX LYF1 MINI20 NMYC NRF2 E4F1 ZID AIRE PEBP ETS2 GC MIZF CEBPGAMMA CDX TEF EGR2 CLOX LMAF HEB E2F4DP1 RORA2 EVI1 E2 NERF RP58 GATA4 NGFIC CDC5 AFP1 IRF2 RFX1 SREBP PAX3 CDP IK3 TFIIA SRF ZBRK1 EGR1 PAX8 OLF1 ZIC1 RREB1 LFA1 DMRT7 AMEF2 COUPTF NFKAPPAB50 STAF CREBP1CJUN FXR POLY BACH1 TAXCREB ATF4 ATF3 HTF ACAAT GLI STAT5B PPAR IK2 HP1SITEFACTOR HMEF2 EBF GABP CACCCBINDINGFACTOR ATF6 STRA13 MTF1 HOX13 HLF CREBP1 HMX1 DMRT1 CMYC POU6F1 DMRT4 COUP PPARG MINI19 RSRFC4 MEIS1AHOXA9 NRF1 ARP1 MIF1 DMRT3 LXR ZEC NFMUE1 DTYPEPA ROAZ PAX5 DR1 DEAF1 ATF1 MEF3 SZF11 TCF11MAFG EFC MAZR HEN1 PAX VJUN CDPCR3 APOLYA TEL2 PPARA DR3 DMRT2 GRE VMAF PAX6 VBP R DR4 SAP1A PITX2

2

1

-Log(PP)

-Log(PP)

ATF6IRF7 MOVOB HNF1 KROX RORA MAX NMYC CACD SREBP2 CDX2 CKROX HSF HIC1 USF2 CLOCKBMAL MYC EBOX PTF1BETA CDC5 PAX3 PIT1 ZID CMAF XBP1 EGR ETF RP58 BLIMP1 KID3 DMRT3 ATF4 SP1 UF1H3BETA FREAC4 MIZF NKX22 VDR ALPHACP1 E47 CMYB CP2 BACH2 E2F4DP1 MEIS1BHOXA9 DEC CREBP1 HTF MEF2 TAXCREB POU3F2AIRE PADS IK3 CREBP1CJUN GATA4 E4F1 E2F1DP2 TAL1BETAITF2 NFE2 GCM RFX1 CMYC STAF HNF4ALPHA E2F1DP1 HLF TAL1ALPHAE47 E2F4DP2 ZIC2 EGR3 ETS2 SMAD4 EBF RORA2 ZIC3 LMAF AP2 NRF2 COREBINDINGFACTOR LXR NFKAPPAB SREBP AML1 ACAAT TAL1 PAX8 HES1 AML FXRBACH1 LFA1 EVI1 CETS168 AFP1 SRF DMRT2 DMRT7 NERF TAL1BETAE47 MINI19 NGFIC PAX9 XPF1 TFIIA SP3 MUSCLE ATF3 EGR2 HMX1 DELTAEF1 DMRT4 MTF1 AMEF2 HEN1 APOLYA DMRT1 STRA13 POLY DTYPEPA COUP NFMUE1 HEB MAZR SZF11 DR3CDPCR3HD CDPCR1 CDPCR3 MEIS1AHOXA9 PPAR ROAZ ZBRK1 DMRT5 STAT5B CACCCBINDINGFACTOR COUPTF EFC GABP E2 HP1SITEFACTOR OLF1 NFKAPPAB50 HOX13 GRE EGR1 RREB1 ZIC1 NRF1 MIF1 POU6F1 FOXP3 VMAF DR1 PEBP LUN1 DR4 ATF1 PPARG VBP TCF11MAFG ARP1 GLI RSRFC4 MINI20 MEF3 PPARA PAX5 DEAF1 PITX2 CLOX GZF1 PAX HMEF2 TEL2 PAX6 SAP1A GCNF VJUN CDP R NRSF GC

3

2

1

0

0

-1 -1

0

1

2

3

4

5

USF

E2A

LBP1

KAISO LYF1MYOGENINIK2

NANOG RORA1 MYCMAX MYOGENIN HFH4 FOXD3 ARNT HSF2 MEF2 ZTAOCT1 OCT4 OCT NFKB GCM ERR1

E12

4

E12 MYOD E2A

3

E47

-1

6

-1

0

1

-Log(PE)

2

3

4

5

6

-Log(PE)

c

d

6

% of motif presence in no. of promoters

100 5

4

-Log(PP)

