Cancer Cell Metabolism Gene Database

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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 PDE4B
Basic gene info.Gene symbolPDE4B
Gene namephosphodiesterase 4B, cAMP-specific
SynonymsDPDE4|PDEIVB
CytomapUCSC genome browser: 1p31
Genomic locationchr1 :66797792-66840262
Type of geneprotein-coding
RefGenesNM_001037339.2,
NM_001037340.2,NM_001037341.1,NM_001297440.1,NM_001297441.1,
NM_001297442.1,NM_002600.3,
Ensembl idENSG00000184588
DescriptioncAMP-specific 3',5'-cyclic phosphodiesterase 4Bdunce-like phosphodiesterase E4phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)
Modification date20141207
dbXrefs MIM : 600127
HGNC : HGNC
Ensembl : ENSG00000184588
HPRD : 02528
Vega : OTTHUMG00000009088
ProteinUniProt: Q07343
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE4B
BioGPS: 5142
Gene Expression Atlas: ENSG00000184588
The Human Protein Atlas: ENSG00000184588
PathwayNCI Pathway Interaction Database: PDE4B
KEGG: PDE4B
REACTOME: PDE4B
ConsensusPathDB
Pathway Commons: PDE4B
MetabolismMetaCyc: PDE4B
HUMANCyc: PDE4B
RegulationEnsembl's Regulation: ENSG00000184588
miRBase: chr1 :66,797,792-66,840,262
TargetScan: NM_001037339
cisRED: ENSG00000184588
ContextiHOP: PDE4B
cancer metabolism search in PubMed: PDE4B
UCL Cancer Institute: PDE4B
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PDE4B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE4B
Familial Cancer Database: PDE4B
* 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 600127; gene.
Orphanet
DiseaseKEGG Disease: PDE4B
MedGen: PDE4B (Human Medical Genetics with Condition)
ClinVar: PDE4B
PhenotypeMGI: PDE4B (International Mouse Phenotyping Consortium)
PhenomicDB: PDE4B

Mutations for PDE4B
* 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
breastPDE4Bchr16681708566817085PDE4Bchr16683738966837389
breastPDE4Bchr16683856766838567chr16687408366874083
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 PDE4B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ352220NDUFS314150114760393847605919PDE4B13931916683883566839015
L20971PDE4B638916683922766839611PDE4B380405116679768766839942
AA226609PDE4B68616683896066839041PDE4B8217716683895866839057
BF359219S100A1611921153579953153580145PDE4B18424516683630966836370

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 # sample31      2        
GAIN (# sample)21      2        
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=77)
Stat. for Synonymous SNVs
(# total SNVs=24)
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
chr1:66833737-66833737p.D551N3
chr1:66379023-66379023p.T9M2
chr1:66384348-66384348p.I37I2
chr1:66713153-66713153p.E98*2
chr1:66833528-66833528p.D512N2
chr1:66821257-66821257p.S265R2
chr1:66821258-66821258p.R266R2
chr1:66829101-66829101p.L377L2
chr1:66827375-66827375p.Q307*2
chr1:66838112-66838112p.S654R2

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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
# sample153151 7 1  1132  1110 13
# mutation153151 7 1  1132  1010 15
nonsynonymous SNV142101 4 1  831  76 10
synonymous SNV 115  3    3 1  34 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
chr1:66384348p.I37I,PDE4B3
chr1:66829220p.S245L,PDE4B3
chr1:66833737p.D126Y,PDE4B2
chr1:66829176p.I180I,PDE4B2
chr1:66829177p.G146S,PDE4B2
chr1:66713282p.D230D,PDE4B2
chr1:66723334p.V231M,PDE4B2
chr1:66828886p.D379N,PDE4B2
chr1:66713200p.L132L,PDE4B1
chr1:66831427p.V281V,PDE4B1

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 PDE4B 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 PDE4B

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

MB21D1,CFLAR,DOCK7,CCDC71L,FUT4,MPZL1,NCK1,
NCOA7,NFIL3,OSMR,PDE4B,PLD1,PNRC1,PSME4,
RAB29,RNF145,SLC5A6,SOD2,SOX9,TMEM123,VASH2
ANK3,ATL2,CHAF1B,DYRK1A,FAM160A1,FBXO34,ITGB6,
NAA15,NT5C2,PDE4B,PDE7A,PM20D2,PSME4,PSTPIP2,
RPAP3,SACS,SOCS6,SRPK1,TEX10,THAP9,TIAM2

