|
mutLBSgeneDB |
| |
| |
| |
| |
| |
| |
|
| Gene summary for HDAC3 |
 Gene summary |
| Basic gene Info. | Gene symbol | HDAC3 |
| Gene name | histone deacetylase 3 | |
| Synonyms | HD3|RPD3|RPD3-2 | |
| Cytomap | UCSC genome browser: 5q31 | |
| Type of gene | protein-coding | |
| RefGenes | NM_003883.3, | |
| Description | SMAP45 | |
| Modification date | 20141222 | |
| dbXrefs | MIM : 605166 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000171720 | ||
| HPRD : 08950 | ||
| Vega : OTTHUMG00000129629 | ||
| Protein | UniProt: O15379 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_HDAC3 | |
| BioGPS: 8841 | ||
| Pathway | NCI Pathway Interaction Database: HDAC3 | |
| KEGG: HDAC3 | ||
| REACTOME: HDAC3 | ||
| Pathway Commons: HDAC3 | ||
| Context | iHOP: HDAC3 | |
| ligand binding site mutation search in PubMed: HDAC3 | ||
| UCL Cancer Institute: HDAC3 | ||
| Assigned class in mutLBSgeneDB | B: This gene belongs to targetable_mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0000122 | negative regulation of transcription from RNA polymerase II promoter | 16569215 | GO:0001934 | positive regulation of protein phosphorylation | 25190803 | GO:0006476 | protein deacetylation | 17172643 | GO:0031647 | regulation of protein stability | 25190803 | GO:0042993 | positive regulation of transcription factor import into nucleus | 25190803 | GO:0045944 | positive regulation of transcription from RNA polymerase II promoter | 25190803 | GO:0071498 | cellular response to fluid shear stress | 25190803 |
| Top |
| Ligand binding site mutations for HDAC3 |
| Lollipop-style diagram of mutations at LBS in amino-acid sequence. We represented ligand binding site mutations only. (You can see big image via clicking.)  : non-synonymous mutation on LBS, Circle size denotes number of samples. |
 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | Y331 | A333V | STAD | 1 | Y331 | E330K | UCEC | 1 |
| cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma. |
| Top |
| Protein structure related information for HDAC3 |
| Relative protein structure stability change (ΔΔE) using Mupro 1.1 Mupro score denotes assessment of the effect of mutations on thermodynamic stability. (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability) |
 : nsSNV at non-LBS : nsSNV at LBS |
 |
| nsSNVs sorted by the relative stability change of protein structure by each mutation Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene. |
| LBS | AAchange of nsSNV | Relative stability change | Y331 | E330K | -1.3130243 | Y331 | A333V | -0.60035641 |
| (MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132) |
| Structure image for HDAC3 from PDB |
| Top |
| Differential gene expression and gene-gene network for HDAC3 |
| Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types |
| Differential co-expressed gene network based on protein-protein interaction data (CePIN) |
| Top |
| Top |
| Phenotype information for HDAC3 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0018799 | Heart Diseases | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
| Top |
| Pharmacological information for HDAC3 |
| Gene expression profile of anticancer drug treated cell-lines (CCLE) Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient. |
 |
| Gene-centered drug-gene interaction network |
 |
| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Approved|investigational | DB02546 | Vorinostat | Small molecule |  |
| Investigational | DB05223 | SB939 | Small molecule |  |
| Investigational | DB05651 | MGCD-0103 | Small molecule |  |
| Approved|investigational | DB06603 | Panobinostat | Small molecule |  |
| Gene-centered ligand-gene interaction network |
 |
| Ligands binding to mutated ligand binding site of HDAC3 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | I0P | INOSITOL 1,4,5,6-TETRAKISPHOSPHATE | 4a69 | A | Y331 | I0P | INOSITOL 1,4,5,6-TETRAKISPHOSPHATE | 4a69 | B | Y331 |
| Top |
| Conservation information for LBS of HDAC3 |
| Multiple alignments for O15379 in multiple species |
| LBS | AA sequence | # species | Species | D170 | LYIDIDIHHGD | 4 | Homo sapiens, Danio rerio, Gallus gallus, Rattus norvegicus | D170 | LYIDIDVHHGD | 1 | Arabidopsis thaliana | D170 | LYVDIDIHHGD | 1 | Xenopus tropicalis | D259 | LQCGADSLGCD | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus | D259 | LQCGADSLARD | 1 | Arabidopsis thaliana | D259 | LQCGADSLGRD | 1 | Gallus gallus | G21 | FHYGAGHPMKP | 4 | Homo sapiens, Danio rerio, Gallus gallus, Rattus norvegicus | G21 | VYFGPNHPMKP | 1 | Arabidopsis thaliana | G21 | FHYGTGHPMKP | 1 | Xenopus tropicalis | H17 | DVGNFHYGAGH | 4 | Homo sapiens, Danio rerio, Gallus gallus, Rattus norvegicus | H17 | DVGSVYFGPNH | 1 | Arabidopsis thaliana | H17 | DVGNFHYGTGH | 1 | Xenopus tropicalis | H172 | IDIDIHHGDGV | 4 | Homo sapiens, Danio rerio, Gallus gallus, Rattus norvegicus | H172 | IDIDVHHGDGV | 1 | Arabidopsis thaliana | H172 | VDIDIHHGDGV | 1 | Xenopus tropicalis | K25 | AGHPMKPHRLA | 3 | Homo sapiens, Gallus gallus, Rattus norvegicus | K25 | PNHPMKPHRLC | 1 | Arabidopsis thaliana | K25 | AGHPMKPHRLS | 1 | Danio rerio | K25 | TGHPMKPHRLS | 1 | Xenopus tropicalis | R265 | SLGCDRLGCFN | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus | R265 | SLARDRLGCFN | 1 | Arabidopsis thaliana | R265 | SLGRDRLGCFN | 1 | Gallus gallus | R301 | GGYTVRNVARC | 5 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Rattus norvegicus | R301 | GGYTKENVARC | 1 | Arabidopsis thaliana | V300 | GGGYTVRNVAR | 5 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Rattus norvegicus | V300 | GGGYTKENVAR | 1 | Arabidopsis thaliana | Y331 | SEYFEYFAPDF | 5 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Rattus norvegicus | Y331 | NDYIKYFAPDF | 1 | Arabidopsis thaliana |
 |
Copyright © 2016-Present - The University of Texas Health Science Center at Houston |