AP4 RFX HELIOSA STAT5A GEN SOX10 NFAT HIC1

3

LEF1STAT1 FOXO1 FOXO4 TTF1PAX4

E2F1 CEBP AR MEF3

P53

HNF3 HMGIY ETS TEFDMRT4 STAT4 MYB AP2GAMMAE2F NFE2 FOXP3 SMAD CART1 PAX2 DBP T3R NFKAPPAB65 CDP SF1 BACH2 NFYCREL BARBIE P300 MZF1 BCL6 GATA2 STAT6 SRY E2F1DP1RB NFKB BEL1 OCT4 CEBPDELTA BACH1 ATF4 CREB PEA3 CDXA PIT1 PAX SREBP1 AP2 AHR NKX25 TITF1 ZIC3 LEF1TCF1 AHRHIF BRCA LMAF IK CHCH FOXJ2 SP1 AP2ALPHA SOX17 CAP PXR CLOX GATA4 TBX5 CBF ATF GFI1 EGR RBPJK ALPHACP1 TBP CETS1P54 TGIF TCF11 ZTA KAISO PR WT1 AP1FJ TEF1 CREBATF NFMUE1 YY1 ELK1 STAT GATA3 HOXA7 NKX32 E2F1DP2 HNF4 CEBPA CAAT NF1 LRH1 HAND1E47 CMAF CETS168 SMAD3 GATA HEB RFX1 HFH3 FXR HNF3B SPZ1 POU1F1 STAF CEBPB SREBP2 DTYPEPA STAT3 XPF1 CIZNCX EVI1 FREAC2 MRF2 KID3 AP1 FOXO3A GATA6 XFD2 OCT ATF3 TAL1BETAITF2 GR NKX3A LBP1 E2F4DP2 E2F1DP1 PBX1 WHN MSX1 LPOLYA PU1 AHRARNT HNF1 IPF1 ZF5 MEIS1 GFI1B HSF IRF ATF1 SREBP FREAC7 VDR PTF1BETA E4F1 ACAAT DR4 AFP1 ETF AML MYCMAX NRF2 GRE CDX HNF6 HES1 MOVOB GATA1 ETS1 SOX9 HSF2 ZID COREBINDINGFACTOR TAL1ALPHAE47 TFE TFIII HFH8 SOX5 SRF AML1 FOXO3 ELF1 SP3 PPAR MAF LRF CRX ATATA EGR3 ER PXRRXR PAX8 TAL1 MAZ IK1R CDPCR1 MIZF LHX3 VMAF LMO2COM NANOG GC CDPCR3HD TAL1BETAE47 XBP1 DELTAEF1 DR3 DMRT3 NKX61 HNF4ALPHA PBX IK2 EGR1 E4BP4 EGR2 CACBINDINGPROTEIN FOX BRN2 CHX10 BLIMP1 HFH1 IRF1 TCF4 PAX3 CACD NKX62 HOXA3 TFIIA XVENT1 AREB6 VMYB MTATA OTX LDSPOLYA CREBP1CJUN PAX6 ICSBP OSF2 CACCCBINDINGFACTOR HNF3ALPHA FOXM1 LYF1 XFD3 PEBP EN1 GLI POU3F2 VJUN CP2 SAP1A CHOP CMYC AP3 NFKAPPAB TEL2 TST1 OG2 MYOGENIN HSF1 FREAC4 CMYB DR1 HMX1 CDX2 FAC1 NGFIC AIRE XFD1 TCF11MAFG COUP NERF ETS2 AP2REP ARNT FOXD3 CDC5 LFA1 PADS S8OCT1 UF1H3BETA MMEF2 SOX HOXA4 ISRE CREBP1 PPARA RORA TATA E2F4DP1 MUSCLE IK3 EBF CKROX MINI20 HEN1 ZIC1 HP1SITEFACTOR NFKAPPAB50 SMAD4 KROX RUSH1A ZNF219 E47 GCM GABP ERR1 NKX22 RORA1 POLY E2A HIF1 MEIS1BHOXA9 RREB1 PITX2 MYOD E12 IRF7 NRF1 STAT5B MEF2 DEC HFH4 STRA13 USF OLF1 HTF HLF CEBPGAMMA CLOCKBMAL TAXCREB COUPTF RSRFC4 NMYC EBOX USF2 ZIC2 MYC MAX FREAC3 RORA2 RP58 ATF6 MTF1 E2