ARHGAP20,ARHGAP24,ARHGAP31,CASS4,CYTIP,ETS1,FMNL1,
ITM2A,LCP2,NLRP3,PDE4B,PDE4D,PRKCH,RAB27A,
RAB8B,SAMSN1,SCARF1,SRGN,STK10,TOX,TRAM2
AREG,ARL4C,CD80,CHST2,CTLA4,CXCL1,CXCL2,
CXCL3,DEFB103B,IL1B,MMP12,NFKBIZ,PDE4B,PFKFB3,
PIM3,PLAU,PRSS27,STX11,WFDC12,YRDC,ZC3H12A
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 PDE4B
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q07343; -.
ChemistryChEMBL CHEMBL2111340; -.
ChemistryGuidetoPHARMACOLOGY 1301; -.
Organism-specific databasesPharmGKB PA33129; -.
Organism-specific databasesCTD 5142; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00131phosphodiesterase 4B, cAMP-specificapproved; nutraceuticalAdenosine monophosphate
DB00201phosphodiesterase 4B, cAMP-specificapprovedCaffeine
DB00277phosphodiesterase 4B, cAMP-specificapprovedTheophylline
DB00651phosphodiesterase 4B, cAMP-specificapprovedDyphylline
DB00806phosphodiesterase 4B, cAMP-specificapproved; investigationalPentoxifylline
DB00824phosphodiesterase 4B, cAMP-specificapprovedEnprofylline
DB00920phosphodiesterase 4B, cAMP-specificapprovedKetotifen
DB01088phosphodiesterase 4B, cAMP-specificapproved; investigationalIloprost
DB01113phosphodiesterase 4B, cAMP-specificapprovedPapaverine
DB01412phosphodiesterase 4B, cAMP-specificapprovedTheobromine
DB01427phosphodiesterase 4B, cAMP-specificapprovedAmrinone
DB01647phosphodiesterase 4B, cAMP-specificexperimental(R)-Mesopram
DB01791phosphodiesterase 4B, cAMP-specificexperimentalPiclamilast
DB01954phosphodiesterase 4B, cAMP-specificexperimental4-[3-(Cyclopentyloxy)-4-Methoxyphenyl]-2-Pyrrolidinone
DB01959phosphodiesterase 4B, cAMP-specificexperimental3,5-Dimethyl-1-(3-Nitrophenyl)-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester
DB02660phosphodiesterase 4B, cAMP-specificexperimentalFilaminast
DB03349phosphodiesterase 4B, cAMP-specificexperimental8-Bromo-Adenosine-5'-Monophosphate
DB03606phosphodiesterase 4B, cAMP-specificexperimental(S)-Rolipram
DB03807phosphodiesterase 4B, cAMP-specificexperimental1-(2-Chlorophenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester
DB03849phosphodiesterase 4B, cAMP-specificexperimentalCis-4-Cyano-4-[3-(Cyclopentyloxy)-4-Methoxyphenyl]Cyclohexanecarboxylic Acid
DB04149phosphodiesterase 4B, cAMP-specificexperimental(R)-Rolipram
DB04530phosphodiesterase 4B, cAMP-specificexperimentalS,S-(2-Hydroxyethyl)Thiocysteine
DB05266phosphodiesterase 4B, cAMP-specificapproved; investigationalIbudilast
DB06909phosphodiesterase 4B, cAMP-specificexperimental1-ethyl-N-(phenylmethyl)-4-(tetrahydro-2H-pyran-4-ylamino)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide
DB08299phosphodiesterase 4B, cAMP-specificexperimental4-[8-(3-nitrophenyl)-1,7-naphthyridin-6-yl]benzoic acid
DB01151phosphodiesterase 4B, cAMP-specificapprovedDesipramine
DB00472phosphodiesterase 4B, cAMP-specificapprovedFluoxetine


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Cross referenced IDs for PDE4B
* 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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