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 PDE5A
Basic gene info.Gene symbolPDE5A
Gene namephosphodiesterase 5A, cGMP-specific
SynonymsCGB-PDE|CN5A|PDE5
CytomapUCSC genome browser: 4q27
Genomic locationchr4 :120415549-120549981
Type of geneprotein-coding
RefGenesNM_001083.3,
NM_033430.2,NM_033437.3,
Ensembl idENSG00000138735
DescriptioncGMP-binding cGMP-specific 3',5'-cyclic nucleotide phosphodiesterasecGMP-specific 3',5'-cyclic phosphodiesterasecGMP-specific phosphodiesterase PDE5A2cGMP-specific phosphodiesterase type 5Aphosphodiesterase isozyme 5
Modification date20141207
dbXrefs MIM : 603310
HGNC : HGNC
Ensembl : ENSG00000138735
HPRD : 04497
Vega : OTTHUMG00000132971
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE5A
BioGPS: 8654
Gene Expression Atlas: ENSG00000138735
The Human Protein Atlas: ENSG00000138735
PathwayNCI Pathway Interaction Database: PDE5A
KEGG: PDE5A
REACTOME: PDE5A
ConsensusPathDB
Pathway Commons: PDE5A
MetabolismMetaCyc: PDE5A
HUMANCyc: PDE5A
RegulationEnsembl's Regulation: ENSG00000138735
miRBase: chr4 :120,415,549-120,549,981
TargetScan: NM_001083
cisRED: ENSG00000138735
ContextiHOP: PDE5A
cancer metabolism search in PubMed: PDE5A
UCL Cancer Institute: PDE5A
Assigned class in ccmGDBC

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Phenotypic Information for PDE5A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE5A
Familial Cancer Database: PDE5A
* 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: PDE5A
MedGen: PDE5A (Human Medical Genetics with Condition)
ClinVar: PDE5A
PhenotypeMGI: PDE5A (International Mouse Phenotyping Consortium)
PhenomicDB: PDE5A

Mutations for PDE5A
* 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
ovaryPDE5Achr4120529791120529811PDE5Achr4120529850120529870
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 PDE5A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW102720PDE5A101634120420968120421121EHBP115820326325118563251232
CV345100LOC1001315643352919380139393801890PDE5A5226424120436849120436969
BG996672PDE5A141124120471311120471408ARGLU110230713107196119107196325
BG980189CEACAM51276194221257642260645PDE5A2722944120432019120432047

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 # sample1           1   1
GAIN (# sample)1                
LOSS (# sample)            1   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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=60)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=2)
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
chr4:120446754-120446754p.R577W3
chr4:120484024-120484024p.Q365H2
chr4:120528215-120528215p.K130N2
chr4:120463730-120463730p.R486*2
chr4:120446851-120446851p.?2
chr4:120428814-120428814p.T712P2
chr4:120463665-120463665p.Q507Q2
chr4:120419875-120419875p.E837K2
chr4:120488258-120488258p.N291N2
chr4:120528376-120528376p.E77K2

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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
# sample52 11  7 12 74   65111
# mutation52 13  7 12 74   67115
nonsynonymous SNV51 10  7  1 44   57111
synonymous SNV 1 3    11 3    1  4
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
chr4:120446754p.R577W,PDE5A3
chr4:120427082p.S381C,PDE5A2
chr4:120481508p.E837Q,PDE5A2
chr4:120419875p.R732Q,PDE5A2
chr4:120473732p.G703G,PDE5A1
chr4:120549736p.K457Q,PDE5A1
chr4:120419774p.L213M,PDE5A1
chr4:120425693p.E31K1
chr4:120517749p.G870G,PDE5A1
chr4:120446753p.H684H,PDE5A1

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 PDE5A 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 PDE5A

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

AFP,ASH2L,BAG4,C16orf52,C8orf86,CACNG1,DDHD2,
ERLIN2,HGSNAT,HTR7P1,KIAA1107,MOCS1,NTRK3,PDE5A,
RAB11FIP1,RASSF6,SEMA5A,TAPT1,TBX3,TCEAL1,ULK2
AEBP2,ARHGAP5,ATXN7,C7orf60,ISPD,LEMD3,MAP4K5,
NUDT21,PDE5A,PLEKHA1,PPP1R12A,RSBN1,SCAMP1,SENP6,
SOCS5,SORBS2,TRIM33,USP1,WASL,ZNF148,ZNF800

ATP2B4,BVES,CAND2,CNTNAP1,FILIP1,GNAO1,KANK2,
KCNMA1,KIAA2022,LRCH2,MAB21L2,MEIS1,MYLK,MYOCD,
PDE5A,PDZRN4,PGR,PLN,PPP1R12B,RNF150,TMEM200B
ANKS1B,C20orf166-AS1,CAMK2G,CCBE1,DIXDC1,IL17RD,KCNMA1,
LMO3,LMOD1,LOXL4,MEIS1,MEIS2,MRVI1,PDE5A,
PGM5,PPP1R12A,RBFOX2,SCD5,SEMA3A,SEMA3C,TBC1D1
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 PDE5A
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
DB00203phosphodiesterase 5A, cGMP-specificapproved; investigationalSildenafil
DB00277phosphodiesterase 5A, cGMP-specificapprovedTheophylline
DB00806phosphodiesterase 5A, cGMP-specificapproved; investigationalPentoxifylline
DB00820phosphodiesterase 5A, cGMP-specificapproved; investigationalTadalafil
DB00862phosphodiesterase 5A, cGMP-specificapprovedVardenafil
DB00975phosphodiesterase 5A, cGMP-specificapprovedDipyridamole
DB01972phosphodiesterase 5A, cGMP-specificexperimentalGuanosine-5'-Monophosphate
DB03597phosphodiesterase 5A, cGMP-specificexperimentalGamma-Glutamyl[S-(2-Iodobenzyl)Cysteinyl]Glycine
DB04272phosphodiesterase 5A, cGMP-specificexperimentalCitric Acid
DB06267phosphodiesterase 5A, cGMP-specificapproved; investigationalUdenafil
DB07954phosphodiesterase 5A, cGMP-specificexperimental3-ISOBUTYL-1-METHYLXANTHINE
DB08729phosphodiesterase 5A, cGMP-specificexperimental5-ethoxy-4-(1-methyl-7-oxo-3-propyl-6,7-dihydro-1H-pyrazolo[4,3-d]pyrimidin-5-yl)thiophene-2-sulfonamide
DB01151phosphodiesterase 5A, cGMP-specificapprovedDesipramine
DB00472phosphodiesterase 5A, cGMP-specificapprovedFluoxetine


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Cross referenced IDs for PDE5A
* 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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