mutLBSgeneDB |
Gene summary for HDAC4 |
Gene summary |
Basic gene Info. | Gene symbol | HDAC4 |
Gene name | histone deacetylase 4 | |
Synonyms | AHO3|BDMR|HA6116|HD4|HDAC-4|HDAC-A|HDACA | |
Cytomap | UCSC genome browser: 2q37.3 | |
Type of gene | protein-coding | |
RefGenes | NM_006037.3, | |
Description | histone deacetylase A | |
Modification date | 20141219 | |
dbXrefs | MIM : 605314 | |
HGNC : HGNC | ||
Ensembl : ENSG00000068024 | ||
HPRD : 05610 | ||
Vega : OTTHUMG00000133344 | ||
Protein | UniProt: P56524 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_HDAC4 | |
BioGPS: 9759 | ||
Pathway | NCI Pathway Interaction Database: HDAC4 | |
KEGG: HDAC4 | ||
REACTOME: HDAC4 | ||
Pathway Commons: HDAC4 | ||
Context | iHOP: HDAC4 | |
ligand binding site mutation search in PubMed: HDAC4 | ||
UCL Cancer Institute: HDAC4 | ||
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 | 10869435 | GO:0006338 | chromatin remodeling | 18850004 | GO:0016575 | histone deacetylation | 10869435 | GO:0033235 | positive regulation of protein sumoylation | 17696781 | GO:0034983 | peptidyl-lysine deacetylation | 18614528 | GO:0045892 | negative regulation of transcription, DNA-templated | 10869435 | GO:0070932 | histone H3 deacetylation | 12590135 | GO:0070933 | histone H4 deacetylation | 12590135 |
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Ligand binding site mutations for HDAC4 |
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 | R681 | R681K | LUSC | 1 | P942 | P942H | SKCM | 1 | D934 | F933L | SKCM | 1 | G975 | D977N | STAD | 1 | H665 | L663V | STAD | 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. |
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Protein structure related information for HDAC4 |
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 | P942 | P942H | -1.4575842 | H665 | L663V | -1.1832811 | D934 | F933L | -1.0853421 | R681 | R681K | -0.96707605 | G975 | D977N | -0.16414282 |
(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 HDAC4 from PDB |
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Differential gene expression and gene-gene network for HDAC4 |
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) |
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Phenotype information for HDAC4 |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
umls:C2931817 | Chromosome 2q37 deletion syndrome | 5 | Biomarker |
umls:C3714756 | Intellectual Disability | 2 | Biomarker |
umls:C0221357 | Brachydactyly | 1 | Biomarker |
umls:C0236736 | Cocaine-Related Disorders | 1 | Therapeutic |
umls:C0005695 | Urinary Bladder Neoplasms | 1 | Biomarker |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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Pharmacological information for HDAC4 |
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 | DB06176 | Romidepsin | Small molecule | |
Approved|investigational | DB06603 | Panobinostat | Small molecule | |
Experimental | DB07879 | N-hydroxy-5-[(3-phenyl-5,6-dihydroimidazo[1,2-a]pyrazin-7(8H)-yl)carbonyl]thiophene-2-carboxamide | Small molecule | |
