| CEBP_a | CCAAT-enhancer-binding protein alpha |
| CEBP_all | CCAAT-enhancer-binding proteins |
| CLOCK | Circadian Locomotor Output Cycles Kaput |
| cMyc_can | Regulator gene coding for transcription factor; often mutated in cancer |
| CRE | Cyclic AMP response element |
| E2F1 | Transcription factor E2F1, encoded by E2F1 gene |
| E2F1/DP1sel1 | E2F-DP1 dimers binding DNA |
| EGR1 | Early growth response protein 1 |
| EKLf | Erythroid Kruppel-like Factor |
| ER2 | Estrogen receptor beta |
| GATA_all | Family binding “GATA” DNA sequence |
| GATA-1 | GATA-binding factor 1 |
| GATA-2 | GATA-binding protein 2 |
| GATA-3 | Trans-acting T-cell transcription factor GATA-3 |
| HMG-1 | High-mobility group protein 1 |
| HNF-1 | Hepatocyte nuclear factor 1 |
| HNF-3 | Hepatocyte nuclear factor 3 |
| HNF-4 | Hepatocyte nuclear factor 4 |
| IRF | Interferon regulatory factors |
| isre | Interferon stimulation response element |
| MyoD | Myogenic regulatory factor |
| MyOGsel3 | Myogenin |
| NF-1 | Neurofibromin 1 |
| NF-E2 | NF-E2 45 kDa subunit, encoded by NFE2 |
| NFATp | Nuclear factor of activated T-cells (NFAT) complex component |
| NFkB_all | Nuclear factor kappa-light-chain-enhancer of activated B cells |
| NFkB_hetero | p50/p65 (RELA) heterodimer form of NF-kB |
| NFkB_homo | c-Rel protein, member of NF-kB family |
| Nfy | Nuclear transcription factor Y |
| Nrf2 | Nuclear factor (erythroid-derived 2)-like 2 |
| Oct-1 | Octamer transcription factor 1 |
| Oct_all | Octamer transcription factors |
| p53 | Protein 53 |
| PPRF | Paramedian pontine reticular formation |
| Pu1 | SPI1 gene-encoded protein |
| setCREB | cAMP response element-binding |
| setCREBzag | cAMP response element-binding |
| SRE_san | Serum response element |
| SRF | Serum response factor |
| STAT1 | Signal Transducer and Activator of Transcription 1 |
| STAT | Signal Transducer and Activator of Transcription |
| TTF1 | Thyroid transcription factor 1 |
| USF | Upstream stimulatory factors |
| yy1 | YY1 gene-encoded protein |