HCSGD entry for HDAC3
1. General information
| Official gene symbol | HDAC3 |
|---|---|
| Entrez ID | 8841 |
| Gene full name | histone deacetylase 3 |
| Other gene symbols | HD3 RPD3 RPD3-2 |
| Links to Entrez Gene | Links to Entrez Gene |
2. Neighbors in the network
3. Gene ontology annotation
GO ID | GO term | Evidence | Category |
|---|---|---|---|
| GO:0000118 | Histone deacetylase complex | TAS | cellular_component |
| GO:0000122 | Negative regulation of transcription from RNA polymerase II promoter | IDA IMP | biological_process |
| GO:0003682 | Chromatin binding | IDA | molecular_function |
| GO:0003714 | Transcription corepressor activity | IDA IMP | molecular_function |
| GO:0004407 | Histone deacetylase activity | IEA IMP TAS | molecular_function |
| GO:0005515 | Protein binding | IPI | molecular_function |
| GO:0005634 | Nucleus | IDA TAS | cellular_component |
| GO:0005654 | Nucleoplasm | TAS | cellular_component |
| GO:0005737 | Cytoplasm | TAS | cellular_component |
| GO:0005876 | Spindle microtubule | IDA | cellular_component |
| GO:0006351 | Transcription, DNA-templated | IEA | biological_process |
| GO:0006476 | Protein deacetylation | IDA | biological_process |
| GO:0007219 | Notch signaling pathway | TAS | biological_process |
| GO:0007346 | Regulation of mitotic cell cycle | IEA | biological_process |
| GO:0008134 | Transcription factor binding | IPI TAS | molecular_function |
| GO:0010832 | Negative regulation of myotube differentiation | IMP | biological_process |
| GO:0016568 | Chromatin modification | TAS | biological_process |
| GO:0016787 | Hydrolase activity | IEA | molecular_function |
| GO:0017053 | Transcriptional repressor complex | IDA | cellular_component |
| GO:0019899 | Enzyme binding | IPI | molecular_function |
| GO:0030332 | Cyclin binding | IPI | molecular_function |
| GO:0031490 | Chromatin DNA binding | IEA | molecular_function |
| GO:0032041 | NAD-dependent histone deacetylase activity (H3-K14 specific) | IEA | molecular_function |
| GO:0032922 | Circadian regulation of gene expression | IEA | biological_process |
| GO:0033558 | Protein deacetylase activity | IDA | molecular_function |
| GO:0040014 | Regulation of multicellular organism growth | IEA | biological_process |
| GO:0042826 | Histone deacetylase binding | IPI | molecular_function |
| GO:0043066 | Negative regulation of apoptotic process | TAS | biological_process |
| GO:0044255 | Cellular lipid metabolic process | TAS | biological_process |
| GO:0044281 | Small molecule metabolic process | TAS | biological_process |
| GO:0045786 | Negative regulation of cell cycle | TAS | biological_process |
| GO:0045892 | Negative regulation of transcription, DNA-templated | IMP | biological_process |
| GO:0046329 | Negative regulation of JNK cascade | IMP | biological_process |
| GO:0046969 | NAD-dependent histone deacetylase activity (H3-K9 specific) | IEA | molecular_function |
| GO:0046970 | NAD-dependent histone deacetylase activity (H4-K16 specific) | IEA | molecular_function |
| GO:0048011 | Neurotrophin TRK receptor signaling pathway | TAS | biological_process |
| GO:0051225 | Spindle assembly | IMP | biological_process |
| GO:0097372 | NAD-dependent histone deacetylase activity (H3-K18 specific) | IEA | molecular_function |
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4. Expression levels in datasets
- Meta-analysis result
| p-value up | p-value down | FDR up | FDR down |
|---|---|---|---|
| 0.9508058053 | 0.0832090650 | 0.9999902473 | 0.5471261054 |
- Individual experiment result
( "-" represent NA in the specific microarray platform )
( "-" represent NA in the specific microarray platform )
| Data source | Up or down | Log fold change |
|---|---|---|
| GSE11954 | Down | -0.3816781928 |
| GSE13712_SHEAR | Down | -0.3097092853 |
| GSE13712_STATIC | Down | -0.0969904944 |
| GSE19018 | Up | 0.3039447661 |
| GSE19899_A1 | Up | 0.0759345927 |
| GSE19899_A2 | Up | 0.2902374556 |
| PubMed_21979375_A1 | Up | 0.0729853013 |
| PubMed_21979375_A2 | Down | -0.1885901363 |
| GSE35957 | Down | -0.1163505974 |
| GSE36640 | Down | -0.5204521062 |
| GSE54402 | Up | 0.2876630890 |
| GSE9593 | Down | -0.2401119908 |
| GSE43922 | Down | -0.0485490959 |
| GSE24585 | Down | -0.1200881356 |
| GSE37065 | Down | -0.0537283319 |
| GSE28863_A1 | Down | -0.0725937289 |
| GSE28863_A2 | Up | 0.0221830780 |
| GSE28863_A3 | Down | -0.5412960381 |
| GSE28863_A4 | Down | -0.1921385967 |
| GSE48662 | Down | -0.3928912046 |
5. Regulation relationships with compounds/drugs/microRNAs
- Compounds
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- Drugs
Name | Drug | Accession number |
|---|---|---|
| Vorinostat | DB02546 | EXPT02902 |
| SB939 | DB05223 | - |
| MGCD-0103 | DB05651 | - |
| Panobinostat | DB06603 | - |
- MicroRNAs
- mirTarBase
No target information from mirTarBase
- mirRecord
No target information from mirRecord
6. Text-mining results about the gene
Gene occurances in abstracts of cellular senescence-associated articles: 4 abstracts the gene occurs.
PubMed ID of the article | Sentenece the gene occurs |
|---|---|
| 24992635 | Finally, we found that DBC1 participates in the onset of cellular senescence in response to cell damage by mechanism that involves binding and inhibition of HDAC3 |
| 24992635 | We propose that by regulating HDAC3 activity during cellular damage, DBC1 participates in the fate decision that leads to the establishment of cellular senescence and consequently to inflammation and tissue dysfunction during obesity |
| 22117195 | We have previously reported that MageA2 binds histone deacetylase (HDAC)3 and represses p53-dependent apoptosis in response to chemotherapeutic drugs |
| 19583777 | Furthermore, chromatin immunoprecipitation assays verified that HDAC3 was recruited to the p16(INK4a) promoter by ZBP-89 through an epigenetic mechanism involving histone acetylation modification |
| 19583777 | Moreover, immunofluorescence and coimmunoprecipitation assays revealed that ZBP-89 and HDAC3 formed a complex |
| 19583777 | These data suggest that ZBP-89 and HDAC3, but not HDAC4, can work coordinately to restrain cell senescence by downregulating p16(INK4a) expression through an epigenetic modification of histones |
| 18558095 | Specifically, HDAC3 and HDAC4 inhibited the p16(INK4a) promoter activity |
| 18558095 | The chromatin immunoprecipitation (ChIP) assays verified that HDAC3 and HDAC4 were recruited to p16(INK4a) promoter by YY1 |
| 18558095 | Overall, data from this study suggest that YY1, HDAC3 and HDAC4 restrained cell senescence by repressing p16(INK4a) expression through an epigenetic modification of histones |
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