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Table 6 The predicted regulatory signature of the developing human heart

From: Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs

Pair

E-value p

Pair

E-value p

Pair

E-value p

ZF5 & SZF11

12.5

E2F & HIC1

12.5

IRF1 & HIC1

12.5

SOX2 & ZFX

11.2

GATA1 & ZFX

12.5

TGIF & COREBINDINGFACTOR

11.2

AP2 & GATA

11.2

LTF & E2F1

12.5

FOXJ2 & CREL

11.2

MSX3 & CKROX

11.2

AIRE & LMX1

11.2

EGR & NFY

11.2

DAX1 & LXR

11.2

E2F & MYOD

12.5

MEF2 & AP4

11.2

CETS1P54 & DEAF1

11.2

FPM315 & LMO2COM

12.0

ZFP206 & LUN1

11.2

MAZ & BARX2

11.2

BACH2 & COUP

11.2

ZF5 & CAAT

11.2

ATF1 & ZFX

11.2

ALPHACP1 & RNF96

11.2

LHX8 & IK

11.2

SP1SP3 & RFX1

11.0

SP1 & MSX1

11.2

PEA3 & SMAD4

11.0

MOVOB & ELK1

11.0

ZNF219 & GATA2

10.8

ETS & GABP

10.7

STAT1 & RNF96

10.0

PXRRXR & SP1

10.0

XPF1 & EGR1

10.0

POU6F1 & AP2GAMMA

10.0

GATA6 & KROX

10.0

AP2ALPHA & LMX1

10.0

RXRG & RNF96

10.0

GATA1 & AP2

10.0

NFY & CNOT3

10.0

ZIC2 & CMYB

10.0

HIC1 & FOX

10.0

FPM315 & ATF

10.0

EBF & CNOT3

10.0

LMX1 & NKX12

10.0

LEF1 & WT1

10.0

LIM1 & LHX61

10.0

SP4 & GATA

10.0

NFKB & PAX4

10.0

AR & PAX4

10.0

AP2 & AHRARNT

10.0

CNOT3 & LUN1

10.0

ZNF515 & BEN

10.0

NF1 & CAAT

10.0

CNOT3 & ARNT

10.0

AREB6 & RNF96

10.0

AP2ALPHA & NMYC

10.0

NFKB & NGFIC

10.0

MAZR & LMO2COM

10.0

TAL1BETAITF2 & ZIC1

10.0

MYOGNF1 & PAX5

10.0

HEB & EN2

10.0

MINI19 & LIM1

10.0

CPHX & VDR

10.0

SPZ1 & GATA3

10.0

EBF & E2F1

10.0

MEF2 & E2A

10.0

GLI3 & FOXO4

10.0

NFKB & MEIS1AHOXA9

10.0

MSX2 & UF1H3BETA

10.0

ETF & TBX22

10.0

ZBED6 & MEF2

10.0

CNOT3 & PXRRXR

10.0

KROX & NFY

10.0

SP2 & GATA2

10.0

MYOD & MEF2

10.0

ROAZ & E2F1

10.0

GATA6 & UF1H3BETA

10.0

SP1 & GATA

10.0

AML2 & KLF15

10.0

ZF5 & TTF1

10.0

MZF1 & MIF1

10.0

MECP2 & GC

10.0

NFY & WT1

9.1

AREB6 & WT1

9.3

ZIC1 & E2F1

9.3

HIC1 & FOX

9.1

ZNF219 & GTF2IRD1

9.1

EGR & GATA2

9.1

CNOT3 & PU1

9.2

MINI19 & AREB6

9.1

GATA & SP1

9.0

MUSCLE & CREBATF

9.0

STAT3 & E2F1

9.0

HIC1 & HFH4

9.0

MUSCLE & MEF2

9.0

TBX15 & SP3

9.0

CTCF & CPHX

9.0

FOXO3 & PAX5

9.0

PAX9 & PAX4

8.7

NFY & SP1

8.7

EGR & GATA2

8.6

SPZ1 & ZF5

8.4

LBP1 & POLY

8.3

PEA3 & MINI19

8.3

CNOT3 & AHRARNT

8.3

SP1 & SOX10

8.3

BARHL1 & CKROX

8.3

AP2 & ATF1

8.3

AP2 & MEF2

8.3

EGR & DEAF1

8.2

COUPTF & ZF5

8.2

SP1 & NFY

8.1

AMEF2 & TBX15

8.0

TAL1BETAITF2 & SP2

8.0

PXRRXR & HIC1

8.0

AP2 & E2F1

8.0

TGIF & MRG2

8.0

RXRG & ZBED6

8.0

E2A & SRF

8.0

SP3 & ELK1

8.0

CEBP & CEBP

8.0

TATA & ERR1

8.0

E2F1 & SP1

8.0

AML2 & GC

8.0

XPF1 & SREBP

8.0

EGR1 & SMAD

8.0

ZIC1 & PPARG

8.0

DBP & E47

8.0

KROX & HMEF2

8.0

CTCF & GATA3

8.0

EAR2 & ETF

8.0

SP1 & PXRRXR

8.0

  1. CrmMiner predicted 132 motif pairs that comprise the regulatory signature of the developing human heart. The score of a sequence is the sum of the enrichment values (E-value p , Equation 1) of any of the 132 pairs present in the sequence provided that a pair of motifs meets the distance requirement (≤ 100 bp). A sequence that has a score equal to or above 23.8 is predicted to be a CRM specific to the developing heart. The 23.8 is the threshold that was determined at the training and the parameter-optimization stages. The unit of E-value p is fold.