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 PDE1C
Basic gene info.Gene symbolPDE1C
Gene namephosphodiesterase 1C, calmodulin-dependent 70kDa
SynonymsHcam3|cam-PDE 1C|hCam-3
CytomapUCSC genome browser: 7p14.3
Genomic locationchr7 :31792631-32110980
Type of geneprotein-coding
RefGenesNM_001191056.2,
NM_001191057.2,NM_001191058.2,NM_001191059.2,NM_005020.3,
Ensembl idENSG00000154678
DescriptionHuman 3',5' cyclic nucleotide phosphodiesterase (HSPDE1C1A)calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C
Modification date20141207
dbXrefs MIM : 602987
HGNC : HGNC
Ensembl : ENSG00000154678
HPRD : 04287
Vega : OTTHUMG00000023836
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE1C
BioGPS: 5137
Gene Expression Atlas: ENSG00000154678
The Human Protein Atlas: ENSG00000154678
PathwayNCI Pathway Interaction Database: PDE1C
KEGG: PDE1C
REACTOME: PDE1C
ConsensusPathDB
Pathway Commons: PDE1C
MetabolismMetaCyc: PDE1C
HUMANCyc: PDE1C
RegulationEnsembl's Regulation: ENSG00000154678
miRBase: chr7 :31,792,631-32,110,980
TargetScan: NM_001191056
cisRED: ENSG00000154678
ContextiHOP: PDE1C
cancer metabolism search in PubMed: PDE1C
UCL Cancer Institute: PDE1C
Assigned class in ccmGDBC

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Phenotypic Information for PDE1C(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE1C
Familial Cancer Database: PDE1C
* 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: PDE1C
MedGen: PDE1C (Human Medical Genetics with Condition)
ClinVar: PDE1C
PhenotypeMGI: PDE1C (International Mouse Phenotyping Consortium)
PhenomicDB: PDE1C

Mutations for PDE1C
* 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
breastPDE1Cchr73181806431818064LINSchr15101125974101125974
breastPDE1Cchr73196540931965409chr73367660733676607
breastPDE1Cchr73196660831966608chr159066556490665564
breastPDE1Cchr73198355931983559chr8123026791123026791
ovaryPDE1Cchr73196375831963778PDE1Cchr73196189731961917
ovaryPDE1Cchr73204659832046618PDE1Cchr73204666432046684
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 PDE1C related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
H11830SETX13489135145001135150759PDE1C33635873210893532108957
AV724221PDE1C142573208872432089152LAT242160477364377873643964
AA247844PDE1C120173182561131825812PDE1C19625573182955731829617

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 # sample22   13 7 1 1 115
GAIN (# sample)12   13 6 1 1 115
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=133)
Stat. for Synonymous SNVs
(# total SNVs=34)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
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
chr7:31890295-31890295p.E271Q4
chr7:32109912-32109912p.R32C4
chr7:31918727-31918727p.R103*4
chr7:31904603-31904603p.D235N4
chr7:31917638-31917638p.R146Q3
chr7:31864584-31864584p.V435M3
chr7:31848706-31848706p.G610G3
chr7:31890345-31890345p.T254M3
chr7:31862790-31862790p.P493P3
chr7:31918638-31918638p.H132H3

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample431174 9 11 26134124711 14
# mutation431174 9 11 30154126311 16
nonsynonymous SNV321144 7 1  18124 1425 10
synonymous SNV11 3  2  1 123 11216 6
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
chr7:31862790p.E595K,PDE1C3
chr7:31855568p.S468W,PDE1C3
chr7:31864484p.P493P,PDE1C3
chr7:31862779p.K353K,PDE1C2
chr7:32109934p.S468S,PDE1C2
chr7:31904603p.G63G2
chr7:31855612p.I702I,PDE1C2
chr7:32209516p.T273T,PDE1C2
chr7:31877484p.R518Q,PDE1C2
chr7:31793022p.G63W2

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 PDE1C 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 PDE1C

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

A2M,ANKRD1,CHST3,CYP1A2,FAM126A,GRAMD3,GRIN2A,
HEPH,ISM1,KLHL38,LOC285830,MAML2,OR2S2,PALM2,
PALM2-AKAP2,PDE1C,PROS1,SLC7A5P1,SOCS5,TTC7A,WWTR1
ABI2,ARHGAP19,CACNA1C,ESYT3,FAM83B,FAT2,GPR75,
GTF3C4,ITGA2,KIAA1217,LY75,NFASC,PAK3,PAK7,
PAWR,PCNXL2,PDE1C,SEMA5A,SIPA1L1,ZNF37BP,ZNF618

ABCG4,ADAMTS3,AKT3,CD93,CYP46A1,DYSF,EHD3,
GIPC3,IL7R,KIAA1614,LPHN2,NHSL2,PDE1C,PREX2,
PTPRN,RPH3A,SCN1B,SDK1,SLC6A17,XKR5,ZNF366
ABCA8,BMPER,PCNXL4,DIEXF,TRMT44,ERCC6L2,EIF2AK4,
FMNL2,IRAK3,KIAA0355,LOX,MYH13,PDE1C,PREX2,
PRLHR,RCAN2,SDK2,SHPRH,TGFBRAP1,TTC37,TXLNG
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 PDE1C
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
DB01151phosphodiesterase 1C, calmodulin-dependent 70kDaapprovedDesipramine


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Cross referenced IDs for PDE1C
* 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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