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 PDE2A
Basic gene info.Gene symbolPDE2A
Gene namephosphodiesterase 2A, cGMP-stimulated
SynonymsCGS-PDE|PDE2A1|PED2A4|cGSPDE
CytomapUCSC genome browser: 11q13.4
Genomic locationchr11 :72287183-72353504
Type of geneprotein-coding
RefGenesNM_001143839.3,
NM_001146209.2,NM_001243784.1,NM_002599.4,
Ensembl idENSG00000186642
DescriptioncGMP-dependent 3',5'-cyclic phosphodiesterasecGMP-stimulated phosphodiesterase 1cGMP-stimulated phosphodiesterase 4cyclic GMP-stimulated phosphodiesterase
Modification date20141207
dbXrefs MIM : 602658
HGNC : HGNC
Ensembl : ENSG00000186642
HPRD : 04041
Vega : OTTHUMG00000102045
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE2A
BioGPS: 5138
Gene Expression Atlas: ENSG00000186642
The Human Protein Atlas: ENSG00000186642
PathwayNCI Pathway Interaction Database: PDE2A
KEGG: PDE2A
REACTOME: PDE2A
ConsensusPathDB
Pathway Commons: PDE2A
MetabolismMetaCyc: PDE2A
HUMANCyc: PDE2A
RegulationEnsembl's Regulation: ENSG00000186642
miRBase: chr11 :72,287,183-72,353,504
TargetScan: NM_001143839
cisRED: ENSG00000186642
ContextiHOP: PDE2A
cancer metabolism search in PubMed: PDE2A
UCL Cancer Institute: PDE2A
Assigned class in ccmGDBC

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Phenotypic Information for PDE2A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE2A
Familial Cancer Database: PDE2A
* 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: PDE2A
MedGen: PDE2A (Human Medical Genetics with Condition)
ClinVar: PDE2A
PhenotypeMGI: PDE2A (International Mouse Phenotyping Consortium)
PhenomicDB: PDE2A

Mutations for PDE2A
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 PDE2A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE938766PDE2A40397117228997372291982KIAA184139352226131595361316082
BQ677895CAMTA22656981748733034875682PDE2A699720117230578672305807
BE924919CAPZB119911966574119665940PDE2A186266117232371172323798
AB209076KCNIP31365829596308695979644PDE2A36534512117236108472361943

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 # sample4  1    1        
GAIN (# sample)4  1    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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=64)
Stat. for Synonymous SNVs
(# total SNVs=25)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=1)

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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
chr11:72301503-72301503p.T224I3
chr11:72299876-72299876p.D341V2
chr11:72289953-72289953p.T819T2
chr11:72295250-72295250p.A549T2
chr11:72293532-72293532p.F603L2
chr11:72289292-72289292p.A867V2
chr11:72295251-72295251p.I548I2
chr11:72319797-72319797p.?2
chr11:72295734-72295734p.A466A2
chr11:72296617-72296617p.K401N2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13 101 2 3  1162 21612 12
# mutation13 111 2 3  1262 21812 14
nonsynonymous SNV12 71   3  742 2148 11
synonymous SNV 1 4  2    52   44 3
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
chr11:72295250p.R749H,PDE2A2
chr11:72296617p.A860V,PDE2A2
chr11:72289292p.T812T,PDE2A2
chr11:72290417p.K394N,PDE2A2
chr11:72292005p.A542T,PDE2A2
chr11:72289953p.I679I,PDE2A2
chr11:72290019p.R880H,PDE2A1
chr11:72294556p.M754L,PDE2A1
chr11:72307659p.P646T,PDE2A1
chr11:72290599p.A476D,PDE2A1

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 PDE2A 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 PDE2A

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

ADCY4,AOC3,ARHGEF15,BMX,CCL14,CD300LG,CD34,
CDH5,CXorf36,ERG,GPIHBP1,GPR146,LDB2,MMRN2,
NPR1,PDE2A,PEAR1,ROBO4,S1PR1,SDPR,VWF
ABHD6,ARHGEF15,BMP6,BTNL9,CD300LG,CDH5,CXorf36,
EPAS1,ERG,FGD5,GIMAP6,GNAZ,KIAA1462,MMRN2,
NRP1,PDE2A,PTPRM,ROBO4,TEK,TENC1,VWF

ABCC9,ANK2,AOC3,CACNA2D1,CCDC69,CCL14,CLIP3,
ACKR1,FAM13C,FILIP1,JAM2,NPR1,PDE2A,RBMS3,
S1PR1,SDPR,SLC9A9,SPARCL1,SV2B,TLL1,ZEB1
AOC3,ATP1A2,CD109,CLIP3,CPXM2,FAM127C,FBXL7,
GJC2,LOXL4,MPP2,NLGN1,NPTXR,PCDHGB7,PDE2A,
RBFOX2,RGAG4,RGMA,SEMA4C,SLC29A1,TGFB1I1,TSPAN18
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 PDE2A
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
DB02315phosphodiesterase 2A, cGMP-stimulatedexperimentalCyclic Guanosine Monophosphate
DB07954phosphodiesterase 2A, cGMP-stimulatedexperimental3-ISOBUTYL-1-METHYLXANTHINE
DB08811phosphodiesterase 2A, cGMP-stimulatedapprovedTofisopam
DB00131phosphodiesterase 2A, cGMP-stimulatedapproved; nutraceuticalAdenosine monophosphate
DB00125phosphodiesterase 2A, cGMP-stimulatedapproved; nutraceuticalL-Arginine
DB00155phosphodiesterase 2A, cGMP-stimulatedapproved; nutraceuticalL-Citrulline
DB00435phosphodiesterase 2A, cGMP-stimulatedapprovedNitric Oxide
DB01151phosphodiesterase 2A, cGMP-stimulatedapprovedDesipramine
DB00472phosphodiesterase 2A, cGMP-stimulatedapprovedFluoxetine


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Cross referenced IDs for PDE2A
* 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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