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 PDE4C
Basic gene info.Gene symbolPDE4C
Gene namephosphodiesterase 4C, cAMP-specific
SynonymsDPDE1
CytomapUCSC genome browser: 19p13.11
Genomic locationchr19 :18318770-18337285
Type of geneprotein-coding
RefGenesNM_000923.4,
NM_001098818.2,NM_001098819.2,NR_040546.1,
Ensembl idENSG00000105650
DescriptionPDE21cAMP-specific 3',5'-cyclic phosphodiesterase 4Cphosphodiesterase 4C, cAMP-specific (phosphodiesterase E1 dunce homolog, Drosophila)phosphodiesterase E1 dunce homolog
Modification date20141207
dbXrefs MIM : 600128
HGNC : HGNC
Ensembl : ENSG00000105650
HPRD : 02529
Vega : OTTHUMG00000183353
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE4C
BioGPS: 5143
Gene Expression Atlas: ENSG00000105650
The Human Protein Atlas: ENSG00000105650
PathwayNCI Pathway Interaction Database: PDE4C
KEGG: PDE4C
REACTOME: PDE4C
ConsensusPathDB
Pathway Commons: PDE4C
MetabolismMetaCyc: PDE4C
HUMANCyc: PDE4C
RegulationEnsembl's Regulation: ENSG00000105650
miRBase: chr19 :18,318,770-18,337,285
TargetScan: NM_000923
cisRED: ENSG00000105650
ContextiHOP: PDE4C
cancer metabolism search in PubMed: PDE4C
UCL Cancer Institute: PDE4C
Assigned class in ccmGDBC

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Phenotypic Information for PDE4C(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE4C
Familial Cancer Database: PDE4C
* 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: PDE4C
MedGen: PDE4C (Human Medical Genetics with Condition)
ClinVar: PDE4C
PhenotypeMGI: PDE4C (International Mouse Phenotyping Consortium)
PhenomicDB: PDE4C

Mutations for PDE4C
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PDE4C related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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                
GAIN (# sample)1                
LOSS (# sample)                 
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=50)
Stat. for Synonymous SNVs
(# total SNVs=29)
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
chr19:18327613-18327613p.D475N3
chr19:18331215-18331215p.K236*3
chr19:18321934-18321934p.P648P2
chr19:18329784-18329784p.R344Q2
chr19:18333048-18333048p.P110S2
chr19:18331077-18331077p.S254F2
chr19:18328995-18328995p.H432Y2
chr19:18322678-18322678p.T561M2
chr19:18332983-18332983p.S131S2
chr19:18327665-18327665p.L457L2

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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
# sample27 72 3 6  55211204 6
# mutation27 82 3 6  55211274 6
nonsynonymous SNV15 5  2 5  34111183 4
synonymous SNV12 32 1 1  211  91 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
chr19:18328995p.D443N,PDE4C2
chr19:18327613p.T529M,PDE4C2
chr19:18327665p.L425L,PDE4C2
chr19:18327666p.L425P,PDE4C2
chr19:18322678p.P616P,PDE4C2
chr19:18321934p.H400N,PDE4C2
chr19:18327582p.R232R,PDE4C1
chr19:18331127p.R60R,PDE4C1
chr19:18321983p.D590N,PDE4C1
chr19:18332997p.L456Q,PDE4C1

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 PDE4C 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 PDE4C

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

ALPP,ALPPL2,C1orf87,DEFB104A,DNAJB13,FAM181A,GDA,
IHH,LEFTY1,LIMS3,LIMS3-LOC440895,LOC647309,MOS,NKX6-2,
ONECUT3,PDE4C,PKHD1L1,SCGB1A1,SERPINA4,SOX17,TRIM31
ALDH1B1,C20orf166-AS1,MAP3K7CL,CAMK2G,CASQ2,DGKG,DMPK,
INPP5A,ITIH4,KCNA5,LGI1,LOC401093,MT3,MUSTN1,
PDE4C,POU4F1,PPP1R12B,PRKG1,RCAN2,SUSD5,TYRP1

ABCC3,B3GALT5,CIB1,DNM2,ETHE1,GPA33,HYAL1,
IL1R2,KIAA1522,KIAA1683,LIMA1,LIPH,MPPE1,NPAS1,
OCEL1,PDE4C,SCAMP2,SULT1C2,TMEM92,TSPAN1,TSPAN15
ARHGAP36,SMIM14,CRYM,EVPLL,GGT7,HPCA,ILDR1,
IMPA2,IP6K2,LOC100130872,LRRC31,PDE4C,PLBD1,RAB40B,
SAMD13,SMPDL3B,TSSK6,VSIG2,ZNF223,ZNF552,ZNF774
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 PDE4C
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
DB00651phosphodiesterase 4C, cAMP-specificapprovedDyphylline
DB00920phosphodiesterase 4C, cAMP-specificapprovedKetotifen
DB01088phosphodiesterase 4C, cAMP-specificapproved; investigationalIloprost
DB01791phosphodiesterase 4C, cAMP-specificexperimentalPiclamilast
DB05266phosphodiesterase 4C, cAMP-specificapproved; investigationalIbudilast
DB01151phosphodiesterase 4C, cAMP-specificapprovedDesipramine
DB00472phosphodiesterase 4C, cAMP-specificapprovedFluoxetine


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Cross referenced IDs for PDE4C
* 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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