Table 3 Comparison of optimal motifs for TFs common to MatBase, Transfac and the union of public databases

ATF3

0.710

V$CREB.02

0.693

M00981

–

–

0.694

M00015

–

–

–

–

Ap2alpha

0.809

V$AP2.02

0.807

M01045

0.816

MA0003.2

0.777

M00004

0.779

selex292

0.754

TFAP2A,C.p2

Ap2gamma

0.799

V$AP2.02

0.765

M00470

0.792

MA0524.1

0.781

M00006

0.784

selex298

0.751

TFAP2A,C.p2

BHLHE40

0.947

V$BHLHB2.01

0.799

M01034

0.885

MA0464.1

0.955

M00022

0.958

selex316

0.917

ARNT_ARNT2_BHLHB2_

MAX_MYC_USF1.p2

CTCF

0.929

V$CTCF.04

0.931

M01259

0.942

MA0139.1

0.940

M00045

0.922

selex2

0.934

CTCF.p2

Cfos

0.751

V$AP1.01

0.759

M00517

0.744

MA0476.1

0.760

M00093

–

–

0.742

FOS_FOSB,L1_JUNB,D.p2

Cjun

0.814

V$AP1.01

0.820

M00925

0.799

MA0099.1

0.827

M00183

–

–

0.570

JUN.p2

Cmyc

0.700

V$CMYC.01

0.685

M00322

0.702

MA0147.1

0.690

M00216

–

–

0.659

ARNT_ARNT2_BHLHB2_

MAX_MYC_USF1.p2

E2F1

0.802

V$E2F3.01

0.764

M00938

0.753

MA0024.2

0.694

M00052

0.723

selex750

0.674

E2F1..5.p2

E2F4

0.682

V$E2F4.01

0.678

M00920

0.689

MA0470.1

0.650

M00055

0.502

selex753

0.654

E2F1..5.p2

E2F6

0.698

V$E2F4.01

0.435

M01252

0.653

MA0471.1

0.681

M00057

–

–

–

–

EBF

0.740

V$EBF1.01

0.736

M01871

0.721

MA0154.2

0.746

M00037

0.751

selex79

0.692

EBF1.p2

ELF1

0.862

V$ELK1.03

0.835

M02053

0.800

MA0473.1

0.832

M00065

0.836

selex81

0.797

ELF1,2,4.p2

ETS1

0.765

V$ELK3.01

0.753

M02063

0.680

MA0098.1

0.708

M00082

0.765

selex100

0.683

ETS1,2.p2

Egr1

0.831

V$EGR1.01

0.848

M01972

0.822

PB0010.1

0.844

M00060

0.853

selex3

0.841

EGR1..3.p2

FOSL1

0.885

V$AP1.02

0.890

M00517

0.890

MA0477.1

0.865

M00091

–

–

0.881

FOS_FOSB,L1_JUNB,D.p2

FOSL2

0.877

V$AP1.01

0.870

M00925

0.865

MA0478.1

0.885

M00092

–

–

0.852

FOSL2.p2

FOXA1

0.763

V$FREAC4.01

0.826

M01261

0.832

MA0148.3

0.808

M00094

–

–

–

–

FOXA2

0.759

V$FREAC4.01

0.735

M02014

0.834

MA0047.2

0.816

M00095

–

–

0.834

FOXA2.p3

Gabp

0.873

V$ELK1.03

0.867

M02074

0.879

MA0062.2

0.876

M00116

0.871

selex116

0.870

ELK1,4_GABPA,B1.p3

Gata1

0.711

V$GATA5.01

0.685

M00203

0.683

MA0035.3

0.697

M00117

–

–

0.479

GATA1..3.p2

Gata2

0.853

V$GATA2.03

0.834

M00789

0.834

MA0036.2

0.843

M00118

–

–

0.538

GATA1..3.p2

HNF4A

0.801

V$HNF4.01

0.838

M02220

0.847

MA0114.2

0.850

M00147

0.837

selex673

0.809

HNF4A_NR2F1,2.p2

HNF4G

0.864

V$HNF4.01

0.811

M00764

0.898

MA0484.1

0.788

M00148

–

–

–

–

IRF4

0.669

V$ISRE.01

0.641

M00772

0.648

PB0034.1

0.603

M00174

0.665

selex148

–

–

Junb

0.912

V$AP1.01

0.912

M00925

0.920

MA0490.1

0.911

M00181