2

1

0

80

60

40

20

STAT5A ETS KID3 STAT6 GATA1 LEF1 BCL6 AREB6 STAT1 GEN HNF4 HELIOSA SMAD PAX4 HIC1 CEBP IK2IKAP4 HMGIY NFAT SREBP2 PEA3 NKX32 YY1 WT1 MZF1 SOX10 AR DELTAEF1 STAT3 E2F SPZ1 T3R NKX25 NF1 FOXO1 FOXO4 SRY LMO2COM DBP LRH1 TTF1 CHCH MYB P300 TBX5 PAX2 STAT4 AP2ALPHA BRCA CDXA RFX AHRHIF AHRIK1 OCT1 MYOGENIN AP1FJ CETS1P54 MOVOB HAND1E47 SP1 CIZ CAP OTX GATA2 LRF HNF3 CRX GATA3 PR AP1 EN1 TBP GR PU1 ETF SF1 MEIS1 CETS168 CBFER NFY GFI1 AP2GAMMA AP2REP SREBP AP2 TCF11 ELK1LBP1 SOX17 SREBP1 WHN E2F1 MAZ LEF1TCF1 RBPJK ZIC3 OG2 E2A GATA ELF1 TFIII NKX62 MYOD E12 GATA6 OSF2 ZF5 TGIF S8 LYF1 ETS1 CREB HOXA7 AHRARNT IPF1 E47 CREBATF ATF PXRRXR STAT LPOLYA CMAF KAISOEGR SOX9 COREBINDINGFACTOR AML1 CAAT AML FOXO3A PITX2 HOXA3 RUSH1A HNF3B TEF1 FREAC7 NRF2 PXRGC VMYB TATA TCF4HFH3 CACBINDINGPROTEIN HNF3ALPHA HOXA4 CACD TAL1 PBX1 LMAF VDR NCX CEBPA CEBPB MYCMAX FOXJ2 CKROX HIF1 TFE RORA1 PAX8 ERR1 BRN2 AP3 HEB RFX1 LFA1XVENT1 MAF FREAC2 SOX5BARBIE ZTA SMAD3 PEBP CEBPDELTA GABP CP2 PADS HFH8 TITF1 FOXM1 NFKAPPAB65 CREL NERF IRF ETS2 ARNT CMYB XFD2 OCT MRF2 BACH2 KROX NKX3A TAL1ALPHAE47 HES1 RORA XPF1 E2F4DP2 E2F1DP1 NFKB USF TAL1BETAE47 POU1F1 E2F1DP1RB HSF1 SAP1A NANOG LDSPOLYA HNF6 NFMUE1 FAC1 TAL1BETAITF2 IRF1 XBP1 LHX3 MSX1 MTATA CHOP TST1 GFI1B HFH1 ZNF219 MUSCLE EBF ZIC1 ACAAT XFD1 HSF2 BACH1 ATF4 MMEF2 PBX CHX10 NFE2 DEC ZIC2 FOXD3 TEL2 E2F1DP2 CART1 CLOCKBMAL NMYC EBOX USF2 MYC MAX CREBP1 E4F1 FOX ZID GLI HNF1PIT1 MEF3 HNF4ALPHA NRF1 IK3 CMYC TFIIA EVI1 FOXO3 TEF NKX22 XFD3 MIZF ALPHACP1 CDX NKX61 GATA4 CACCCBINDINGFACTOR UF1H3BETA BLIMP1 PTF1BETA STAF OCT4 PAX NFKAPPAB50 MEF2 NFKAPPAB IRF7 GCM AIRE PAX3 CREBP1CJUN ATATA ICSBP SOX CDX2 ATF1 SRF ATF3 DMRT4 RP58 STRA13 MINI20 CDPCR3HD E4BP4 CDPCR1 PPAR DTYPEPA VMAF SP3 AFP1 CLOX CDP CEBPGAMMA ATF6 SMAD4 FREAC4 STAT5B ISRE NGFIC COUP EGR2 EGR3 DMRT3 MEIS1BHOXA9 RORA2 HFH4 HTF HLF HEN1 POU3F2 HMX1 EGR1 DR1 GRE DR4 HSFR FXR FOXP3 HP1SITEFACTOR TAXCREB COUPTF FREAC3 RSRFC4 MTF1 OLF1 TCF11MAFG RREB1 E2F4DP1 E2 POLY CDC5 PAX6 VJUN PPARA DR3 BEL1

P53

0 -1 -1

0

1

2

3

-Log(PE)

4

5

6

0

1

2

-Log(PP)

3

4

5