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 PDE8A
Basic gene info.Gene symbolPDE8A
Gene namephosphodiesterase 8A
SynonymsHsT19550
CytomapUCSC genome browser: 15q25.3
Genomic locationchr15 :85525204-85682372
Type of geneprotein-coding
RefGenesNM_001243137.1,
NM_002605.2,NM_173454.1,NM_173455.1,NM_173456.1,
NM_173457.1,
Ensembl idENSG00000073417
DescriptioncAMP-specific cyclic nucleotide phosphodiesterase 8Ahigh affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A
Modification date20141207
dbXrefs MIM : 602972
HGNC : HGNC
Ensembl : ENSG00000073417
HPRD : 09114
Vega : OTTHUMG00000148670
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE8A
BioGPS: 5151
Gene Expression Atlas: ENSG00000073417
The Human Protein Atlas: ENSG00000073417
PathwayNCI Pathway Interaction Database: PDE8A
KEGG: PDE8A
REACTOME: PDE8A
ConsensusPathDB
Pathway Commons: PDE8A
MetabolismMetaCyc: PDE8A
HUMANCyc: PDE8A
RegulationEnsembl's Regulation: ENSG00000073417
miRBase: chr15 :85,525,204-85,682,372
TargetScan: NM_001243137
cisRED: ENSG00000073417
ContextiHOP: PDE8A
cancer metabolism search in PubMed: PDE8A
UCL Cancer Institute: PDE8A
Assigned class in ccmGDBC

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Phenotypic Information for PDE8A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE8A
Familial Cancer Database: PDE8A
* 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: PDE8A
MedGen: PDE8A (Human Medical Genetics with Condition)
ClinVar: PDE8A
PhenotypeMGI: PDE8A (International Mouse Phenotyping Consortium)
PhenomicDB: PDE8A

Mutations for PDE8A
* 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
breastPDE8Achr158552823285528232chr15102064754102064754
pancreasPDE8Achr158563662785636647PDE8Achr158561916885619188
pancreasPDE8Achr158563834085638360chr153206831232068332
pancreasPDE8Achr158563998485640004chr159717791697177936
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 PDE8A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF770537PDE8A10267158564517085645428IPO5257386139866238798662516
BF951597PDE8A173158566632885666402PDE8A62441158566094785666329
W92044FAM20A189176653125866531346PDE8A78533158568173085682185
W91923FAM20A189176653125866531346PDE8A78536158568173385682185

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    1   
GAIN (# sample)1  1         1   
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=39)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr15:85610364-85610364p.L121L2
chr15:85669540-85669540p.P730S2
chr15:85664054-85664054p.V587V2
chr15:85610362-85610362p.L121M1
chr15:85659299-85659299p.E495V1
chr15:85669589-85669589p.E746A1
chr15:85632630-85632630p.E233K1
chr15:85664067-85664067p.A592T1
chr15:85656658-85656658p.I389F1
chr15:85666404-85666404p.A689P1

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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
# sample11 91 1 4  362 158 7
# mutation11 91 1 4  362 158 7
nonsynonymous SNV11 31   4  351 136 5
synonymous SNV   6  1     11  22 2
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
chr15:85610364p.L49L,PDE8A2
chr15:85619136p.R95T,PDE8A1
chr15:85666319p.R409R,PDE8A1
chr15:85643423p.T622I,PDE8A1
chr15:85681058p.E96Q,PDE8A1
chr15:85659326p.P432P,PDE8A1
chr15:85619149p.T660N,PDE8A1
chr15:85666327p.E97D,PDE8A1
chr15:85652331p.E449V,PDE8A1
chr15:85681096p.R673Q,PDE8A1

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 PDE8A 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 PDE8A

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

ADPGK,ARIH1,ASB7,BTBD1,DMXL2,FOXN2,GOLGA6L10,
HMG20A,IDH3A,IREB2,MAN2A2,MAP2K1,MEF2A,MYO5A,
PDE8A,PTPN9,RCN2,SLC41A2,VPS54,WHAMM,ZNF592
ACER3,ANO6,PQLC2L,CAT,CD36,CELF2,COL4A3BP,
DDHD2,EBF1,EIF4EBP2,FERMT2,GNAI1,GTDC1,HRASLS5,
MDFIC,PDE8A,PLIN1,RRAGC,SEPT11,SH3KBP1,UVRAG

ABCA5,ARFGEF2,EPB41L4B,TMEM236,KIAA1161,LRRK1,MAGI3,
MCTP2,NR5A2,PDE8A,PHLPP2,PPARA,SEMA6D,SGK2,
TRPM7,TUG1,USP53,ZNF587,ZNF592,ZNF774,ZNF91
AGFG2,AHCYL2,RHOV___CHP1,CPT1A,DTX4,EPB41L4B,FZD5,
KIAA1522,LRRFIP2,MTMR11,MYO1D,NCEH1,PDE8A,PPM1B,
RAPGEFL1,RAVER2,SGK2,SH3BGRL2,SLC26A2,SNX30,TMEM63B
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 PDE8A
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
DB00920phosphodiesterase 8AapprovedKetotifen
DB07954phosphodiesterase 8Aexperimental3-ISOBUTYL-1-METHYLXANTHINE
DB01151phosphodiesterase 8AapprovedDesipramine
DB00472phosphodiesterase 8AapprovedFluoxetine


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Cross referenced IDs for PDE8A
* 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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