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mutLBSgeneDB |
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| Gene summary for HDAC2 |
 Gene summary |
| Basic gene Info. | Gene symbol | HDAC2 |
| Gene name | histone deacetylase 2 | |
| Synonyms | HD2|RPD3|YAF1 | |
| Cytomap | UCSC genome browser: 6q21 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001527.3, NR_033441.1,NR_073443.1, | |
| Description | YY1-associated factor 1transcriptional regulator homolog RPD3 | |
| Modification date | 20141222 | |
| dbXrefs | MIM : 605164 | |
| HGNC : HGNC | ||
| HPRD : 05521 | ||
| Protein | UniProt: Q92769 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_HDAC2 | |
| BioGPS: 3066 | ||
| Pathway | NCI Pathway Interaction Database: HDAC2 | |
| KEGG: HDAC2 | ||
| REACTOME: HDAC2 | ||
| Pathway Commons: HDAC2 | ||
| Context | iHOP: HDAC2 | |
| ligand binding site mutation search in PubMed: HDAC2 | ||
| UCL Cancer Institute: HDAC2 | ||
| 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:0043044 | ATP-dependent chromatin remodeling | 16217013 |
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| Ligand binding site mutations for HDAC2 |
| 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. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | F206 | E204K | BLCA | 1 | D175 | D175N | BRCA | 1 | D175 | D175N | LAML | 1 | H29 | G28R | LUAD | 1 | D100 | P102A | LUAD | 1 | F206 | E204K | SKCM | 1 | Y304 | I306N | STAD | 1 | D177 | D177N | STAD | 1 | H200 | K201E | 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. |
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| Protein structure related information for HDAC2 |
| 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 |
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| 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 | D100 | P102A | -1.6588211 | F206 | E204K | -1.6549996 | Y304 | I306N | -1.402377 | D175 | D175N | -1.1420521 | D177 | D177N | -0.91336098 | H200 | K201E | -0.56714182 | H29 | G28R | -0.13951358 |
| (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 HDAC2 from PDB |
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| Differential gene expression and gene-gene network for HDAC2 |
| 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 HDAC2 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0024117 | Pulmonary Disease, Chronic Obstructive | 10 | Biomarker, Therapeutic |
| umls:C0014175 | Endometriosis | 3 | Biomarker, Therapeutic |
| umls:C0007137 | Carcinoma, Squamous Cell | 2 | Biomarker |
| umls:C0023470 | Leukemia, Myeloid | 1 | Biomarker |
| umls:C0018800 | Cardiomegaly | 1 | Biomarker |
| umls:C0025202 | Melanoma | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for HDAC2 |
| 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. |
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| Gene-centered drug-gene interaction network |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Approved|investigational | DB00227 | Lovastatin | Small molecule |  |
| Approved | DB00277 | Theophylline | Small molecule |  |
| Approved|investigational | DB00313 | Valproic Acid | Small molecule |  |
| Approved | DB01223 | Aminophylline | Small molecule |  |
| Approved | DB01303 | Oxtriphylline | Small molecule |  |
| Approved|investigational | DB02546 | Vorinostat | Small molecule |  |
| Investigational | DB05223 | SB939 | Small molecule |  |
| Investigational | DB05651 | MGCD-0103 | Small molecule |  |
| Approved|investigational | DB06176 | Romidepsin | Small molecule |  |
| Approved|investigational | DB06603 | Panobinostat | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of HDAC2 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS |
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| Conservation information for LBS of HDAC2 |
| Multiple alignments for Q92769 in multiple species |
