Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 PDE3B
Basic gene info.Gene symbolPDE3B
Gene namephosphodiesterase 3B, cGMP-inhibited
SynonymsHcGIP1|cGIPDE1
CytomapUCSC genome browser: 11p15.1
Genomic locationchr11 :14665268-14893604
Type of geneprotein-coding
RefGenesNM_000922.3,
Ensembl idENSG00000261923
DescriptionCGI-PDE BCGIP1cGMP-inhibited 3',5'-cyclic phosphodiesterase Bcyclic GMP-inhibited phosphodiesterase Bcyclic nucleotide phosphodiesterase
Modification date20141207
dbXrefs MIM : 602047
HGNC : HGNC
Ensembl : ENSG00000152270
HPRD : 03626
Vega : OTTHUMG00000165898
ProteinUniProt: Q13370
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE3B
BioGPS: 5140
Gene Expression Atlas: ENSG00000261923
The Human Protein Atlas: ENSG00000261923
PathwayNCI Pathway Interaction Database: PDE3B
KEGG: PDE3B
REACTOME: PDE3B
ConsensusPathDB
Pathway Commons: PDE3B
MetabolismMetaCyc: PDE3B
HUMANCyc: PDE3B
RegulationEnsembl's Regulation: ENSG00000261923
miRBase: chr11 :14,665,268-14,893,604
TargetScan: NM_000922
cisRED: ENSG00000261923
ContextiHOP: PDE3B
cancer metabolism search in PubMed: PDE3B
UCL Cancer Institute: PDE3B
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PDE3B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE3B
Familial Cancer Database: PDE3B
* 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 602047; gene.
Orphanet
DiseaseKEGG Disease: PDE3B
MedGen: PDE3B (Human Medical Genetics with Condition)
ClinVar: PDE3B
PhenotypeMGI: PDE3B (International Mouse Phenotyping Consortium)
PhenomicDB: PDE3B

Mutations for PDE3B
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPDE3Bchr111484989814849918chr237379677273796792
ovaryPDE3Bchr111486313914863339chr237379687873797078
pancreasPDE3Bchr111471458714714787chr111507308815073288
pancreasPDE3Bchr111471468014714700chr111507397715073997
pancreasPDE3Bchr111471504514715245chr111507387215074072
pancreasPDE3Bchr111471512714715147chr111507315715073177
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PDE3B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI969380SPATA81228159732860997328836PDE3B223412111466644414793516
AI651372SPATA81228159732860997328836PDE3B223460111466639614793516

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 # sample21      5        
GAIN (# sample)2       5        
LOSS (# sample) 1               
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=82)
Stat. for Synonymous SNVs
(# total SNVs=19)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr11:14865418-14865418p.S789L4
chr11:14839801-14839801p.R532Q3
chr11:14880728-14880728p.I887S2
chr11:14839900-14839900p.Y565C2
chr11:14880774-14880774p.L902L2
chr11:14666364-14666364p.L248P2
chr11:14808095-14808095p.R381Q2
chr11:14856585-14856585p.R755L2
chr11:14889184-14889184p.G1007S2
chr11:14808117-14808117p.G388G2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample43 123   3  125  1614 10
# mutation43 123   3  135  1616 15
nonsynonymous SNV12 73   3  124  1514 10
synonymous SNV31 5       11   12 5
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
chr11:14865418p.S789L3
chr11:14808095p.R755L2
chr11:14856585p.R532Q2
chr11:14839801p.R381Q2
chr11:14666552p.P24L1
chr11:14853310p.G388G1
chr11:14889185p.K585T1
chr11:14808182p.I887S1
chr11:14865471p.Y31C1
chr11:14665692p.F390F1

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 PDE3B 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 PDE3B

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

ABCD2,ACVR1C,ADH1A,ADH1B,ADIPOQ,AQPEP,CD28,
CELF2,CHRDL1,DOCK11,FLI1,GVINP1,IKZF1,KBTBD8,
KCNIP2,KLB,LOC339524,PDE3B,PLIN1,PTPRC,SLC19A3
ABCD2,ACO1,ADIPOQ,ANO6,AQPEP,CAT,GYG2,
HEPACAM,HRASLS5,KCNIP2,LPL,MARC1,PDE3B,PECR,
PEX19,PLIN1,PPARG,PPP2R5A,PRKAR2B,SIK2,SLC16A7

ARID4A,ATAD2B,BMPR2,CHD9,EPM2AIP1,GAB1,GPR125,
KIDINS220,KLHL24,LPHN3,PBRM1,PDCD4,PDE3B,PHC3,
PIK3C2A,PRKACB,SATB1,SNX30,SOS2,TEAD1,ZBED5
ABI2,ADARB1,VSTM4,C3orf58,CRYBG3,DCBLD2,FOXJ2,
JMY,LOC92249,MTMR9,NFIA,PDE3B,PDE5A,POU3F4,
PTGS1,RABGAP1,RBFOX2,RNF38,SATB1,SEMA3C,SETBP1
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 PDE3B
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q13370; -.
ChemistryChEMBL CHEMBL2095153; -.
ChemistryGuidetoPHARMACOLOGY 1299; -.
Organism-specific databasesPharmGKB PA33127; -.
Organism-specific databasesCTD 5140; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01640phosphodiesterase 3B, cGMP-inhibitedexperimental(5r)-6-(4-{[2-(3-Iodobenzyl)-3-Oxocyclohex-1-En-1-Yl]Amino}Phenyl)-5-Methyl-4,5-Dihydropyridazin-3(2h)-One
DB01970phosphodiesterase 3B, cGMP-inhibitedexperimentalHg9a-9, Nonanoyl-N-Hydroxyethylglucamide
DB07954phosphodiesterase 3B, cGMP-inhibitedexperimental3-ISOBUTYL-1-METHYLXANTHINE
DB00131phosphodiesterase 3B, cGMP-inhibitedapproved; nutraceuticalAdenosine monophosphate
DB00125phosphodiesterase 3B, cGMP-inhibitedapproved; nutraceuticalL-Arginine
DB00155phosphodiesterase 3B, cGMP-inhibitedapproved; nutraceuticalL-Citrulline
DB00435phosphodiesterase 3B, cGMP-inhibitedapprovedNitric Oxide


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Cross referenced IDs for PDE3B
* 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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