Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for PDE1B
Basic gene info.Gene symbolPDE1B
Gene namephosphodiesterase 1B, calmodulin-dependent
SynonymsPDE1B1|PDES1B
CytomapUCSC genome browser: 12q13
Genomic locationchr12 :54955227-54973023
Type of geneprotein-coding
RefGenesNM_000924.3,
NM_001165975.2,NM_001288768.1,NM_001288769.1,
Ensembl idENSG00000123360
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
Gene Expression Atlas: ENSG00000123360
The Human Protein Atlas: ENSG00000123360
PathwayNCI Pathway Interaction Database: PDE1B
KEGG: PDE1B
REACTOME: PDE1B
ConsensusPathDB
Pathway Commons: PDE1B
MetabolismMetaCyc: PDE1B
HUMANCyc: PDE1B
RegulationEnsembl's Regulation: ENSG00000123360
miRBase: chr12 :54,955,227-54,973,023
TargetScan: NM_000924
cisRED: ENSG00000123360
ContextiHOP: PDE1B
cancer metabolism search in PubMed: PDE1B
UCL Cancer Institute: PDE1B
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PDE1B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE1B
Familial Cancer Database: PDE1B
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_PURINE_METABOLISM

check002.gifOthers
OMIM 171891; gene.
Orphanet
DiseaseKEGG Disease: PDE1B
MedGen: PDE1B (Human Medical Genetics with Condition)
ClinVar: PDE1B
PhenotypeMGI: PDE1B (International Mouse Phenotyping Consortium)
PhenomicDB: PDE1B

Mutations for PDE1B
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PDE1B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample 2        1      
GAIN (# sample) 2        1      
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=59)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr12:54943667-54943667p.S4F2
chr12:54966478-54966478p.D230N2
chr12:54971078-54971078p.E526A2
chr12:54970410-54970410p.V478M2
chr12:54963049-54963049p.S103S2
chr12:54969417-54969417p.?2
chr12:54970454-54970454p.N492N2
chr12:54963142-54963142p.F134F2
chr12:54968884-54968884p.I356T2
chr12:54971043-54971043p.S514S2

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2 7  3 5  1041  168 6
# mutation 2 8  3 5  1041  187 7
nonsynonymous SNV 2 5  2 2  831  105 7
synonymous SNV   3  1 3  21   82  
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr12:54968993p.F372L,PDE1B3
chr12:54943667p.S4F2
chr12:54963142p.V458M,PDE1B2
chr12:54970410p.A209A,PDE1B2
chr12:54966477p.S494S,PDE1B2
chr12:54971043p.F114F,PDE1B2
chr12:54967229p.A155T,PDE1B1
chr12:54968916p.M289I,PDE1B1
chr12:54966424p.P5S1
chr12:54970398p.D157V,PDE1B1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for PDE1B in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, 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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Gene Expression for PDE1B

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

ACVRL1,AOC3,AQP7,ARHGEF15,CDH5,CNRIP1,CXorf36,
ENG,ERG,FABP4,GNG11,GPX3,LOC339524,NPR1,
PDE1B,PECAM1,ROBO4,STARD8,TIE1,TMEM37,VWF
ABHD15,ACAA2,ACACB,ADH1A,ADH1B,ANKRD53,AQP7,
AQPEP,CAMK1,CIDEA,CIDEC,CNTFR,GHR,GYG2,
KCNIP2,MLXIPL,PDE1B,PECR,PLA2G16,SLC19A3,TMEM132C

ABCA6,ABCA9,ACSM5,ADAMTS10,ADH1B,BHMT2,C1orf162,
CCDC80,CD36,CDO1,CLDN11,CYP1B1,EBF2,EXTL1,
FABP4,LOC339524,MFAP5,PDE1B,PLAC9,RBP7,SEMA3G
ABCC9,ANXA6,BOC,CHRM2,CHST10,DEGS1,EFEMP2,
EMP3,FIBIN,IGSF11,KCNJ8,MEIS3,NAB2,NAT14,
PDE1B,SALL2,SGCA,SHISA4,SULF1,SYT11,TMEM200B
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for PDE1B
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q01064; -.
ChemistryChEMBL CHEMBL2363066; -.
ChemistryGuidetoPHARMACOLOGY 1295; -.
Organism-specific databasesPharmGKB PA33123; -.
Organism-specific databasesCTD 5153; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00622phosphodiesterase 1B, calmodulin-dependentapprovedNicardipine
DB01023phosphodiesterase 1B, calmodulin-dependentapproved; investigationalFelodipine
DB01244phosphodiesterase 1B, calmodulin-dependentapprovedBepridil
DB04530phosphodiesterase 1B, calmodulin-dependentexperimentalS,S-(2-Hydroxyethyl)Thiocysteine
DB01151phosphodiesterase 1B, calmodulin-dependentapprovedDesipramine
DB00472phosphodiesterase 1B, calmodulin-dependentapprovedFluoxetine


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Cross referenced IDs for PDE1B
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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