Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 PDE4D
Basic gene info.Gene symbolPDE4D
Gene namephosphodiesterase 4D, cAMP-specific
SynonymsACRDYS2|DPDE3|HSPDE4D|PDE43|PDE4DN2|STRK1
CytomapUCSC genome browser: 5q12
Genomic locationchr5 :58264865-58295759
Type of geneprotein-coding
RefGenesNM_001104631.1,
NM_001165899.1,NM_001197218.1,NM_001197219.1,NM_001197220.1,
NM_001197221.1,NM_001197222.1,NM_001197223.1,NM_006203.4,
Ensembl idENSG00000113448
DescriptioncAMP-specific 3',5'-cyclic phosphodiesterase 4DcAMP-specific phosphodiesterase PDE4D6phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila)
Modification date20141207
dbXrefs MIM : 600129
HGNC : HGNC
Ensembl : ENSG00000113448
HPRD : 02530
Vega : OTTHUMG00000162218
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE4D
BioGPS: 5144
Gene Expression Atlas: ENSG00000113448
The Human Protein Atlas: ENSG00000113448
PathwayNCI Pathway Interaction Database: PDE4D
KEGG: PDE4D
REACTOME: PDE4D
ConsensusPathDB
Pathway Commons: PDE4D
MetabolismMetaCyc: PDE4D
HUMANCyc: PDE4D
RegulationEnsembl's Regulation: ENSG00000113448
miRBase: chr5 :58,264,865-58,295,759
TargetScan: NM_001104631
cisRED: ENSG00000113448
ContextiHOP: PDE4D
cancer metabolism search in PubMed: PDE4D
UCL Cancer Institute: PDE4D
Assigned class in ccmGDBC

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Phenotypic Information for PDE4D(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE4D
Familial Cancer Database: PDE4D
* 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: PDE4D
MedGen: PDE4D (Human Medical Genetics with Condition)
ClinVar: PDE4D
PhenotypeMGI: PDE4D (International Mouse Phenotyping Consortium)
PhenomicDB: PDE4D

Mutations for PDE4D
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
prostatePDE4Dchr55962198559623985NCOR2chr12124837154124839154
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 PDE4D related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA282561PDE4D110055912953759129636AGPAT41015756161587303161695030
DB236218PDE4D121055906407159064280SLC16A9208580106141407261424081
BE928480REPS1682996139228509139228740PDE4D29932555938675159386781
AW993560TAB281606149684678149684831PDE4D14634255895080258950999
BI019872RAB3714226177270077672700988PDE4D21937355835130158351453
DA522054PDE4D126755888368458883950KCTD2261561177305985773060153
BF367933PDE4D113955949555859495702PDE4D13341455949567859495960
DW442273PDE4D1714955867644158676572PDE4D14523555867708558677175
BF917173PDE4D144555844597658446420KIAA1217431605102483509524835269

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        1 2      
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=52)
Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr5:58511596-58511596p.?3
chr5:58270597-58270597p.S639C2
chr5:58285638-58285638p.H330N2
chr5:58271593-58271593p.T499M2
chr5:58271602-58271602p.R496H1
chr5:58289244-58289244p.R188W1
chr5:58270586-58270586p.P643S1
chr5:58273027-58273027p.V430V1
chr5:58489358-58489358p.G82R1
chr5:58511757-58511757p.P29S1

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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
# sample26 10  6 2  751  103 10
# mutation26 10  6 2  751  103 14
nonsynonymous SNV26 9  5 1  521  81 10
synonymous SNV   1  1 1  23   22 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
chr5:58271593p.R237Q,PDE4D2
chr5:58481063p.R44P2
chr5:59284456p.T411M,PDE4D2
chr5:58273031p.A15A1
chr5:59064319p.P555S,PDE4D1
chr5:58270586p.D383N,PDE4D1
chr5:58289223p.E107Q,PDE4D1
chr5:59284542p.H3H1
chr5:58271518p.R61I1
chr5:58511729p.S551C,PDE4D1

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 PDE4D 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 PDE4D

