| ACTL6B | actin-like 6B | 21 |
| ACTN2 | actinin, alpha 2 | 40 |
| AEBP1 | AE binding protein 1 | 20 |
| JUB | ajuba LIM protein | 1 |
| PRMT2 | protein arginine methyltransferase 2 | 1 |
| TEX2 | transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha) | 1 |
| TF | transcription factor AP-2 beta (activating enhancer binding protein 2 beta) | 675 |
| ARNTL | aryl hydrocarbon receptor nuclear translocator | 1 |
| ASCL1 | achaete-scute complex homolog 1 (Drosophila) | 20 |
| BASP1 | brain abundant, membrane attached signal protein 1 | 30 |
| BCL11A | B-cell CLL/lymphoma 11A (zinc finger protein) | 1 |
| BCL10 | B-cell CLL/lymphoma 10 | 9 |
| BCORL1 | BCL6 corepressor | 10 |
| ARNT | aryl hydrocarbon receptor nuclear translocator-like | 10 |
| TM6SF1 | T, brachyury homolog (mouse) | 22 |
| T | T, brachyury homolog (mouse) | 25493 |
| BRCA1 | breast cancer 1, early onset | 101 |
| CREBBP | CREB binding protein | 13 |
| CBX4 | chromobox homolog 4 | 29 |
| CCNE1 | cyclin E1 | 10 |
| CDX2 | caudal type homeobox 2 | 10 |
| CITED1 | Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 1 | 1 |
| NR2F1 | nuclear receptor subfamily 2, group F, member 1 | 10 |
| NR2F2 | nuclear receptor subfamily 2, group F, member 2 | 10 |
| CREB1 | cAMP responsive element binding protein 1 | 9 |
| CREM | cAMP responsive element modulator | 1 |
| KCNIP3 | Kv channel interacting protein 3, calsenilin | 1 |
| CTBP1 | C-terminal binding protein 1 | 10 |
| CTBP2 | C-terminal binding protein 2 | 1 |
| DCC | deleted in colorectal carcinoma | 192 |
| DNMT3B | DNA (cytosine-5-)-methyltransferase 3 beta | 14 |
| E4F1 | E4F transcription factor 1 | 1 |
| ENO1 | enolase 1, (alpha) | 1 |
| ESRRB | estrogen-related receptor beta | 10 |
| FEV | FEV (ETS oncogene family) | 1 |
| FGF22 | fibroblast growth factor 2 (basic) | 9 |
| ZFPM2 | zinc finger protein, FOG family member 2 | 1 |
| GATA3 | GATA binding protein 3 | 11 |
| GATA4 | GATA binding protein 4 | 21 |
| HAND1 | heart and neural crest derivatives expressed 1 | 54 |
| HAND2 | heart and neural crest derivatives expressed 2 | 30 |
| HCFC1 | host cell factor C1 (VP16-accessory protein) | 9 |
| HDAC1 | histone deacetylase 1 | 13 |
| HDAC4 | histone deacetylase 4 | 1 |
| HEY1 | hairy/enhancer-of-split related with YRPW motif 1 | 9 |
| HEYL | hairy/enhancer-of-split related with YRPW motif-like | 20 |
| HSF4 | heat shock transcription factor 4 | 11 |
| ID4 | inhibitor of DNA binding 4, dominant negative helix-loop-helix protein | 10 |
| IRF3 | interferon regulatory factor 3 | 1 |
| ISL1 | ISL LIM homeobox 1 | 1 |
| TCF21 | transcription factor 4 | 30 |
| JMY | junction mediating and regulatory protein, p53 cofactor | 1 |
| JUNB | jun B proto-oncogene | 9 |
| KCTD1 | potassium channel tetramerization domain containing 1 | 29 |
| KDM1 | lysine (K)-specific demethylase 1A | 1 |
| PRKCB | protein kinase C, beta | 31 |
| PRKCB1 | protein kinase C, beta | 21 |
| LHX1 | LIM homeobox 1 | 95 |
| LHX2 | LIM homeobox 2 | 41 |
| LHX3 | LIM homeobox 3 | 11 |
| LHX9 | LIM homeobox 9 | 10 |
| LIF | leukemia inhibitory factor | 13 |
| MAP3K1 | mitogen-activated protein kinase kinase kinase 10 | 22 |
| MAML3 | mastermind-like 3 (Drosophila) | 10 |
| FLJ36070 | MEF2 activating motif and SAP domain containing transcriptional regulator | 20 |
| MED12L | mediator complex subunit 12-like | 1 |
| MED16 | mediator complex subunit 16 | 1 |
| MED17 | mediator complex subunit 17 | 1 |
| MED22 | mediator complex subunit 22 | 9 |
| MED7 | mediator complex subunit 7 | 9 |
| MEIS2 | Meis homeobox 2 | 1 |
| MSX2 | msh homeobox 2 | 1 |
