|
mutLBSgeneDB |
| |
| |
| |
| |
| |
| |
|
| Gene summary for KDM5D |
 Gene summary |
| Basic gene Info. | Gene symbol | KDM5D |
| Gene name | lysine (K)-specific demethylase 5D | |
| Synonyms | HY|HYA|JARID1D|SMCY | |
| Cytomap | UCSC genome browser: Yq11 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001146705.1, NM_001146706.1,NM_004653.4, | |
| Description | H-YJumonji, AT rich interactive domain 1D (RBP2-like)SMC homolog, Y chromosomeSmcy homolog, Y-linkedhistocompatibility Y antigenhistone demethylase JARID1Djumonji/ARID domain-containing protein 1Dlysine-specific demethylase 5Dprotein SmcYselected | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 426000 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000012817 | ||
| Ensembl : ENSG00000278871 | ||
| Ensembl : ENSG00000280101 | ||
| Ensembl : ENSG00000280358 | ||
| HPRD : 02464 | ||
| Vega : OTTHUMG00000036508 | ||
| Protein | UniProt: Q9BY66 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_KDM5D | |
| BioGPS: 8284 | ||
| Pathway | NCI Pathway Interaction Database: KDM5D | |
| KEGG: KDM5D | ||
| REACTOME: KDM5D | ||
| Pathway Commons: KDM5D | ||
| Context | iHOP: KDM5D | |
| ligand binding site mutation search in PubMed: KDM5D | ||
| UCL Cancer Institute: KDM5D | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0034720 | histone H3-K4 demethylation | 17320160 |
| Top |
| Ligand binding site mutations for KDM5D |
| 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 | C320 | S321Y | GBM | 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 KDM5D |
| 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 | C320 | S321Y | -0.88998689 |
| (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 KDM5D from PDB |
| Top |
| Differential gene expression and gene-gene network for KDM5D |
| 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 KDM5D |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
| Top |
| Pharmacological information for KDM5D |
| 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|nutraceutical | DB00126 | Vitamin C | Small molecule |  |
| Gene-centered ligand-gene interaction network |
 |
| Ligands binding to mutated ligand binding site of KDM5D go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS |
| Top |
| Conservation information for LBS of KDM5D |
| Multiple alignments for Q9BY66 in multiple species |
| LBS | AA sequence | # species | Species | C317 | IDSYICQVCSR | 2 | Homo sapiens, Pan troglodytes | C317 | MNSYVCRICSR | 1 | Mus musculus | C320 | YICQVCSRGDE | 2 | Homo sapiens, Pan troglodytes | C320 | YVCRICSRGDE | 1 | Mus musculus | C332 | DKLLFCDGCDD | 2 | Homo sapiens, Pan troglodytes | C332 | DKFLLCDGCSD | 1 | Mus musculus | C335 | LFCDGCDDNYH | 2 | Homo sapiens, Pan troglodytes | C335 | LLCDGCSDNYH | 1 | Mus musculus | C343 | NYHIFCLLPPL | 3 | Homo sapiens, Mus musculus, Pan troglodytes | C358 | RGIWRCPKCIL | 2 | Homo sapiens, Pan troglodytes | C358 | KGVWRCPKCIL | 1 | Mus musculus | C361 | WRCPKCILAEC | 3 | Homo sapiens, Mus musculus, Pan troglodytes | H340 | CDDNYHIFCLL | 2 | Homo sapiens, Pan troglodytes | H340 | CSDNYHIFCLL | 1 | Mus musculus |
 |
Copyright © 2016-Present - The University of Texas Health Science Center at Houston |