| AEBP1 | AE binding protein 1 | 20 |
| ALX3 | ALX homeobox 3 | 10 |
| ALX4 | ALX homeobox 4 | 230 |
| ARID3A | AT rich interactive domain 3A (BRIGHT-like) | 1 |
| ARNT | aryl hydrocarbon receptor nuclear translocator-like | 10 |
| ARNTL | aryl hydrocarbon receptor nuclear translocator | 1 |
| ARX | aristaless related homeobox | 29 |
| ASCL1 | achaete-scute complex homolog 1 (Drosophila) | 20 |
| ASCL2 | achaete-scute complex homolog 2 (Drosophila) | 44 |
| ATOH1 | atonal homolog 1 (Drosophila) | 1 |
| BAPX1 | NK3 homeobox 2 | 20 |
| BARHL1 | BarH-like homeobox 1 | 31 |
| BARHL2 | BarH-like homeobox 2 | 49 |
| BARX1 | BARX homeobox 1 | 10 |
| BARX2 | BARX homeobox 2 | 9 |
| BCL11B | B-cell CLL/lymphoma 11B (zinc finger protein) | 10 |
| BCL6 | B-cell CLL/lymphoma 6 | 1 |
| BHLHB5 | basic helix-loop-helix family, member e22 | 20 |
| BHLHE22 | basic helix-loop-helix family, member e22 | 10 |
| BNC1 | basonuclin 1 | 150 |
| BSX | brain-specific homeobox | 1 |
| BUD31 | BUD31 homolog (S. cerevisiae) | 1 |
| C11orf9 | myelin regulatory factor | 11 |
| CBFA2T3 | core-binding factor, runt domain, alpha subunit 2; translocated to, 3 | 10 |
| CDX2 | caudal type homeobox 2 | 10 |
| CEBPA | CCAAT/enhancer binding protein (C/EBP), alpha | 13 |
| CEBPD | CCAAT/enhancer binding protein (C/EBP), delta | 1 |
| CEBPE | CCAAT/enhancer binding protein (C/EBP), epsilon | 20 |
| CEBPG | CCAAT/enhancer binding protein (C/EBP), gamma | 1 |
| CITED1 | Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 1 | 1 |
| CREB1 | cAMP responsive element binding protein 1 | 9 |
| CREB3L1 | cAMP responsive element binding protein 3-like 1 | 10 |
| CREB5 | cAMP responsive element binding protein 5 | 1 |
| CREBBP | CREB binding protein | 13 |
| CREM | cAMP responsive element modulator | 1 |
| CTBP1 | C-terminal binding protein 1 | 10 |
| CUTL2 | cut-like homeobox 2 | 50 |
| CUX2 | cut-like homeobox 2 | 1 |
| DBX1 | developing brain homeobox 1 | 11 |
| DBX2 | developing brain homeobox 2 | 10 |
| DLX1 | distal-less homeobox 1 | 30 |
| DLX2 | distal-less homeobox 2 | 10 |
| DLX4 | distal-less homeobox 4 | 11 |
| DLX5 | distal-less homeobox 5 | 70 |
| DMRT1 | doublesex and mab-3 related transcription factor 1 | 51 |
| DMRT2 | doublesex and mab-3 related transcription factor 2 | 30 |
| DRGX | dorsal root ganglia homeobox | 9 |
| E2F3 | E2F transcription factor 3 | 1 |
| E2F5 | E2F transcription factor 5, p130-binding | 14 |
| E4F1 | E4F transcription factor 1 | 1 |
