mutLBSgeneDB

mutLBSgeneDB
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 NDP
Gene summary
Basic gene Info.Gene symbolNDP
Gene nameNorrie disease (pseudoglioma)
SynonymsEVR2|FEVR|ND
CytomapUCSC genome browser: Xp11.4
Type of geneprotein-coding
RefGenesNM_000266.3,
DescriptionX-linked exudative vitreoretinopathy 2 proteinnorrie disease proteinnorrin
Modification date20141219
dbXrefs MIM : 300658
HGNC : HGNC
Ensembl : ENSG00000124479
HPRD : 02404
Vega : OTTHUMG00000021391
ProteinUniProt: Q00604
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NDP
BioGPS: 4693
PathwayNCI Pathway Interaction Database: NDP
KEGG: NDP
REACTOME: NDP
Pathway Commons: NDP
ContextiHOP: NDP
ligand binding site mutation search in PubMed: NDP
UCL Cancer Institute: NDP
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:0016055Wnt signaling pathway17955262
GO:0045893positive regulation of transcription, DNA-templated15035989
GO:0060070canonical Wnt signaling pathway15035989


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Ligand binding site mutations for NDP
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
R107R109QLUAD1
R107R107LLUSC1
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.


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Protein structure related information for NDP
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
R107R109Q-1.1517799
R107R107L-0.31976177
(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 NDP from PDB

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


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Phenotype information for NDP
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0266526Norrie disease23Biomarker, GeneticVariation
umls:C1844579Exudative Vitreoretinopathy, Familial, X-Linked Recessive1Biomarker, GeneticVariation

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

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Pharmacological information for NDP
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 NDP go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
SCRSUCROSE OCTASULFATE5bqcAR107


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Conservation information for LBS of NDP
Multiple alignments for Q00604 in multiple species
LBSAA sequence# speciesSpecies
A72GHCSQASRSEP3Homo sapiens, Bos taurus, Mus musculus
C126RYILSCHCEEC3Homo sapiens, Bos taurus, Mus musculus
C128ILSCHCEECSS2Bos taurus, Mus musculus
C128ILSCHCEECNS1Homo sapiens
C39SDPRRCMRHHY1Homo sapiens
C39SDPQRCMRHHY1Bos taurus
C39S--QRCMRHHY1Mus musculus
C69RCEGHCSQASR3Homo sapiens, Bos taurus, Mus musculus
H127YILSCHCEECS2Bos taurus, Mus musculus
H127YILSCHCEECN1Homo sapiens
H43RCMRHHYVDSI3Homo sapiens, Bos taurus, Mus musculus
K58YKCSSKMVLLA3Homo sapiens, Bos taurus, Mus musculus
L106SKLKALRLRCS3Homo sapiens, Bos taurus, Mus musculus
L124TYRYILSCHCE3Homo sapiens, Bos taurus, Mus musculus
M40DPRRCMRHHYV1Homo sapiens
M40DPQRCMRHHYV1Bos taurus
M40--QRCMRHHYV1Mus musculus
Q71EGHCSQASRSE3Homo sapiens, Bos taurus, Mus musculus
R107KLKALRLRCSG3Homo sapiens, Bos taurus, Mus musculus
R115CSGGMRLTATY3Homo sapiens, Bos taurus, Mus musculus
R38DSDPRRCMRHH1Homo sapiens
R38DSDPQRCMRHH1Bos taurus
R38DS--QRCMRHH1Mus musculus
R41PRRCMRHHYVD1Homo sapiens
R41PQRCMRHHYVD1Bos taurus
R41-QRCMRHHYVD1Mus musculus
S125YRYILSCHCEE3Homo sapiens, Bos taurus, Mus musculus
S70CEGHCSQASRS3Homo sapiens, Bos taurus, Mus musculus
Y122TATYRYILSCH3Homo sapiens, Bos taurus, Mus musculus


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