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 ISPD
Gene summary
Basic gene Info.Gene symbolISPD
Gene nameisoprenoid synthase domain containing
CytomapUCSC genome browser: 7p21.2
Type of geneprotein-coding
Description2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase-like protein4-diphosphocytidyl-2C-methyl-D-erythritol synthase homologisoprenoid synthase domain-containing proteinnotch1-induced protein
Modification date20141219
dbXrefs MIM : 614631
ProteinUniProt: A4D126
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ISPD
BioGPS: 729920
PathwayNCI Pathway Interaction Database: ISPD
Pathway Commons: ISPD
ContextiHOP: ISPD
ligand binding site mutation search in PubMed: ISPD
UCL Cancer Institute: ISPD
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

Ligand binding site mutations for ISPD
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 ISPD
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 ISPD from PDB

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


Phenotype information for ISPD
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0265221Walker-Warburg Syndrome4Biomarker
umls:C0015393Eye Abnormalities1Biomarker
umls:C0026848Muscular Diseases1Biomarker

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

Pharmacological information for ISPD
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 ISPD go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
MGMAGNESIUM(2+)4cvhAH127 E235

Conservation information for LBS of ISPD
Multiple alignments for A4D126 in multiple species
LBSAA sequence# speciesSpecies
E235SDYDLEFGTEC2Homo sapiens, Bos taurus
E235SDFDLEFGTEC2Mus musculus, Rattus norvegicus
E235SEFDLEFGTEC1Danio rerio
E235TDYDLDFGTEC1Xenopus tropicalis
G237FDLEFGTECLQ2Mus musculus, Rattus norvegicus
G237YDLEFGTECLQ1Homo sapiens
G237FDLEFGTECLH1Danio rerio
G237YDLDFGTECLH1Xenopus tropicalis
G237YDLEFGTECLH1Bos taurus
H127AGVTRHRSIFN2Homo sapiens, Bos taurus
H127AGATRHRSIFN2Mus musculus, Rattus norvegicus
H127GGTTRHRSIYN1Danio rerio
H127GGETRHRSIFN1Xenopus tropicalis
L234CSDYDLEFGTE2Homo sapiens, Bos taurus
L234CSDFDLEFGTE2Mus musculus, Rattus norvegicus
L234CSEFDLEFGTE1Danio rerio
L234CTDYDLDFGTE1Xenopus tropicalis
R126EAGVTRHRSIF2Homo sapiens, Bos taurus
R126EAGATRHRSIF2Mus musculus, Rattus norvegicus
R126HGGTTRHRSIY1Danio rerio
R126KGGETRHRSIF1Xenopus tropicalis
T125VEAGVTRHRSI2Homo sapiens, Bos taurus
T125AEAGATRHRSI2Mus musculus, Rattus norvegicus
T125VHGGTTRHRSI1Danio rerio
T125VKGGETRHRSI1Xenopus tropicalis

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