mutated Ligand Binding Site gene DataBase





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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 PHF8
Gene summary
Basic gene Info.Gene symbolPHF8
Gene namePHD finger protein 8
CytomapUCSC genome browser: Xp11.22
Type of geneprotein-coding
Descriptionhistone lysine demethylase PHF8jumonji C domain-containing histone demethylase 1F
Modification date20141222
dbXrefs MIM : 300560
Ensembl : ENSG00000172943
HPRD : 06599
Vega : OTTHUMG00000021622
ProteinUniProt: Q9UPP1
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PHF8
BioGPS: 23133
PathwayNCI Pathway Interaction Database: PHF8
Pathway Commons: PHF8
ContextiHOP: PHF8
ligand binding site mutation search in PubMed: PHF8
UCL Cancer Institute: PHF8
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0033169histone H3-K9 demethylation20023638
GO:0035574histone H4-K20 demethylation20622853
GO:0045893positive regulation of transcription, DNA-templated20622853
GO:0045943positive regulation of transcription from RNA polymerase I promoter20208542
GO:0061188negative regulation of chromatin silencing at rDNA20208542
GO:0070544histone H3-K36 demethylation20208542
GO:0071557histone H3-K27 demethylation20622853

Ligand binding site mutations for PHF8
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
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.

Protein structure related information for PHF8
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
(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 PHF8 from PDB

Differential gene expression and gene-gene network for PHF8
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 PHF8 and the right PPI network was created from samples without mutations in the LBS of PHF8. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for PHF8
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1846055Siderius X-linked mental retardation syndrome2Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