| MUC17 | mucin 1, cell surface associated | 24 |
| MSC | musculin | 21 |
| MYOD1 | myogenic differentiation 1 | 104 |
| NCOA4 | nuclear receptor coactivator 4 | 9 |
| NCOR2 | nuclear receptor corepressor 2 | 10 |
| NEUROD1 | neuronal differentiation 1 | 49 |
| NEUROD2 | neuronal differentiation 2 | 20 |
| NFATC4 | nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4 | 1 |
| NFIL3 | nuclear factor, interleukin 3 regulated | 1 |
| NEUROG1 | neurogenin 1 | 91 |
| NGN1 | neurogenin 1 | 24 |
| NEUROG3 | neurogenin 3 | 30 |
| NKX2-2 | NK2 homeobox 2 | 30 |
| NKX2-5 | NK2 homeobox 5 | 30 |
| NMI | N-myc (and STAT) interactor | 1 |
| NOTCH1 | notch 1 | 1 |
| NR0B1 | nuclear receptor subfamily 0, group B, member 1 | 1 |
| NR1D1 | nuclear receptor subfamily 1, group D, member 1 | 1 |
| NR1I2 | nuclear receptor subfamily 1, group I, member 2 | 10 |
| NR1I3 | nuclear receptor subfamily 1, group I, member 3 | 20 |
| NRG1 | neuregulin 1 | 23 |
| PITX1 | paired-like homeodomain 1 | 10 |
| PITX2 | paired-like homeodomain 2 | 63 |
| PMF1 | polyamine-modulated factor 1 | 1 |
| POU3F1 | POU class 3 homeobox 1 | 30 |
| POU3F2 | POU class 3 homeobox 2 | 30 |
| PPARGC1B | peroxisome proliferator-activated receptor gamma | 1 |
| PRDM16 | PR domain containing 16 | 19 |
| PPARG | peroxisome proliferator-activated receptor gamma, coactivator 1 beta | 14 |
| PRRX1 | paired related homeobox 1 | 21 |
| PSMC3 | proteasome (prosome, macropain) 26S subunit, ATPase, 3 | 1 |
| RARA | retinoic acid receptor, alpha | 96 |
| RBPMS | RNA binding protein with multiple splicing | 1 |
| RCOR2 | REST corepressor 2 | 9 |
| RIPK3 | receptor-interacting serine-threonine kinase 3 | 33 |
| SETD8 | SET domain containing (lysine methyltransferase) 8 | 9 |
| SIN3A | SIN3 transcription regulator homolog A (yeast) | 1 |
| SKI | v-ski sarcoma viral oncogene homolog (avian) | 41 |
| LBXCOR1 | SKI family transcriptional corepressor 1 | 10 |
| SMARCD3 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 | 10 |
| SND1 | staphylococcal nuclease and tudor domain containing 1 | 1 |
| SMARCB1 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 | 9 |
| SKIP | SNW domain containing 1 | 40 |
| SOX1 | SRY (sex determining region Y)-box 10 | 229 |
| SOX10 | SRY (sex determining region Y)-box 11 | 1 |
| SOX15 | SRY (sex determining region Y)-box 17 | 51 |
| SOX3 | SRY (sex determining region Y)-box 3 | 10 |
| NR5A1 | nuclear receptor subfamily 5, group A, member 1 | 10 |
| TACR3 | TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa | 20 |
| TAF1 | TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa | 1 |
| TAF4 | TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa | 10 |
| TBKBP1 | transducin (beta)-like 1X-linked | 9 |
| TBR1 | T-box 15 | 10 |
| TBX1 | T-box 18 | 33 |
| TBX18 | T-box 20 | 10 |
| TBX5 | T-box 6 | 50 |
| TGFBR2 | TGFB-induced factor homeobox 1 | 1 |
| TJP2 | transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila) | 30 |
| NFKBIL2 | tonsoku-like, DNA repair protein | 9 |
| TSG101 | tumor susceptibility gene 101 | 13 |
| UBE3A | ubiquitin protein ligase E3A | 1 |
| UBP1 | upstream binding protein 1 (LBP-1a) | 9 |
| UTF1 | undifferentiated embryonic cell transcription factor 1 | 30 |
| VGLL2 | vestigial like 2 (Drosophila) | 40 |
| WNT3 | wingless-type MMTV integration site family, member 3A | 31 |
| WWTR1 | WW domain containing transcription regulator 1 | 1 |
| YAP1 | Yes-associated protein 1 | 65 |
| ZEB1 | zinc finger E-box binding homeobox 1 | 1 |
| ZNF593 | zinc finger protein 593 | 20 |
| ZSCAN18 | zinc finger and SCAN domain containing 1 | 1 |
