Table 1.
Examples of gene-expression changes in response to HDACi treatment or single class I HDAC enzyme depletion.
| Gene symbol | Gene name | Probe nr. | Belinostat | Valproic acid | HDAC1 KD | HDAC2 KD | HDAC3 KD |
| Transcription | |||||||
| HDAC1 | Histone deacetylase 1 | 201209_at | 0.10 | ||||
| HDAC2 | Histone deacetylase 2 | 201833_at | 0.10 | ||||
| HDAC3 | Histone deacetylase 3 | 216326_s_at | 0.14 | ||||
| JUN | Jun oncogene (AP-1) | 201465_s_at | 0.38 | 0.41 | 0.42 | ||
| SMAD3 | SMAD family member 3 | 218284_at | 0.53 | 0.49 | 0.55 | ||
| RAF1 | v-raf-1 murine leukemia viral oncogene homolog | 201244_s_at | 2.88 | 2.94 | 2.93 | ||
| Metabolism | |||||||
| CTPS | CTP synthase | 202613_at | 0.39 | 0.44 | |||
| TYMS | Thymidylate synthase | 202589_at | 0.62 | 0.43 | |||
| FUCA | Fucosidase, alpha-L-1, tissue | 202838_at | 5.86 | 5.41 | |||
| SAT1 | Spermidine/spermine N1-acetyltransferase 1 | 210592_s_at | 3.81 | 3.54 | |||
| Cell cycle | |||||||
| CDKN1A | Cyclin-dependent kinase inhibitor 1A (p21, Cip1) | 202284_s_at | 4.15 | 3.16 | |||
| CDC25B | Cell division cycle 25 homolog B | 201853_s_at | 0.68 | 0.58 | |||
| HRASLS3 | HRAS-like suppressor 3 | 209581_at | 5.96 | 4.70 | 4.14 | 2.31 | 2.11 |
| CCNB1 | Cyclin B1 | 214710_s_at | 0.55 | 0.39 | |||
| CCND1 | Cyclin D1 | 208712_at | 0.38 | ||||
| CCND2 | Cyclin D2 | 200951_s_at | 2.29 | ||||
| CCNE1 | Cyclin E1 | 213523_at | 2.04 | 1.69 | |||
| CCNG1 | Cyclin G1 | 208796_s_at | 4.39 | 4.11 | 3.31 | ||
| Apoptosis | |||||||
| FAIM | Fas apoptotic inhibitory molecule | 220643_s_at | 0.32 | 0.17 | |||
| BCL2L11 | BCL2-like 11 (apoptosis facilitator) (BIM) | 1555372_at | 1.95 | ||||
| CASP3 | Caspase 3 | 202763_at | 0.51 | 0.52 | |||
| CASP7 | Caspase 7 | 207181_s_at | 1.86 | 1.72 | 1.53 | ||
| CASP9 | Caspase 9 | 203984_s_at | 1.57 | 3.24 | 1.87 | ||
| FAS | FAS (TNF receptor superfamily, member 6) | 216252_x_at | 1.55 | 0.65 | |||
| Cell signaling | |||||||
| RASGRP2 | RAS guanyl releasing protein 2 | 214369_s_at | 3.16 | 6.06 | |||
| MYC | v-myc myelocytomatosis viral oncogene homolog | 202431_s_at | 0.43 | ||||
| MINA | MYC induced nuclear antigen | 213189_at | 0.31 | 0.40 | |||
| TGFα | Transforming growth factor, alpha | 205016_at | 3.24 | ||||
| RASGRP1 | RAS guanyl releasing protein 1 | 205590_at | 0.12 | 0.10 | 0.25 | ||
| CGA | glycoprotein hormones, alpha polypeptide | 204637_at | 5.30 | 4.36 | 2.66 | 16.53 | 6.27 |
| Miscellaneous | |||||||
| KPNB1 | Importin β | 208975_s_at | 0.67 | 0.57 | |||
| SERPINE1 | Serpin peptidase inhibitor, clade E | 202627_s_at | 0.21 | 0.23 | 0.22 | ||
| EDN1 | Endothelin 1 | 218995_s_at | 0.45 | 0.45 | 0.45 | ||
| THBS1 | Thrombospondin 1 | 201108_s_at | 0.30 | 0.30 | 0.51 | ||
| ADAM19 | ADAM metallopeptidase domain 19 | 209765_at | 0.33 | 0.37 | |||
| PDK4 | Pyruvate dehydrogenase kinase 4 | 205960_at | 4.13 | 7.34 | 2.74 | 3.31 | 4.38 |
| ATP10D | ATPase, Class V, type 10D | 213238_at | 3.85 | 3.46 | 2.40 | 2.04 | 2.88 |
Absolute fold-changes related to untreated or scrambled control for HDACi (VPA or belinostat) or HDAC 1, 2, or 3 KD samples respectively are listed. Blank fields correspond to no significant changes above 1.5-fold. The complete gene list of all genes regulated by 2-fold or more is accessible as supplementary material (Table A).