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