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 PDE1A
Basic gene info.Gene symbolPDE1A
Gene namephosphodiesterase 1A, calmodulin-dependent
SynonymsCAM-PDE-1A|HCAM-1|HCAM1|HSPDE1A
CytomapUCSC genome browser: 2q32.1
Genomic locationchr2 :183004761-183387572
Type of geneprotein-coding
RefGenesNM_001003683.2,
NM_001258312.1,NM_001258313.1,NM_001258314.1,NM_005019.4,
Ensembl idENSG00000115252
Description61 kDa Cam-PDEcalcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1Acalcium/calmodulin-stimulated cyclic nucleotide phosphodiesterasecam-PDE 1A
Modification date20141207
dbXrefs MIM : 171890
HGNC : HGNC
Ensembl : ENSG00000115252
HPRD : 01387
Vega : OTTHUMG00000132596
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE1A
BioGPS: 5136
Gene Expression Atlas: ENSG00000115252
The Human Protein Atlas: ENSG00000115252
PathwayNCI Pathway Interaction Database: PDE1A
KEGG: PDE1A
REACTOME: PDE1A
ConsensusPathDB
Pathway Commons: PDE1A
MetabolismMetaCyc: PDE1A
HUMANCyc: PDE1A
RegulationEnsembl's Regulation: ENSG00000115252
miRBase: chr2 :183,004,761-183,387,572
TargetScan: NM_001003683
cisRED: ENSG00000115252
ContextiHOP: PDE1A
cancer metabolism search in PubMed: PDE1A
UCL Cancer Institute: PDE1A
Assigned class in ccmGDBC

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Phenotypic Information for PDE1A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE1A
Familial Cancer Database: PDE1A
* 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: PDE1A
MedGen: PDE1A (Human Medical Genetics with Condition)
ClinVar: PDE1A
PhenotypeMGI: PDE1A (International Mouse Phenotyping Consortium)
PhenomicDB: PDE1A

Mutations for PDE1A
* 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
breastPDE1Achr2183109919183109919PDE1Achr2183160405183160405
ovaryPDE1Achr2183096810183096830chr2182255924182255944
ovaryPDE1Achr2183100158183100178PDE1Achr2183100213183100233
ovaryPDE1Achr2183142203183142223PDE1Achr2183132979183132999
ovaryPDE1Achr2183154196183154396PDE1Achr2183153714183153914
ovaryPDE1Achr2183199308183199328PDE1Achr2183203436183203456
ovaryPDE1Achr2183216139183216159PDE1Achr2183225576183225596
ovaryPDE1Achr2183216144183216164PDE1Achr2183225576183225596
ovaryPDE1Achr2183333201183333221PDE1Achr2183333598183333618
pancreasPDE1Achr2183044703183044723PDE1Achr2183191703183191723
pancreasPDE1Achr2183187964183187984PDE1Achr2183192328183192348
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 PDE1A 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 # sample2       4 5      
GAIN (# sample)2       3 5      
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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=73)
Stat. for Synonymous SNVs
(# total SNVs=12)
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
chr2:183104880-183104880p.R119W5
chr2:183053786-183053786p.G392E5
chr2:183104955-183104955p.R94W5
chr2:183095762-183095762p.D188N4
chr2:183066172-183066172p.F389F4
chr2:183387016-183387016p.R30C3
chr2:183104895-183104895p.E114K3
chr2:183070702-183070702p.M305I3
chr2:183053739-183053739p.R408W3
chr2:183104852-183104852p.G128E2

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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
# sample22 82 3 1  961  337115
# mutation22 82 3 1  961  317117
nonsynonymous SNV22 71 3 1  731  256114
synonymous SNV   11      23   61 3
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
chr2:183104955p.R60R,PDE1A4
chr2:183095762p.G358V,PDE1A3
chr2:183053786p.D154N,PDE1A3
chr2:183104880p.R85W,PDE1A3
chr2:183070702p.M271I,PDE1A2
chr2:183099217p.F355F,PDE1A2
chr2:183053739p.R102Q,PDE1A2
chr2:183104855p.V34V,PDE1A2
chr2:183066172p.A93G,PDE1A2
chr2:183104895p.R374W,PDE1A2

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 PDE1A 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 PDE1A

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

CCDC80,CD93,CNRIP1,COL14A1,CXorf36,ELTD1,EMCN,
ERG,IGF1,JAM2,LDB2,LHFP,MYCT1,PDE1A,
PEAR1,PREX2,PTPRB,RHOJ,SLIT2,SPARCL1,TEK
CD34,CLIC2,EMCN,HOXD8,HSD17B11,JAZF1,LHFP,
LOC644538,MEOX2,MYCT1,NEGR1,OLFML1,PDE1A,PGM5,
PLS3,PMP22,PRRX1,SEPT7,SYT11,TCF4,TEK

BOC,C1R,C1S,CNRIP1,COL14A1,DOK5,DZIP1,
FAM110B,FBLN1,FBLN5,FLRT2,JAM2,LHFP,LOC399959,
MGP,PABPC5,PDE1A,PODN,RBMS3,RNF180,RUNX1T1
AP1S2,ARL3,ARL6,FAM229B,CFAP36,DNAJC18,EID1,
FAM195B,FAM92A1,FEZ1,FKBP7,GNG11,IGFBP7,KIAA0895,
KPNA5,MAGED2,PDE1A,SELM,TAF9B,TCEAL1,ZNF25
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 PDE1A
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
DB00622phosphodiesterase 1A, calmodulin-dependentapprovedNicardipine
DB01023phosphodiesterase 1A, calmodulin-dependentapproved; investigationalFelodipine
DB01244phosphodiesterase 1A, calmodulin-dependentapprovedBepridil
DB00472phosphodiesterase 1A, calmodulin-dependentapprovedFluoxetine


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Cross referenced IDs for PDE1A
* 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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