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

AVPI1,C19orf57,LINC00473,CXCL5,ECEL1,EYA4,FLJ45079,
FYN,LOC441177,LSAMP,MAPK4,MCTP2,PDE3A,PDE4D,
PLD1,PON1,PPARGC1A,PTP4A1,SLC7A5,SMOC1,SPINK6
ACTC1,AGL,ART3,ASB2,ATP2A2,BVES,CTNNA3,
DCAF6,DES,FLNC,FNDC5,KCNT1,LRRC2,MEF2C,
NEXN,PDE4D,PHTF2,PLN,SGCA,SLC8A3,TMEM233

AKAP13,TMEM263,CRYBG3,ELL2,FAM114A1,IKZF2,IL6ST,
KLF9,LHFPL2,MEF2A,PDE4B,PDE4D,PDE5A,PJA2,
PLCL2,PPP1R12A,RAB27A,RAB8B,SGMS2,SNRK,TMTC2
ABI2,AMIGO2,ARHGAP23,DCBLD2,DENND5A,ENAH,FAM124A,
FAM129A,FGF12,HSPA2,MAP9,MASP1,MPDZ,MTMR9,
MYOCD,PDE4D,PKD2,PRKAA2,SRF,VGLL3,WWC2
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 PDE4D
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
DB00131phosphodiesterase 4D, cAMP-specificapproved; nutraceuticalAdenosine monophosphate
DB00651phosphodiesterase 4D, cAMP-specificapprovedDyphylline
DB00920phosphodiesterase 4D, cAMP-specificapprovedKetotifen
DB01088phosphodiesterase 4D, cAMP-specificapproved; investigationalIloprost
DB01791phosphodiesterase 4D, cAMP-specificexperimentalPiclamilast
DB01954phosphodiesterase 4D, cAMP-specificexperimental4-[3-(Cyclopentyloxy)-4-Methoxyphenyl]-2-Pyrrolidinone
DB01959phosphodiesterase 4D, cAMP-specificexperimental3,5-Dimethyl-1-(3-Nitrophenyl)-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester
DB02676phosphodiesterase 4D, cAMP-specificexperimental2-[3-(2-Hydroxy-1,1-Dihydroxymethyl-Ethylamino)-Propylamino]-2-Hydroxymethyl-Propane-1,3-Diol
DB02918phosphodiesterase 4D, cAMP-specificexperimental6-(4-Difluoromethoxy-3-Methoxy-Phenyl)-2h-Pyridazin-3-One
DB03183phosphodiesterase 4D, cAMP-specificexperimental1-(4-Aminophenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester
DB03606phosphodiesterase 4D, cAMP-specificexperimental(S)-Rolipram
DB03849phosphodiesterase 4D, cAMP-specificexperimentalCis-4-Cyano-4-[3-(Cyclopentyloxy)-4-Methoxyphenyl]Cyclohexanecarboxylic Acid
DB04149phosphodiesterase 4D, cAMP-specificexperimental(R)-Rolipram
DB04271phosphodiesterase 4D, cAMP-specificexperimental3,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester
DB04469phosphodiesterase 4D, cAMP-specificexperimental1-(4-Methoxyphenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester
DB05266phosphodiesterase 4D, cAMP-specificapproved; investigationalIbudilast
DB06842phosphodiesterase 4D, cAMP-specificexperimental(4R)-4-(3-butoxy-4-methoxybenzyl)imidazolidin-2-one
DB07051phosphodiesterase 4D, cAMP-specificexperimental3,5-DIMETHYL-1-PHENYL-1H-PYRAZOLE-4-CARBOXYLIC ACID ETHYL ESTER
DB07954phosphodiesterase 4D, cAMP-specificexperimental3-ISOBUTYL-1-METHYLXANTHINE
DB08299phosphodiesterase 4D, cAMP-specificexperimental4-[8-(3-nitrophenyl)-1,7-naphthyridin-6-yl]benzoic acid
DB01151phosphodiesterase 4D, cAMP-specificapprovedDesipramine
DB00472phosphodiesterase 4D, cAMP-specificapprovedFluoxetine
DB00465phosphodiesterase 4D, cAMP-specificapprovedKetorolac
DB00533phosphodiesterase 4D, cAMP-specificwithdrawn; investigationalRofecoxib


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Cross referenced IDs for PDE4D
* 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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