|
mutLBSgeneDB |
| |
| |
| |
| |
| |
| |
|
| Gene summary for KDM8 |
 Gene summary |
| Basic gene Info. | Gene symbol | KDM8 |
| Gene name | lysine (K)-specific demethylase 8 | |
| Synonyms | JMJD5 | |
| Cytomap | UCSC genome browser: 16p12.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001145348.1, NM_024773.2, | |
| Description | jmjC domain-containing protein 5jumonji domain containing 5jumonji domain-containing protein 5lysine-specific demethylase 8 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 611917 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000155666 | ||
| HPRD : 07836 | ||
| Vega : OTTHUMG00000131677 | ||
| Protein | UniProt: Q8N371 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_KDM8 | |
| BioGPS: 79831 | ||
| Pathway | NCI Pathway Interaction Database: KDM8 | |
| KEGG: KDM8 | ||
| REACTOME: KDM8 | ||
| Pathway Commons: KDM8 | ||
| Context | iHOP: KDM8 | |
| ligand binding site mutation search in PubMed: KDM8 | ||
| UCL Cancer Institute: KDM8 | ||
| 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:0070544 | histone H3-K36 demethylation | 20457893 |
| Top |
| Ligand binding site mutations for KDM8 |
| 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 | V402 | V402M | BRCA | 1 | V402,H400 | Y401C | KIRC | 1 | W414 | S416L | 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 KDM8 |
| 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 | V402 | V402M | -0.5002972 | H400 | Y401C | -0.24568211 | V402 | Y401C | -0.24568211 | W414 | S416L | -0.015240816 |
| (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 KDM8 from PDB |
| Top |
| Differential gene expression and gene-gene network for KDM8 |
| 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 KDM8 |
| 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 KDM8 |
| 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 KDM8 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | CO | COBALT(2+) | 4gjy | A | H400 | CO | COBALT(2+) | 4gjz | A | H400 | AKG | 2-OXOGLUTARIC ACID | 3uyj | A | H400 V402 W414 | AKG | 2-OXOGLUTARIC ACID | 3uyj | B | H400 V402 W414 | OGA | N-OXALYLGLYCINE | 4gjy | A | H400 V402 W414 | AKG | 2-OXOGLUTARIC ACID | 4gjz | A | H400 V402 W414 | AKG | 2-OXOGLUTARIC ACID | 4qu1 | A | H400 V402 W414 |
| Top |
| Conservation information for LBS of KDM8 |
| Multiple alignments for Q8N371 in multiple species |
| LBS | AA sequence | # species | Species | D245 | GSRYTDEEWSQ | 2 | Homo sapiens, Bos taurus | D245 | GSRYTDEDWSQ | 2 | Mus musculus, Rattus norvegicus | D245 | GKNYLCSDWKQ | 1 | Arabidopsis thaliana | D245 | GSRYTDAEWSQ | 1 | Xenopus tropicalis | D323 | SPLHQDPQQNF | 5 | Homo sapiens, Xenopus tropicalis, Mus musculus, Rattus norvegicus, Bos taurus | D323 | TPLHHDPHHNI | 1 | Arabidopsis thaliana | H321 | TISPLHQDPQQ | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | H321 | TVSPLHQDPQQ | 2 | Xenopus tropicalis, Bos taurus | H321 | TVTPLHHDPHH | 1 | Arabidopsis thaliana | H400 | PAKYWHYVRSL | 2 | Mus musculus, Rattus norvegicus | H400 | PVKYWHYVRAL | 1 | Homo sapiens | H400 | PPKWWHYVRSL | 1 | Arabidopsis thaliana | H400 | PVKWWHYIRAL | 1 | Xenopus tropicalis | H400 | PVKHWHYVRAL | 1 | Bos taurus | K336 | QVMGRKYIRLY | 2 | Homo sapiens, Bos taurus | K336 | QVLGRKYIRLY | 2 | Mus musculus, Rattus norvegicus | K336 | QVVGKKYIRLY | 1 | Arabidopsis thaliana | K336 | QIVGRKYIRVY | 1 | Xenopus tropicalis | N327 | QDPQQNFLVQV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N327 | HDPHHNILAQV | 1 | Arabidopsis thaliana | N327 | QDPQQNFLAQI | 1 | Xenopus tropicalis | N327 | QDPQQNFLAQV | 1 | Bos taurus | S318 | PQGTISPLHQD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S318 | PAGTVTPLHHD | 1 | Arabidopsis thaliana | S318 | PAGTVSPLHQD | 1 | Xenopus tropicalis | S318 | PQGTVSPLHQD | 1 | Bos taurus | S412 | LSFSVSFWWS- | 5 | Homo sapiens, Xenopus tropicalis, Mus musculus, Rattus norvegicus, Bos taurus | S412 | MSLSVSFWWSN | 1 | Arabidopsis thaliana | V402 | KYWHYVRSLDL | 2 | Mus musculus, Rattus norvegicus | V402 | KYWHYVRALDL | 1 | Homo sapiens | V402 | KWWHYVRSLTM | 1 | Arabidopsis thaliana | V402 | KWWHYIRALDL | 1 | Xenopus tropicalis | V402 | KHWHYVRALDL | 1 | Bos taurus | W310 | ITINAWFGPQG | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus | W310 | -SLNAWFGPAG | 1 | Arabidopsis thaliana | W310 | ITINAWFGPAG | 1 | Xenopus tropicalis | W414 | FSVSFWWS--- | 5 | Homo sapiens, Xenopus tropicalis, Mus musculus, Rattus norvegicus, Bos taurus | W414 | LSVSFWWSNEA | 1 | Arabidopsis thaliana | Y272 | AKDVGYLAQHQ | 2 | Mus musculus, Rattus norvegicus | Y272 | PRDVGYLAQHQ | 1 | Homo sapiens | Y272 | PMEPTYLAQHP | 1 | Arabidopsis thaliana | Y272 | QNGIGYLAQHQ | 1 | Xenopus tropicalis | Y272 | PKDIGYLAQHQ | 1 | Bos taurus |
 |
Copyright © 2016-Present - The University of Texas Health Science Center at Houston |