| LBS | AA sequence | # species | Species | C152 | EASGFCYVNDI | 3 | Homo sapiens, Arabidopsis thaliana, Mus musculus | C152 | EASGFCYTNDI | 1 | Caenorhabditis elegans | D100 | FNVGEDCPVFD | 3 | Homo sapiens, Arabidopsis thaliana, Mus musculus | D100 | FNVGEDCPLFD | 1 | Caenorhabditis elegans | D175 | RVLYIDIDIHH | 2 | Homo sapiens, Mus musculus | D175 | RVLYIDIDVHH | 1 | Arabidopsis thaliana | D175 | RVLYVDIDVHH | 1 | Caenorhabditis elegans | D177 | LYIDIDIHHGD | 2 | Homo sapiens, Mus musculus | D177 | LYIDIDVHHGD | 1 | Arabidopsis thaliana | D177 | LYVDIDVHHGD | 1 | Caenorhabditis elegans | D265 | LQCGADSLSGD | 3 | Homo sapiens, Arabidopsis thaliana, Mus musculus | D265 | LQCGADSLNGD | 1 | Caenorhabditis elegans | F110 | DGLFEFCQLST | 2 | Homo sapiens, Mus musculus | F110 | DGLFDFCRASA | 1 | Arabidopsis thaliana | F110 | DGLYEFCQLSS | 1 | Caenorhabditis elegans | F151 | SEASGFCYVND | 3 | Homo sapiens, Arabidopsis thaliana, Mus musculus | F151 | SEASGFCYTND | 1 | Caenorhabditis elegans | F199 | VMTVSFHKYGE | 2 | Homo sapiens, Mus musculus | F199 | VMTVSFHKFGD | 1 | Arabidopsis thaliana | F199 | VMTVSFHKYGD | 1 | Caenorhabditis elegans | F206 | KYGEYFPGTGD | 2 | Homo sapiens, Mus musculus | F206 | KFGDFFPGTGH | 1 | Arabidopsis thaliana | F206 | KYGDFFPGTGD | 1 | Caenorhabditis elegans | G139 | VNWAGGLHHAK | 2 | Homo sapiens, Mus musculus | G139 | INWGGGLHHAK | 1 | Arabidopsis thaliana | G139 | INWMGGLHHAK | 1 | Caenorhabditis elegans | G150 | KSEASGFCYVN | 3 | Homo sapiens, Arabidopsis thaliana, Mus musculus | G150 | KSEASGFCYTN | 1 | Caenorhabditis elegans | G301 | LLMLGGGGYTI | 2 | Homo sapiens, Mus musculus | G301 | LMVLGGGGYTI | 1 | Arabidopsis thaliana | G301 | LMMVGGGGYTP | 1 | Caenorhabditis elegans | G302 | LMLGGGGYTIR | 2 | Homo sapiens, Mus musculus | G302 | MVLGGGGYTIR | 1 | Arabidopsis thaliana | G302 | MMVGGGGYTPR | 1 | Caenorhabditis elegans | H141 | WAGGLHHAKKS | 2 | Homo sapiens, Mus musculus | H141 | WGGGLHHAKKS | 1 | Arabidopsis thaliana | H141 | WMGGLHHAKKS | 1 | Caenorhabditis elegans | H142 | AGGLHHAKKSE | 2 | Homo sapiens, Mus musculus | H142 | GGGLHHAKKSE | 1 | Arabidopsis thaliana | H142 | MGGLHHAKKSE | 1 | Caenorhabditis elegans | H179 | IDIDIHHGDGV | 2 | Homo sapiens, Mus musculus | H179 | IDIDVHHGDGV | 1 | Arabidopsis thaliana | H179 | VDIDVHHGDGV | 1 | Caenorhabditis elegans | H200 | MTVSFHKYGEY | 2 | Homo sapiens, Mus musculus | H200 | MTVSFHKFGDF | 1 | Arabidopsis thaliana | H200 | MTVSFHKYGDF | 1 | Caenorhabditis elegans | H29 | YYGQGHPMKPH | 3 | Homo sapiens, Arabidopsis thaliana, Mus musculus | H29 | YYGQGHVMKPH | 1 | Caenorhabditis elegans | I176 | VLYIDIDIHHG | 2 | Homo sapiens, Mus musculus | I176 | VLYIDIDVHHG | 1 | Arabidopsis thaliana | I176 | VLYVDIDVHHG | 1 | Caenorhabditis elegans | L140 | NWAGGLHHAKK | 2 | Homo sapiens, Mus musculus | L140 | NWGGGLHHAKK | 1 | Arabidopsis thaliana | L140 | NWMGGLHHAKK | 1 | Caenorhabditis elegans | L272 | LSGDRLGCFNL | 3 | Homo sapiens, Arabidopsis thaliana, Mus musculus | L272 | LNGDRLGPFNL | 1 | Caenorhabditis elegans | M31 | GQGHPMKPHRI | 3 | Homo sapiens, Arabidopsis thaliana, Mus musculus | M31 | GQGHVMKPHRI | 1 | Caenorhabditis elegans | P30 | YGQGHPMKPHR | 3 | Homo sapiens, Arabidopsis thaliana, Mus musculus | P30 | YGQGHVMKPHR | 1 | Caenorhabditis elegans | R35 | PMKPHRIRMTH | 2 | Homo sapiens, Mus musculus | R35 | PMKPHRIRMAH | 1 | Arabidopsis thaliana | R35 | VMKPHRIRMTH | 1 | Caenorhabditis elegans | S198 | RVMTVSFHKYG | 3 | Homo sapiens, Mus musculus, Caenorhabditis elegans | S198 | RVMTVSFHKFG | 1 | Arabidopsis thaliana | Y25 | IGNYYYGQGHP | 2 | Homo sapiens, Mus musculus | Y25 | IGDYYYGQGHP | 1 | Arabidopsis thaliana | Y25 | IGNYYYGQGHV | 1 | Caenorhabditis elegans | Y304 | LGGGGYTIRNV | 3 | Homo sapiens, Arabidopsis thaliana, Mus musculus | Y304 | VGGGGYTPRNV | 1 | Caenorhabditis elegans |
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