–

–

0.900

FOS_FOSB,L1_JUNB,D.p2

Jund

0.820

V$AP1.01

0.823

M00925

0.817

MA0491.1

0.827

M00182

–

–

0.805

FOS_FOSB,L1_JUNB,D.p2

MEF2A

0.643

V$MEF2.02

0.650

M00231

0.653

MA0052.2

0.616

M00204

0.615

selex156

0.604

MEF2A,B,C,D.p2

MEF2C

0.721

V$MEF2.02

0.682

M00941

0.719

MA0497.1

0.664

M00205

–

–

0.669

MEF2A,B,C,D.p2

Max

0.738

V$CMYC.01

0.703

M00322

0.700

PB0043.1

0.720

M00199

0.730

selex326

0.711

ARNT_ARNT2_BHLHB2_

MAX_MYC_USF1.p2

NFKB

0.896

V$NFKAPPAB65.02

0.891

M00774

0.878

MA0105.3

0.872

M00235

0.776

selex189

0.861

NFKB1_REL_RELA.p2

NR4A1

0.512

V$NBRE.01

0.492

M01217

–

–

0.542

M00259

–

–

–

–

Nanog

0.560

V$HOXA2.01

0.631

M01247

–

–

0.556

M00221

–

–

0.630

NANOGmouse.p2

Nfe2

0.855

V$NFE2.01

0.846

M00037

0.877

MA0501.1

0.882

M00231

0.771

selex392

0.835

NFE2.p2

Nrf1

0.951

V$NRF1.01

0.969

M00652

0.963

MA0506.1

0.973

M00264

0.977

selex194

0.968

NRF1.p2

Nrsf

0.838

V$NRSF.02

0.879

M01256

0.850

MA0138.2

0.854

M00316

–

–

0.847

REST.p3

POU2F2

0.513

V$OCT1.02

0.498

M00210

0.481

MA0507.1

0.504

M00290

0.503

selex232

0.503

POU2F1..3.p2

POU5F1

0.868

V$OCT3_4.02

0.857

M01125

0.881

MA0142.1

0.874

M00294

–

–

0.857

POU5F1_SOX2dimer.p2

PU1

0.932

V$SPI1.05

0.884

M01203

0.914

MA0080.3

0.922

M00350

0.860

selex123

0.884

SPI1.p2

Pax5

0.613

V$PAX5.01

0.613

M00143

0.713

MA0014.2

0.729

M00274

0.768

selex200

0.606

PAX5.p2

Pbx3

0.739

V$PBX1_MEIS1.01

0.546

M00998

–

–

0.758

M00280

–

–

–

–

RXRA

0.714

V$PPARG.03

0.608

M02272

0.707

MA0065.1

0.693

M00326

0.731

selex710

0.720

RXRG_dimer.p3

SP1

0.559

V$SP1.03

0.552

M00932

0.561

MA0079.3

0.555

M00346

0.547

selex29

0.551

SP1.p2

SP2

0.711

V$SP4.01

0.719

M01783

0.726

MA0516.1

0.676

M00347

–

–

–

–

Srf

0.681

V$SRF.05

0.693

M00186

0.661

MA0083.1

0.657

M00355

0.657

selex159

0.656

SRF.p3

Tcf12

0.723

V$ASCL2.01

0.679

M00698

0.712

MA0521.1

0.703

M00152

–

–

0.574

TAL1_TCF3,4,12.p2

Tr4

0.601

V$HNF4.01

0.644

M01776

0.652

MA0504.1

0.623

M00256

0.611

selex676

–

–

USF1

0.947

V$USF1.02

0.936

M00121

0.903

MA0093.2

0.945

M00396

0.935

selex352

0.932

ARNT_ARNT2_BHLHB2_

MAX_MYC_USF1.p2

Yy1

0.778

V$YY1.03

0.723

M02044

0.713

MA0095.2

0.735

M00394

0.756

selex33

0.657

YY1.p2

ZBTB33

0.489

V$KAISO.01

0.517

M01119

0.881

MA0527.1

0.749

M00184

–

–

–

–

ZBTB7A

0.699

V$ZF9.01

0.682

M01100

–

–

0.640

M00404

0.632

selex37

–

–

ZEB1

0.766

V$ZEB1.01

0.689

M00414

0.752

MA0103.2

0.686

M00409

–

–

0.734

ZEB1.p2

Znf263

0.685

V$ZNF263.01

0.762

M01587

0.653

MA0528.1

–

–

–

–

–

–