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Table 1 TF cluster identified with pluripotency of human embryonic stem cells

From: TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM)

Genes

Symbol

Description

Evidence

Cluster 1: TFs control pluripotency renewal of human stem cells

   

NM_024865

NANOG

Nanog homeobox

[96]

BC099704

NANOGP8

Nanog homeobox pseudogene 8

Pseudogene with similarity to Nanog.

NM_003106

SOX2

SRY box 2

[96]

NM_002701

POU5F1

POU class 5 homeobox 1

[96]

NM_006892

DNMT3B

DNS methyltransferase 3 beta

[26, 97]

NM_004078

CSRP1

cysteine-rich protein

 

NM_080618

CTCFL

CCCTC-binding factor (zinc finger protein)-like

[98]

NM_016089

ZNF589

Zinc finger 589

[25, 32]

NM_004426

PHC1

Polyhomeotic homolog 1

[22]

NM_005407

SALL2

SAL2 like

[25]

NM_018645

HES6

Hairy and enhancer of split 6

 

NM_173547

TRIM65

Tripartite motif containing 65

 

NM_004427

PHC2

Polyhomeotic homolog 2

[99]

NM_032805

ZFP206

Zinc finger protein 206 (ZSCAN10)

[23, 24]

NM_001421

ELF4

ETS domain TF

 

NM_003325

HIRA

HIR Histone Cell Cycle regulator

[100]

NM_033204

ZNF101

Zinc finger protein 101

 

BC098403

ETV1

ETS variant 1

[28, 29]

NM_006079

CITED2

Cbp/p300-interacting transactivator

[30, 31]

NM_021728

OTX2

Orthodenticle homeobox 2

 

NM_024015

HOXB4

Homeobox B4

 

NM_006074

TRIM22

Tripartite motif-containing 22

[32]

XM_929986

LOC653441

Similar to polyhomeotic 1-like

Gene with sequence similarity to PHC1

NM_004497

FOXA3

Forkhead box 3

 

Cluster 22: TFs control neural development in earlier differentiation of human stem cells

   

BC008687

NEUROG1

Neurogenin 1

[101]

NM_006161

NEUROG1

Neurogenin 1

[101]

NM_001965

EGR4

Early growth response

 

NM_033178

DUX4

Double homeobox 4

[38]

NM_006732

FOSB

FBJ oncogene homolog B

[35]

NM_003317

TITF1

NK2 homeobox 1

[39]

NM_002478

MYOD1

myogenic differentiation 1

[43, 44]

NM_006192

PAX1

Paired box 1

[36]

NM_002700

POU4F3

POU class 4 homeobox 3

[37]

BC10493

POU4F3

POU class 4 homeobox 3

[37]

Cluster 17: TFs control differentiation towards multiple directions in human stem cells

   

NM_001002295

GATA3

GATA binding protein 3

Trophectoderm [45]

NM_012258

HEY1

Hairy/enhancer-of-split related with YRPW motif 1

Trophectoderm [46]

NM_001804

CDX1

Caudal type homeobox 1

 

NM_001430

EPAS1

Endothelial PAS domain protein 1

 

NM_032638

GATA2

GATA binding protein 2

Trophectoderm [47]

NM_030379

GLI2

GLI family zinc finger 2

Mesoderm [48]

NM_017410

HOXC13

Homeobox C13

Ectoderm[51]

NM_002202

ISL1

ISL LIM homeobox 1

Mesoderm [49]

NM_033343

LHX4

LIM homeobox 4

 

NM_002315

LMO1

LIM domain only 1 (rhombotin 1)

 

NM_005461

MAFB

v-maf musculoaponeurotic fibrosarcoma oncogene Homolog B (avian)

Neural [53]

NM_002448

MSX1

Msh homeobox 1

 

NM_002449

MSX2

Msh homeobox 2

Mesoderm[50]

NM_175747

OLIG3

Oligodendrocyte transcription factor 3

Neural [54]

NM_006099

PIAS3

Protein inhibitor of activated STAT, 3

Neural [55]

NM_019854

PRMT8

Protein arginine methyltransferase 8

Neural [56]

NM_030567

PRR7

Proline rich 7 (synaptic)

[102]

BC071571

RFX2

Regulatory factor X, 2 (influences HLA class II expression)

 

NM_003068

SNAI2

Snail homolog 2 (Drosophila)

Neural Crest[57]

NM_031439

SOX7

SRY (sex determining region Y)-box 7

Endoderm (Parietal) [52]

NM_003150

STAT3

Signal transducer and activator of transcription 3 (acute-phase response factor)

 

NM_003221

TFAP2B

Transcription factor AP-2 beta (activating enhancer binding protein 2 beta)

 

NM_016267

VGLL1

Vestigial like 1 (Drosophila)

 

NM_007129

ZIC2

Zic family member 2 (odd-paired homolog, Drosophila)

Neural [103]

NM_152320

ZNF641

zinc finger protein 641

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