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 PDE8B
Basic gene info.Gene symbolPDE8B
Gene namephosphodiesterase 8B
SynonymsADSD|PPNAD3
CytomapUCSC genome browser: 5q13.3
Genomic locationchr5 :76506705-76724080
Type of geneprotein-coding
RefGenesNM_001029851.2,
NM_001029852.2,NM_001029853.2,NM_001029854.2,NM_003719.3,
Ensembl idENSG00000113231
Description3',5' cyclic nucleotide phosphodiesterase 8Bcell proliferation-inducing gene 22 proteinhigh affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8BhsPDE8B
Modification date20141207
dbXrefs MIM : 603390
HGNC : HGNC
Ensembl : ENSG00000113231
HPRD : 04546
Vega : OTTHUMG00000102170
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE8B
BioGPS: 8622
Gene Expression Atlas: ENSG00000113231
The Human Protein Atlas: ENSG00000113231
PathwayNCI Pathway Interaction Database: PDE8B
KEGG: PDE8B
REACTOME: PDE8B
ConsensusPathDB
Pathway Commons: PDE8B
MetabolismMetaCyc: PDE8B
HUMANCyc: PDE8B
RegulationEnsembl's Regulation: ENSG00000113231
miRBase: chr5 :76,506,705-76,724,080
TargetScan: NM_001029851
cisRED: ENSG00000113231
ContextiHOP: PDE8B
cancer metabolism search in PubMed: PDE8B
UCL Cancer Institute: PDE8B
Assigned class in ccmGDBC

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Phenotypic Information for PDE8B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE8B
Familial Cancer Database: PDE8B
* 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: PDE8B
MedGen: PDE8B (Human Medical Genetics with Condition)
ClinVar: PDE8B
PhenotypeMGI: PDE8B (International Mouse Phenotyping Consortium)
PhenomicDB: PDE8B

Mutations for PDE8B
* 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
breastPDE8Bchr57651350876513508PDE8Bchr57672233676722336
breastPDE8Bchr57672220876722208GMDSchr621635492163549
ovaryPDE8Bchr57652129576521315PDE8Bchr57650872776508747
ovaryPDE8Bchr57664662576646645PDE8Bchr57651356276513582
pancreasPDE8Bchr57669112276691322ZNF286Achr171561043015610630
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 PDE8B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
M85313PDE8B118457652325676523439TERF2IP173412167569099975691242

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 # sample      5   1      
GAIN (# sample)                 
LOSS (# sample)      5   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=78)
Stat. for Synonymous SNVs
(# total SNVs=26)
Stat. for Deletions
(# total SNVs=1)
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
chr5:76703223-76703223p.R436C4
chr5:76717755-76717755p.R787H2
chr5:76715631-76715631p.M723I2
chr5:76621417-76621417p.A151A2
chr5:76709105-76709105p.A628T2
chr5:76645262-76645262p.E299K2
chr5:76700600-76700600p.S422S2
chr5:76714204-76714204p.H688Y2
chr5:76646938-76646938p.Q356K2
chr5:76709015-76709015p.R598W2

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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
# sample 1 152 711  114211236 17
# mutation 1 172 711  114211246 20
nonsynonymous SNV   131 5 1  62  1195 19
synonymous SNV 1 41 21   5221 51 1
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
chr5:76714063p.S325S,PDE8B2
chr5:76700600p.R339C,PDE8B2
chr5:76703223p.S195L,PDE8B2
chr5:76709015p.D544N,PDE8B2
chr5:76624876p.R501W,PDE8B2
chr5:76714268p.A531T,PDE8B1
chr5:76621481p.S645N,PDE8B1
chr5:76646927p.G35S,PDE8B1
chr5:76721592p.R180W,PDE8B1
chr5:76627229p.F278F,PDE8B1

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 PDE8B 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 PDE8B

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

BBX,LINC00473,ECEL1,EDARADD,ERBB2IP,ERO1LB,EVX1,
FKTN,GABRR3,HSDL2,MCTP2,MTUS1,PDE4D,PDE8B,
PITX1,PROKR2,SLC6A14,SMAD5,SRFBP1,WDR41,ZBED3
ACO1,AOC3,ASPH,ATP2B4,NPR3,CPED1,CCDC3,
COBLL1,ESYT1,FZD5,MDFIC,MYO1C,PALM2-AKAP2,PARVA,
PDE8B,PLIN1,PLXNA4,PRKAR2B,PYGL,SLC25A16,VKORC1L1

BPIFB3,NAT16,DCHS2,DDHD1,FAM184A,FMNL3,GPM6B,
GREB1,HIP1,ITPR1,TP73-AS1,KRTAP10-11,LOC100272216,MCTP1,
MPP2,NPTXR,PDE8B,PPM1K,TXLNB,ZNF483,ZNF671
ASIC1,ATP1A2,C20orf166-AS1,NPR3,FAXDC2,CAMK2G,PIEZO2,
FBXL22,RBFOX3,LOC92249,LOXL4,MEIS2,NRK,NRXN2,
PDE2A,PDE8B,PLCD4,RGAG4,SLC29A1,SOX11,SRPK3
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 PDE8B
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 8BapprovedKetotifen
DB00472phosphodiesterase 8BapprovedFluoxetine


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Cross referenced IDs for PDE8B
* 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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