|
mutLBSgeneDB |
| |
| |
| |
| |
| |
| |
|
| Gene summary for KDM5A |
 Gene summary |
| Basic gene Info. | Gene symbol | KDM5A |
| Gene name | lysine (K)-specific demethylase 5A | |
| Synonyms | RBBP-2|RBBP2|RBP2 | |
| Cytomap | UCSC genome browser: 12p11 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001042603.2, NM_005056.2, | |
| Description | Jumonji, AT rich interactive domain 1A (RBP2-like)histone demethylase JARID1Ajumonji/ARID domain-containing protein 1Alysine-specific demethylase 5Aretinoblastoma binding protein 2 | |
| Modification date | 20141222 | |
| dbXrefs | MIM : 180202 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000073614 | ||
| HPRD : 08915 | ||
| Vega : OTTHUMG00000168055 | ||
| Protein | UniProt: P29375 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_KDM5A | |
| BioGPS: 5927 | ||
| Pathway | NCI Pathway Interaction Database: KDM5A | |
| KEGG: KDM5A | ||
| REACTOME: KDM5A | ||
| Pathway Commons: KDM5A | ||
| Context | iHOP: KDM5A | |
| ligand binding site mutation search in PubMed: KDM5A | ||
| UCL Cancer Institute: KDM5A | ||
| 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:0045893 | positive regulation of transcription, DNA-templated | 11358960 |
| Top |
| Ligand binding site mutations for KDM5A |
| 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 | E1649 | E1649V | COAD | 1 | E485 | D486N | COAD | 1 | D1633 | D1633G | COAD | 1 | S491,N493 | I492S | 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 KDM5A |
| 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 | E485 | D486N | -1.4824604 | E1649 | E1649V | -1.0363342 | S491 | I492S | -0.96646526 | N493 | I492S | -0.96646526 | D1633 | D1633G | -0.20950631 |
| (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 KDM5A from PDB |
| Top |
| Differential gene expression and gene-gene network for KDM5A |
| 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 KDM5A |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C3714756 | Intellectual Disability | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
| Top |
| Pharmacological information for KDM5A |
| 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. |
 |
| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
 |
| Ligands binding to mutated ligand binding site of KDM5A go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA,ARG) | 3gl6 | A | D1633 E1649 | MN | MANGANESE(2+) | 5e6h | A | E485 | AKG | 2-OXOGLUTARIC ACID | 5e6h | A | E485 S491 N493 |
| Top |
| Conservation information for LBS of KDM5A |
| Multiple alignments for P29375 in multiple species |
| LBS | AA sequence | # species | Species | A1648 | S-PEMAENEDY | 1 | Homo sapiens | A1648 | NRSQIKPDDDY | 1 | Drosophila melanogaster | A1648 | S-AEMAENEDY | 1 | Mus musculus | A583 | YNFAEAVNFCT | 2 | Homo sapiens, Mus musculus | A583 | YNFAEAVNFAP | 1 | Drosophila melanogaster | C1610 | DENAVCAAQNC | 2 | Homo sapiens, Mus musculus | C1610 | DDEEECRAENC | 1 | Drosophila melanogaster | C1615 | CAAQNCQRPCK | 2 | Homo sapiens, Mus musculus | C1615 | CRAENCHKPTG | 1 | Drosophila melanogaster | C1619 | NCQRPCKDKVD | 2 | Homo sapiens, Mus musculus | C1619 | NCHKPTGREVD | 1 | Drosophila melanogaster | C1628 | VDWVQCDGGCD | 2 | Homo sapiens, Mus musculus | C1628 | VDWVQCDGGCN | 1 | Drosophila melanogaster | C1632 | QCDGGCDEWFH | 2 | Homo sapiens, Mus musculus | C1632 | QCDGGCNEWFH | 1 | Drosophila melanogaster | C1640 | WFHQVCVGVS- | 2 | Homo sapiens, Mus musculus | C1640 | WFHMYCVGLNR | 1 | Drosophila melanogaster | C1655 | NEDYICINCAK | 2 | Homo sapiens, Mus musculus | C1655 | DDDYICIRCTK | 1 | Drosophila melanogaster | C558 | YRTNQCAGEFV | 2 | Homo sapiens, Mus musculus | C558 | FRTDQHAGEFV | 1 | Drosophila melanogaster | D1621 | QRPCKDKVDWV | 2 | Homo sapiens, Mus musculus | D1621 | HKPTGREVDWV | 1 | Drosophila melanogaster | D1624 | CKDKVDWVQCD | 2 | Homo sapiens, Mus musculus | D1624 | TGREVDWVQCD | 1 | Drosophila melanogaster | D1629 | DWVQCDGGCDE | 2 | Homo sapiens, Mus musculus | D1629 | DWVQCDGGCNE | 1 | Drosophila melanogaster | D1633 | CDGGCDEWFHQ | 2 | Homo sapiens, Mus musculus | D1633 | CDGGCNEWFHM | 1 | Drosophila melanogaster | E1649 | -PEMAENEDYI | 1 | Homo sapiens | E1649 | RSQIKPDDDYI | 1 | Drosophila melanogaster | E1649 | -AEMAENEDYI | 1 | Mus musculus | E1651 | EMAENEDYICI | 2 | Homo sapiens, Mus musculus | E1651 | QIKPDDDYICI | 1 | Drosophila melanogaster | E485 | FCWHIEDHWSY | 2 | Homo sapiens, Mus musculus | E485 | FCWHNEDHWSY | 1 | Drosophila melanogaster | F480 | MCFSSFCWHIE | 2 | Homo sapiens, Mus musculus | F480 | MCFAAFCWHNE | 1 | Drosophila melanogaster | H1637 | CDEWFHQVCVG | 2 | Homo sapiens, Mus musculus | H1637 | CNEWFHMYCVG | 1 | Drosophila melanogaster | H483 | SSFCWHIEDHW | 2 | Homo sapiens, Mus musculus | H483 | AAFCWHNEDHW | 1 | Drosophila melanogaster | H571 | FPRAYHSGFNQ | 2 | Homo sapiens, Mus musculus | H571 | FPRAYHAGFNQ | 1 | Drosophila melanogaster | K1620 | CQRPCKDKVDW | 2 | Homo sapiens, Mus musculus | K1620 | CHKPTGREVDW | 1 | Drosophila melanogaster | K1622 | RPCKDKVDWVQ | 2 | Homo sapiens, Mus musculus | K1622 | KPTGREVDWVQ | 1 | Drosophila melanogaster | K501 | HWGEPKTWYGV | 3 | Homo sapiens, Drosophila melanogaster, Mus musculus | N493 | WSYSINYLHWG | 3 | Homo sapiens, Drosophila melanogaster, Mus musculus | Q1627 | KVDWVQCDGGC | 2 | Homo sapiens, Mus musculus | Q1627 | EVDWVQCDGGC | 1 | Drosophila melanogaster | Q1638 | DEWFHQVCVGV | 2 | Homo sapiens, Mus musculus | Q1638 | NEWFHMYCVGL | 1 | Drosophila melanogaster | S491 | DHWSYSINYLH | 3 | Homo sapiens, Drosophila melanogaster, Mus musculus | V1623 | PCKDKVDWVQC | 2 | Homo sapiens, Mus musculus | V1623 | PTGREVDWVQC | 1 | Drosophila melanogaster | V1626 | DKVDWVQCDGG | 2 | Homo sapiens, Mus musculus | V1626 | REVDWVQCDGG | 1 | Drosophila melanogaster | W1625 | KDKVDWVQCDG | 2 | Homo sapiens, Mus musculus | W1625 | GREVDWVQCDG | 1 | Drosophila melanogaster | W1635 | GGCDEWFHQVC | 2 | Homo sapiens, Mus musculus | W1635 | GGCNEWFHMYC | 1 | Drosophila melanogaster | W503 | GEPKTWYGVPS | 2 | Homo sapiens, Mus musculus | W503 | GEPKTWYGVPG | 1 | Drosophila melanogaster | Y1653 | AENEDYICINC | 2 | Homo sapiens, Mus musculus | Y1653 | KPDDDYICIRC | 1 | Drosophila melanogaster | Y409 | DVIVEYGADIS | 2 | Homo sapiens, Mus musculus | Y409 | DVTVEYGADLH | 1 | Drosophila melanogaster | Y472 | KVPWLYVGMCF | 2 | Homo sapiens, Mus musculus | Y472 | NAPWMYVGMCF | 1 | Drosophila melanogaster |
 |
Copyright © 2016-Present - The University of Texas Health Science Center at Houston |