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 PDE11A
Basic gene info.Gene symbolPDE11A
Gene namephosphodiesterase 11A
SynonymsPPNAD2
CytomapUCSC genome browser: 2q31.2
Genomic locationchr2 :178487976-178753466
Type of geneprotein-coding
RefGenesNM_001077196.1,
NM_001077197.1,NM_001077358.1,NM_016953.3,
Ensembl idENSG00000128655
DescriptioncAMP and cGMP cyclic nucleotide phosphodiesterase 11Adual 3',5'-cyclic-AMP and -GMP phosphodiesterase 11A
Modification date20141207
dbXrefs MIM : 604961
HGNC : HGNC
Ensembl : ENSG00000128655
HPRD : 05391
Vega : OTTHUMG00000154188
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE11A
BioGPS: 50940
Gene Expression Atlas: ENSG00000128655
The Human Protein Atlas: ENSG00000128655
PathwayNCI Pathway Interaction Database: PDE11A
KEGG: PDE11A
REACTOME: PDE11A
ConsensusPathDB
Pathway Commons: PDE11A
MetabolismMetaCyc: PDE11A
HUMANCyc: PDE11A
RegulationEnsembl's Regulation: ENSG00000128655
miRBase: chr2 :178,487,976-178,753,466
TargetScan: NM_001077196
cisRED: ENSG00000128655
ContextiHOP: PDE11A
cancer metabolism search in PubMed: PDE11A
UCL Cancer Institute: PDE11A
Assigned class in ccmGDBC

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Phenotypic Information for PDE11A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE11A
Familial Cancer Database: PDE11A
* 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: PDE11A
MedGen: PDE11A (Human Medical Genetics with Condition)
ClinVar: PDE11A
PhenotypeMGI: PDE11A (International Mouse Phenotyping Consortium)
PhenomicDB: PDE11A

Mutations for PDE11A
* 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
ovaryPDE11Achr2178540994178541014AGPSchr2178333736178333756
ovaryPDE11Achr2178564144178564164chr2178474299178474319
ovaryPDE11Achr2178586196178586216PDE11Achr2178611116178611136
ovaryPDE11Achr2178599056178599076PDE11Achr2178589388178589408
ovaryPDE11Achr2178710162178710362VPS53chr17501500501700
ovaryPDE11Achr2178712953178712973PDE11Achr2178713040178713060
ovaryPDE11Achr2178716794178716814chr88231428382314303
ovaryPDE11Achr2178747048178747068PDE11Achr2178747635178747655
pancreasPDE11Achr2178506304178506324chr2201026809201026829
pancreasPDE11Achr2178713937178713957DNAH7chr2196766693196766713
pancreasPDE11Achr2178724084178724104AGPSchr2178393876178393896
pancreasPDE11Achr2178729550178729570LRP2chr2170122894170122914
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 PDE11A 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 # sample21 1  1 3 1      
GAIN (# sample)21 1    3 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=12

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=104)
Stat. for Synonymous SNVs
(# total SNVs=43)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=19)
There's no deleted 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
chr2:178494183-178494183p.A918A11
chr2:178494178-178494179p.S920_S921insA10
chr2:178937004-178937004p.S54F3
chr2:178494179-178494180p.S919_S920insP3
chr2:178879164-178879164p.I312I3
chr2:178879077-178879077p.A341A3
chr2:178762794-178762794p.I431I3
chr2:178682603-178682603p.A542A2
chr2:178762823-178762823p.R422C2
chr2:178545555-178545555p.R808*2

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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
# sample842182 4 41 18127  196 12
# mutation842202 4 41 21137  257 12
nonsynonymous SNV742142 2 41 16125  183 10
synonymous SNV1  6  2    512  74 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
chr2:178762794p.I73I,PDE11A3
chr2:178705092p.Y48C,PDE11A2
chr2:178936561p.E18E,PDE11A2
chr2:178565928p.A341V,PDE11A2
chr2:178879182p.A278V,PDE11A2
chr2:178879078p.R185L,PDE11A2
chr2:178705003p.R306R,PDE11A2
chr2:178592803p.R202C2
chr2:178762914p.D50N,PDE11A1
chr2:178936519p.A15V,PDE11A1

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 PDE11A 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 PDE11A

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

BTN1A1,CD14,CD180,DMBT1,EDN3,GNLY,IGFL4,
KIR2DL3,LIPG,MRGPRX3,NOS1,OLAH,PDE11A,PGA5,
PTN,SST,TGFBR2,TMEM100,TMEM233,VNN1,XDH
ANKRD40,EPDR1,HSDL2,IDH3A,LOC100128164,MAP2K1,PDE11A,
QKI,RAD23B,RTN4,SAMD4A,SEC23A,SETD7,SGCB,
SH3GLB1,TMEM56,TTC7B,UGP2,YPEL2,YWHAG,ZEB1

ACACA,ALS2CR11,ATP1A1,CYFIP2,DACH1,DLX3,F10,
FREM2,KSR1,LOC100188947,MAN1A1,PDE11A,SCN8A,SEL1L3,
SLC24A1,SYK,TMC2,EWSAT1,TRPM3,TTTY2,TTTY7
ACSL3,ADAMTS9,C6orf223,DHCR7,DNAJC10,DPY19L1,HIF1A,
IL1RL1,INSIG1,LARP4,LIPG,LRP8,MUC4,MUC5B,
NRGN,PCSK9,PDE11A,SEC23IP,SLC7A1,SQLE,SYNCRIP
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 PDE11A
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
DB00820phosphodiesterase 11Aapproved; investigationalTadalafil
DB00472phosphodiesterase 11AapprovedFluoxetine


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Cross referenced IDs for PDE11A
* 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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