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 PHF2
Gene summary
Basic gene Info.Gene symbolPHF2
Gene namePHD finger protein 2
CytomapUCSC genome browser: 9q22.31
Type of geneprotein-coding
Descriptioncentromere protein 35jumonji C domain-containing histone demethylase 1Elysine-specific demethylase PHF2
Modification date20141207
dbXrefs MIM : 604351
Ensembl : ENSG00000197724
HPRD : 05071
Vega : OTTHUMG00000020253
ProteinUniProt: O75151
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PHF2
BioGPS: 5253
PathwayNCI Pathway Interaction Database: PHF2
Pathway Commons: PHF2
ContextiHOP: PHF2
ligand binding site mutation search in PubMed: PHF2
UCL Cancer Institute: PHF2
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0006482protein demethylation21532585

Ligand binding site mutations for PHF2
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 PHF2
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 PHF2 from PDB

Differential gene expression and gene-gene network for PHF2
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 PHF2 and the right PPI network was created from samples without mutations in the LBS of PHF2. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for PHF2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for PHF2
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 PHF2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR)3kqiAE39

Conservation information for LBS of PHF2
Multiple alignments for O75151 in multiple species
LBSAA sequence# speciesSpecies
C10PVYCVCRLPYD2Homo sapiens, Mus musculus
C10PVYCICRLPYD1Danio rerio
C23RFMIECDACKD2Homo sapiens, Mus musculus
C23QFMIECDACKD1Danio rerio
C240KYCLICVKDSY3Homo sapiens, Danio rerio, Mus musculus
C26IECDACKDWFH3Homo sapiens, Danio rerio, Mus musculus
C34WFHGSCVGVEE2Homo sapiens, Mus musculus
C34WFHGSCVGVDE1Danio rerio
C50IDIYHCPNCEK3Homo sapiens, Danio rerio, Mus musculus
C53YHCPNCEKTHG3Homo sapiens, Danio rerio, Mus musculus
C8TVPVYCVCRLP2Homo sapiens, Mus musculus
D251TDFHIDSGGAS2Homo sapiens, Mus musculus
D251TDFHIECGGAS1Danio rerio
D46EAPDIDIYHCP3Homo sapiens, Danio rerio, Mus musculus
E22TRFMIECDACK2Homo sapiens, Mus musculus
E22TQFMIECDACK1Danio rerio
E39CVGVEEEEAPD2Homo sapiens, Mus musculus
E39CVGVDEDEAPD1Danio rerio
F19YDVTRFMIECD2Homo sapiens, Mus musculus
F19YDVTQFMIECD1Danio rerio
H249SYTDFHIDSGG2Homo sapiens, Mus musculus
H249SYTDFHIECGG1Danio rerio
H31CKDWFHGSCVG3Homo sapiens, Danio rerio, Mus musculus
H335LAFAGHFLHSL2Homo sapiens, Mus musculus
H335LAFSGHFVHSL1Danio rerio
I21VTRFMIECDAC2Homo sapiens, Mus musculus
I21VTQFMIECDAC1Danio rerio
I45EEAPDIDIYHC2Homo sapiens, Mus musculus
I45DEAPDIDIYHC1Danio rerio
K266VLKGEKTFYLI1Homo sapiens
K266VLKGEKIFFLI1Danio rerio
K266VLKGEKIFYLI1Mus musculus
L238VTKYCLICVKD2Homo sapiens, Mus musculus
L238VSKYCLICVKD1Danio rerio
M20DVTRFMIECDA2Homo sapiens, Mus musculus
M20DVTQFMIECDA1Danio rerio
R18PYDVTRFMIEC2Homo sapiens, Mus musculus
R18PYDVTQFMIEC1Danio rerio
T17LPYDVTRFMIE2Homo sapiens, Mus musculus
T17LPYDVTQFMIE1Danio rerio
T193RVLNVTNLEFS2Homo sapiens, Mus musculus
T193KVLNVINLEFS1Danio rerio
T246VKDSYTDFHID2Homo sapiens, Mus musculus
T246VKDSYTDFHIE1Danio rerio
T323GWIYATLTPVD2Homo sapiens, Mus musculus
T323GWINAILTPVD1Danio rerio
W29DACKDWFHGSC3Homo sapiens, Danio rerio, Mus musculus
Y14VCRLPYDVTRF2Homo sapiens, Mus musculus
Y14ICRLPYDVTQF1Danio rerio
Y259GASAWYHVLKG2Homo sapiens, Mus musculus
Y259GASVWYHVLKG1Danio rerio
Y321PSGWIYATLTP2Homo sapiens, Mus musculus
Y321PSGWINAILTP1Danio rerio
Y7ATVPVYCVCRL2Homo sapiens, Mus musculus

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