mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

Home

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for KDM8
Gene summary
Basic gene Info.Gene symbolKDM8
Gene namelysine (K)-specific demethylase 8
SynonymsJMJD5
CytomapUCSC genome browser: 16p12.1
Type of geneprotein-coding
RefGenesNM_001145348.1,
NM_024773.2,
DescriptionjmjC domain-containing protein 5jumonji domain containing 5jumonji domain-containing protein 5lysine-specific demethylase 8
Modification date20141207
dbXrefs MIM : 611917
HGNC : HGNC
Ensembl : ENSG00000155666
HPRD : 07836
Vega : OTTHUMG00000131677
ProteinUniProt: Q8N371
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KDM8
BioGPS: 79831
PathwayNCI Pathway Interaction Database: KDM8
KEGG: KDM8
REACTOME: KDM8
Pathway Commons: KDM8
ContextiHOP: KDM8
ligand binding site mutation search in PubMed: KDM8
UCL Cancer Institute: KDM8
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0070544histone H3-K36 demethylation20457893


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
LBSAAchange of nsSNVCancer type# samples
V402V402MBRCA1
V402,H400Y401CKIRC1
W414S416LUCEC1
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.
LBSAAchange of nsSNVRelative stability change
V402V402M-0.5002972
H400Y401C-0.24568211
V402Y401C-0.24568211
W414S416L-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)
* Left PPI network was created from samples with mutations in the LBS of KDM8 and the right PPI network was created from samples without mutations in the LBS of KDM8. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Top

Top
Phenotype information for KDM8
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype 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 statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of KDM8 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
COCOBALT(2+)4gjyAH400
COCOBALT(2+)4gjzAH400
AKG2-OXOGLUTARIC ACID3uyjAH400 V402 W414
AKG2-OXOGLUTARIC ACID3uyjBH400 V402 W414
OGAN-OXALYLGLYCINE4gjyAH400 V402 W414
AKG2-OXOGLUTARIC ACID4gjzAH400 V402 W414
AKG2-OXOGLUTARIC ACID4qu1AH400 V402 W414


Top
Conservation information for LBS of KDM8
Multiple alignments for Q8N371 in multiple species
LBSAA sequence# speciesSpecies
D245GSRYTDEEWSQ2Homo sapiens, Bos taurus
D245GSRYTDEDWSQ2Mus musculus, Rattus norvegicus
D245GKNYLCSDWKQ1Arabidopsis thaliana
D245GSRYTDAEWSQ1Xenopus tropicalis
D323SPLHQDPQQNF5Homo sapiens, Xenopus tropicalis, Mus musculus, Rattus norvegicus, Bos taurus
D323TPLHHDPHHNI1Arabidopsis thaliana
H321TISPLHQDPQQ3Homo sapiens, Mus musculus, Rattus norvegicus
H321TVSPLHQDPQQ2Xenopus tropicalis, Bos taurus
H321TVTPLHHDPHH1Arabidopsis thaliana
H400PAKYWHYVRSL2Mus musculus, Rattus norvegicus
H400PVKYWHYVRAL1Homo sapiens
H400PPKWWHYVRSL1Arabidopsis thaliana
H400PVKWWHYIRAL1Xenopus tropicalis
H400PVKHWHYVRAL1Bos taurus
K336QVMGRKYIRLY2Homo sapiens, Bos taurus
K336QVLGRKYIRLY2Mus musculus, Rattus norvegicus
K336QVVGKKYIRLY1Arabidopsis thaliana
K336QIVGRKYIRVY1Xenopus tropicalis
N327QDPQQNFLVQV3Homo sapiens, Mus musculus, Rattus norvegicus
N327HDPHHNILAQV1Arabidopsis thaliana
N327QDPQQNFLAQI1Xenopus tropicalis
N327QDPQQNFLAQV1Bos taurus
S318PQGTISPLHQD3Homo sapiens, Mus musculus, Rattus norvegicus
S318PAGTVTPLHHD1Arabidopsis thaliana
S318PAGTVSPLHQD1Xenopus tropicalis
S318PQGTVSPLHQD1Bos taurus
S412LSFSVSFWWS-5Homo sapiens, Xenopus tropicalis, Mus musculus, Rattus norvegicus, Bos taurus
S412MSLSVSFWWSN1Arabidopsis thaliana
V402KYWHYVRSLDL2Mus musculus, Rattus norvegicus
V402KYWHYVRALDL1Homo sapiens
V402KWWHYVRSLTM1Arabidopsis thaliana
V402KWWHYIRALDL1Xenopus tropicalis
V402KHWHYVRALDL1Bos taurus
W310ITINAWFGPQG4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
W310-SLNAWFGPAG1Arabidopsis thaliana
W310ITINAWFGPAG1Xenopus tropicalis
W414FSVSFWWS---5Homo sapiens, Xenopus tropicalis, Mus musculus, Rattus norvegicus, Bos taurus
W414LSVSFWWSNEA1Arabidopsis thaliana
Y272AKDVGYLAQHQ2Mus musculus, Rattus norvegicus
Y272PRDVGYLAQHQ1Homo sapiens
Y272PMEPTYLAQHP1Arabidopsis thaliana
Y272QNGIGYLAQHQ1Xenopus tropicalis
Y272PKDIGYLAQHQ1Bos taurus


Copyright © 2016-Present - The University of Texas Health Science Center at Houston
Site Policies | State of Texas