Pharmacological information for PHF8
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 PHF8 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of PHF8
Multiple alignments for Q9UPP1 in multiple species
LBSAA sequence# speciesSpecies
A202DVTRQADCKMK1Homo sapiens
A202DVSRQADLKMK1Danio rerio
A202DVARQADCKMK1Mus musculus
A392KRLSTADLFKF2Danio rerio, Mus musculus
A392KRLSTADLFRF1Homo sapiens
A78VEEEKAADIDL2Homo sapiens, Mus musculus
A78VEEDKAAEIDL1Danio rerio
C44SVPVYCLCRLP3Homo sapiens, Danio rerio, Mus musculus
C46PVYCLCRLPYD3Homo sapiens, Danio rerio, Mus musculus
C59RFMIECDMCQD2Homo sapiens, Mus musculus
C59RFMIECDVCQD1Danio rerio
C62IECDMCQDWFH2Homo sapiens, Mus musculus
C62IECDVCQDWFH1Danio rerio
C70WFHGSCVGVEE3Homo sapiens, Danio rerio, Mus musculus
C86IDLYHCPNCEV2Homo sapiens, Mus musculus
C86IDLYHCPNCQV1Danio rerio
C89YHCPNCEVLHG2Homo sapiens, Mus musculus
C89YHCPNCQVTHG1Danio rerio
D203VTRQADCKMKL1Homo sapiens
D203VSRQADLKMKL1Danio rerio
D203VARQADCKMKL1Mus musculus
D285TDFHIDFGGTS3Homo sapiens, Danio rerio, Mus musculus
D362VLTPVDCLAFG3Homo sapiens, Danio rerio, Mus musculus
D393RLSTADLFKFP2Danio rerio, Mus musculus
D393RLSTADLFRFP1Homo sapiens
E386KAYEIEKRLST2Homo sapiens, Mus musculus
E386RAYEIEKRLST1Danio rerio
E58TRFMIECDMCQ2Homo sapiens, Mus musculus
E58TRFMIECDVCQ1Danio rerio
F282DSYTDFHIDFG3Homo sapiens, Danio rerio, Mus musculus
F286DFHIDFGGTSV3Homo sapiens, Danio rerio, Mus musculus
F315ANLTLFECWSS2Homo sapiens, Mus musculus
F315ANLSLFERWSS1Danio rerio
F395STADLFKFPNF2Danio rerio, Mus musculus
F395STADLFRFPNF1Homo sapiens
F55YDVTRFMIECD3Homo sapiens, Danio rerio, Mus musculus
G218KYYYSGKREKV2Homo sapiens, Mus musculus
G218EYYNSPNRDRV1Danio rerio
H283SYTDFHIDFGG3Homo sapiens, Danio rerio, Mus musculus
H355PTGWIHAVLTP3Homo sapiens, Danio rerio, Mus musculus
H67CQDWFHGSCVG3Homo sapiens, Danio rerio, Mus musculus
I196KEIDVIDVTRQ1Homo sapiens
I196KEIDVIDVSRQ1Danio rerio
I196KEIDVIDVARQ1Mus musculus
I227KVLNVISLEFS2Homo sapiens, Mus musculus
I227RVLNVISLEFS1Danio rerio
I284YTDFHIDFGGT3Homo sapiens, Danio rerio, Mus musculus
I57VTRFMIECDMC2Homo sapiens, Mus musculus
I57VTRFMIECDVC1Danio rerio
I81EKAADIDLYHC2Homo sapiens, Mus musculus
I81DKAAEIDLYHC1Danio rerio
K300VLKGEKIFYLI2Homo sapiens, Mus musculus
K300VLRGEKIFYLI1Danio rerio
L272VQKYCLMSVRD2Homo sapiens, Mus musculus
L272VQKYCLMGVKD1Danio rerio
L389EIEKRLSTADL3Homo sapiens, Danio rerio, Mus musculus
L394LSTADLFKFPN2Danio rerio, Mus musculus
L394LSTADLFRFPN1Homo sapiens
M56DVTRFMIECDM2Homo sapiens, Mus musculus
M56DVTRFMIECDV1Danio rerio
N225REKVLNVISLE2Homo sapiens, Mus musculus
N225RDRVLNVISLE1Danio rerio
N325SSSNQNEMFFG2Homo sapiens, Mus musculus
N325SSSNQNELFFG1Danio rerio
N369LAFGGNFLHSL3Homo sapiens, Danio rerio, Mus musculus
Q201IDVTRQADCKM1Homo sapiens
Q201IDVSRQADLKM1Danio rerio
Q201IDVARQADCKM1Mus musculus
Q324SSSSNQNEMFF2Homo sapiens, Mus musculus
Q324SSSSNQNELFF1Danio rerio
R220YYSGKREKVLN2Homo sapiens, Mus musculus
R220YNSPNRDRVLN1Danio rerio
R396TADLFKFPNFE2Danio rerio, Mus musculus
R396TADLFRFPNFE1Homo sapiens
S228VLNVISLEFSD3Homo sapiens, Danio rerio, Mus musculus
S319LFECWSSSSNQ2Homo sapiens, Mus musculus
S319LFERWSSSSNQ1Danio rerio
S320FECWSSSSNQN2Homo sapiens, Mus musculus
S320FERWSSSSNQN1Danio rerio
S322CWSSSSNQNEM2Homo sapiens, Mus musculus
S322RWSSSSNQNEL1Danio rerio
S390IEKRLSTADLF3Homo sapiens, Danio rerio, Mus musculus
T280VRDSYTDFHID2Homo sapiens, Mus musculus
T280VKDSYTDFHID1Danio rerio
T391EKRLSTADLFK2Danio rerio, Mus musculus
T391EKRLSTADLFR1Homo sapiens
V357GWIHAVLTPVD3Homo sapiens, Danio rerio, Mus musculus
V52RLPYDVTRFMI3Homo sapiens, Danio rerio, Mus musculus
W65DMCQDWFHGSC2Homo sapiens, Mus musculus
W65DVCQDWFHGSC1Danio rerio
Y215DFVKYYYSGKR2Homo sapiens, Mus musculus
Y215EFVEYYNSPNR1Danio rerio
Y216FVKYYYSGKRE2Homo sapiens, Mus musculus
Y216FVEYYNSPNRD1Danio rerio
Y270PNVQKYCLMSV2Homo sapiens, Mus musculus
Y270PNVQKYCLMGV1Danio rerio
Y293GTSVWYHVLKG2Homo sapiens, Mus musculus
Y293GTSVWYHVLRG1Danio rerio
Y43ASVPVYCLCRL3Homo sapiens, Danio rerio, Mus musculus
Y50LCRLPYDVTRF3Homo sapiens, Danio rerio, Mus musculus

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