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 PDE3A
Basic gene info.Gene symbolPDE3A
Gene namephosphodiesterase 3A, cGMP-inhibited
SynonymsCGI-PDE|CGI-PDE A|CGI-PDE-A
CytomapUCSC genome browser: 12p12
Genomic locationchr12 :20724797-20837041
Type of geneprotein-coding
RefGenesNM_000921.4,
NM_001244683.1,
Ensembl idENSG00000172572
DescriptioncAMP phosphodiesterase, myocardial cGMP-inhibitedcGMP-inhibited 3',5'-cyclic phosphodiesterase Acyclic GMP-inhibited phosphodiesterase A
Modification date20141207
dbXrefs MIM : 123805
HGNC : HGNC
Ensembl : ENSG00000172572
HPRD : 00441
Vega : OTTHUMG00000168962
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE3A
BioGPS: 5139
Gene Expression Atlas: ENSG00000172572
The Human Protein Atlas: ENSG00000172572
PathwayNCI Pathway Interaction Database: PDE3A
KEGG: PDE3A
REACTOME: PDE3A
ConsensusPathDB
Pathway Commons: PDE3A
MetabolismMetaCyc: PDE3A
HUMANCyc: PDE3A
RegulationEnsembl's Regulation: ENSG00000172572
miRBase: chr12 :20,724,797-20,837,041
TargetScan: NM_000921
cisRED: ENSG00000172572
ContextiHOP: PDE3A
cancer metabolism search in PubMed: PDE3A
UCL Cancer Institute: PDE3A
Assigned class in ccmGDBC

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Phenotypic Information for PDE3A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE3A
Familial Cancer Database: PDE3A
* 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
Orphanet
DiseaseKEGG Disease: PDE3A
MedGen: PDE3A (Human Medical Genetics with Condition)
ClinVar: PDE3A
PhenotypeMGI: PDE3A (International Mouse Phenotyping Consortium)
PhenomicDB: PDE3A

Mutations for PDE3A
* 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
There's no inter-chromosomal structural variation.
- 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
breastPDE3Achr122072573020725730PDE3Achr122073263420732634
ovaryPDE3Achr122072538320725403chr124869763948697659
ovaryPDE3Achr122072787020727890chr124869911148699131
ovaryPDE3Achr122079178420791804PDE3Achr122071739020717410
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 PDE3A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA711191PDE3A1402122052282920709645VGLL439955531160634011606496
BF755147PDE3A135160122074901620749041RNF3414133512121838985121839179
AF118076PDE3A1694122059726720597960CENPF69321141214822023214827762

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      2    1   
GAIN (# sample)21      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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=133)
Stat. for Synonymous SNVs
(# total SNVs=48)
Stat. for Deletions
(# total SNVs=5)
Stat. for Insertions
(# total SNVs=2)

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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
chr12:20766419-20766419p.E352K4
chr12:20522252-20522252p.D12N4
chr12:20522722-20522722p.C168C3
chr12:20523043-20523043p.L275L3
chr12:20769164-20769164p.R424C3
chr12:20522723-20522723p.E171fs*363
chr12:20790147-20790147p.R705S3
chr12:20766410-20766410p.V349I3
chr12:20806929-20806929p.R992C3
chr12:20522514-20522514p.E99A2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample7131234 1413  25115  2317116
# mutation6131224 1413  25125  2918121
nonsynonymous SNV381143 11 3  1954  2313116
synonymous SNV35 81 31   671  65 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
chr12:20523043p.L275L5
chr12:20766410p.V27I,PDE3A3
chr12:20799828p.H32H,PDE3A2
chr12:20766427p.D95H,PDE3A2
chr12:20799875p.R102C,PDE3A2
chr12:20522876p.D707N,PDE3A2
chr12:20523121p.P373S,PDE3A2
chr12:20766614p.S301S2
chr12:20803400p.D515N,PDE3A2
chr12:20790115p.D609H,PDE3A2

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 PDE3A 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 PDE3A

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

AVPI1,LINC00473,CALCA,ECEL1,FILIP1,GDF10,KSR1,
LOC154822,LOC441177,MCF2,MCTP2,PDE3A,PDE4D,PLD1,
PTP4A1,SGK1,SLC22A2,SLC7A5,SMOC1,UST,WNT1
ABCA8,ABCC9,ADAMTSL3,ADIPOQ,ANO6,ARHGEF7,AVPR1A,
VSTM4,C1QTNF7,CRYBG3,ESR2,TENM3___TENM1,PDE3A,PHLDB2,
PREX2,PVRL3,SIK2,SLC16A7,SLC22A3,SOX5,TTLL7

ADAM23,ENTPD5,FLVCR1,GAB1,HAVCR1,KCTD4,LGI4,
LRFN2,LRRN2,MERTK,MYH2,OR6T1,PCDHA10,PDE3A,
PTPRD,RAB9BP1,RASSF8,SLC30A1,SOX3,TBPL2,TNFAIP8L3
SOGA1,DAAM1,FAM63B,GPR17,KLF7,NAV2,NKD1,
PARD3B,PDE3A,PRDM11,PTPN13,PTPRM,RBMS3,ROR1,
SCN3B,SNORD116-28,TACC1,TTBK2,WNT9A,ZC3H13,ZNF154
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 PDE3A
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00235phosphodiesterase 3A, cGMP-inhibitedapprovedMilrinone
DB00261phosphodiesterase 3A, cGMP-inhibitedapprovedAnagrelide
DB00277phosphodiesterase 3A, cGMP-inhibitedapprovedTheophylline
DB00922phosphodiesterase 3A, cGMP-inhibitedapproved; investigationalLevosimendan
DB01166phosphodiesterase 3A, cGMP-inhibitedapprovedCilostazol
DB01223phosphodiesterase 3A, cGMP-inhibitedapprovedAminophylline
DB01303phosphodiesterase 3A, cGMP-inhibitedapprovedOxtriphylline
DB01427phosphodiesterase 3A, cGMP-inhibitedapprovedAmrinone
DB04880phosphodiesterase 3A, cGMP-inhibitedapproved; investigationalEnoximone
DB05266phosphodiesterase 3A, cGMP-inhibitedapproved; investigationalIbudilast
DB08811phosphodiesterase 3A, cGMP-inhibitedapprovedTofisopam
DB00131phosphodiesterase 3A, cGMP-inhibitedapproved; nutraceuticalAdenosine monophosphate
DB00125phosphodiesterase 3A, cGMP-inhibitedapproved; nutraceuticalL-Arginine
DB00155phosphodiesterase 3A, cGMP-inhibitedapproved; nutraceuticalL-Citrulline
DB00435phosphodiesterase 3A, cGMP-inhibitedapprovedNitric Oxide
DB01151phosphodiesterase 3A, cGMP-inhibitedapprovedDesipramine
DB00472phosphodiesterase 3A, cGMP-inhibitedapprovedFluoxetine


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Cross referenced IDs for PDE3A
* 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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