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 PDE1B
Gene summary
Basic gene Info.Gene symbolPDE1B
Gene namephosphodiesterase 1B, calmodulin-dependent
SynonymsPDE1B1|PDES1B
CytomapUCSC genome browser: 12q13
Type of geneprotein-coding
RefGenesNM_000924.3,
NM_001165975.2,NM_001288768.1,NM_001288769.1,
Description63 kDa Cam-PDEcalcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1Bcalcium/calmodulin-stimulated cyclic nucleotide phosphodiesterasecalmodulin-stimulated phosphodiesterase PDE1B1cam-PDE 1Bpresumed 63kDa form of the type 1 cyclic n
Modification date20141207
dbXrefs MIM : 171891
HGNC : HGNC
Ensembl : ENSG00000123360
HPRD : 01388
Vega : OTTHUMG00000169844
ProteinUniProt: Q01064
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE1B
BioGPS: 5153
PathwayNCI Pathway Interaction Database: PDE1B
KEGG: PDE1B
REACTOME: PDE1B
Pathway Commons: PDE1B
ContextiHOP: PDE1B
ligand binding site mutation search in PubMed: PDE1B
UCL Cancer Institute: PDE1B
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0006198cAMP catabolic process14687666
GO:0036006cellular response to macrophage colony-stimulating factor stimulus14687666
GO:0046069cGMP catabolic process14687666
GO:0097011cellular response to granulocyte macrophage colony-stimulating factor stimulus14687666


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Ligand binding site mutations for PDE1B
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
H227A228SLUSC1
H263H263YSKCM1
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 PDE1B
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
H227A228S-0.75719955
H263H263Y-0.024121873
(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 PDE1B from PDB

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Differential gene expression and gene-gene network for PDE1B
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 PDE1B and the right PPI network was created from samples without mutations in the LBS of PDE1B. 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 PDE1B
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0023186Learning Disorders1Biomarker

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

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Pharmacological information for PDE1B
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.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
ApprovedDB00622NicardipineSmall molecule
Approved|investigationalDB01023FelodipineSmall molecule
Approved|withdrawnDB01244BepridilSmall molecule
ExperimentalDB04530S,S-(2-Hydroxyethyl)ThiocysteineSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PDE1B go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ZNZINC(2+)1tazAH227 H263


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Conservation information for LBS of PDE1B
Multiple alignments for Q01064 in multiple species
LBSAA sequence# speciesSpecies
D264AAAIHDYEHTG4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
D370LLHAADISHPT4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
H227YHNQIHAADVT4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
H263FAAAIHDYEHT4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus


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