Experimental | DB08613 | 2,2,2-TRIFLUORO-1-{5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHEN-2-YL}ETHANE-1,1-DIOL | Small molecule |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of HDAC4 go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | 9F4 | (1R,2R,3R)-2-[4-(5-FLUORANYLPYRIMIDIN-2-YL) PHENYL]-N-OXIDANYL-3-PHENYL-CYCLOPROPANE-1- CARBOXAMIDE | 4cbt | A | D934 | ZN | ZINC(2+) | 4cbt | A | D934 | ZN | ZINC(2+) | 4cbt | B | D934 | ZN | ZINC(2+) | 4cbt | C | D934 | ZN | ZINC(2+) | 4cby | A | D934 | ZN | ZINC(2+) | 4cby | B | D934 | KEE | (1R,2R,3R)-2-[4-(1,3-OXAZOL-5-YL)PHENYL]-N- OXIDANYL-3-PHENYL-CYCLOPROPANE-1-CARBOXAMIDE | 4cby | C | D934 | ZN | ZINC(2+) | 4cby | C | D934 | ZN | ZINC(2+) | 4cby | D | D934 | KEE | (1R,2R,3R)-2-[4-(1,3-OXAZOL-5-YL)PHENYL]-N- OXIDANYL-3-PHENYL-CYCLOPROPANE-1-CARBOXAMIDE | 4cby | A | R681 D934 | KEE | (1R,2R,3R)-2-[4-(1,3-OXAZOL-5-YL)PHENYL]-N- OXIDANYL-3-PHENYL-CYCLOPROPANE-1-CARBOXAMIDE | 4cby | B | R681 D934 | KEE | (1R,2R,3R)-2-[4-(1,3-OXAZOL-5-YL)PHENYL]-N- OXIDANYL-3-PHENYL-CYCLOPROPANE-1-CARBOXAMIDE | 4cby | D | R681 D934 | 9F4 | (1R,2R,3R)-2-[4-(5-FLUORANYLPYRIMIDIN-2-YL) PHENYL]-N-OXIDANYL-3-PHENYL-CYCLOPROPANE-1- CARBOXAMIDE | 4cbt | C | R681 D934 P942 | 9F4 | (1R,2R,3R)-2-[4-(5-FLUORANYLPYRIMIDIN-2-YL) PHENYL]-N-OXIDANYL-3-PHENYL-CYCLOPROPANE-1- CARBOXAMIDE | 4cbt | B | R681 D934 P942 G975 |
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Conservation information for LBS of HDAC4 |
Multiple alignments for P56524 in multiple species |
LBS | AA sequence | # species | Species | C667 | MLKHQCTCGNT | 3 | Gallus gallus, Mus musculus, Rattus norvegicus | C667 | MLKHQCTCGSS | 1 | Homo sapiens | C669 | KHQCTCGNTNS | 3 | Gallus gallus, Mus musculus, Rattus norvegicus | C669 | KHQCTCGSSSS | 1 | Homo sapiens | C751 | FVRLPCGGVGV | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | D840 | LIVDWDVHHGN | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | D934 | VSSGFDAVEGH | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | E677 | TNSHPEHAGRI | 3 | Gallus gallus, Mus musculus, Rattus norvegicus | E677 | SSSHPEHAGRI | 1 | Homo sapiens | E973 | IVLALEGGHDL | 2 | Homo sapiens, Rattus norvegicus | E973 | VVLALEGGHDL | 1 | Gallus gallus | E973 | LVLALEGGHDL | 1 | Mus musculus | F812 | STPMGFCYFNS | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | F871 | DDGNFFPGSGA | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | G811 | ESTPMGFCYFN | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | G974 | VLALEGGHDLT | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | G975 | LALEGGHDLTA | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | H665 | TLMLKHQCTCG | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | H675 | GNTNSHPEHAG | 3 | Gallus gallus, Mus musculus, Rattus norvegicus | H675 | GSSSSHPEHAG | 1 | Homo sapiens | H678 | NSHPEHAGRIQ | 3 | Gallus gallus, Mus musculus, Rattus norvegicus | H678 | SSHPEHAGRIQ | 1 | Homo sapiens | H802 | VRPPGHHAEES | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | H803 | RPPGHHAEEST | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | H842 | VDWDVHHGNGT | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | L943 | GHPTPLGGYNL | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | P676 | NTNSHPEHAGR | 3 | Gallus gallus, Mus musculus, Rattus norvegicus | P676 | SSSSHPEHAGR | 1 | Homo sapiens | P800 | AVVRPPGHHAE | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | P942 | EGHPTPLGGYN | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | R681 | PEHAGRIQSIW | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus |
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