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 PTGDS
Basic gene info.Gene symbolPTGDS
Gene nameprostaglandin D2 synthase 21kDa (brain)
SynonymsL-PGDS|LPGDS|PDS|PGD2|PGDS|PGDS2
CytomapUCSC genome browser: 9q34.2-q34.3
Genomic locationchr9 :139871955-139876194
Type of geneprotein-coding
RefGenesNM_000954.5,
Ensembl idENSG00000107317
DescriptionPGD2 synthasebeta-trace proteincerebrin-28glutathione-independent PGD synthaseglutathione-independent PGD synthetaselipocalin-type prostaglandin D synthaselipocalin-type prostaglandin-D synthaseprostaglandin D synthaseprostaglandin-D2 synthasepro
Modification date20141207
dbXrefs MIM : 176803
HGNC : HGNC
Ensembl : ENSG00000107317
HPRD : 08904
Vega : OTTHUMG00000020957
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PTGDS
BioGPS: 5730
Gene Expression Atlas: ENSG00000107317
The Human Protein Atlas: ENSG00000107317
PathwayNCI Pathway Interaction Database: PTGDS
KEGG: PTGDS
REACTOME: PTGDS
ConsensusPathDB
Pathway Commons: PTGDS
MetabolismMetaCyc: PTGDS
HUMANCyc: PTGDS
RegulationEnsembl's Regulation: ENSG00000107317
miRBase: chr9 :139,871,955-139,876,194
TargetScan: NM_000954
cisRED: ENSG00000107317
ContextiHOP: PTGDS
cancer metabolism search in PubMed: PTGDS
UCL Cancer Institute: PTGDS
Assigned class in ccmGDBC

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Phenotypic Information for PTGDS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PTGDS
Familial Cancer Database: PTGDS
* 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_ARACHIDONIC_ACID_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PTGDS
MedGen: PTGDS (Human Medical Genetics with Condition)
ClinVar: PTGDS
PhenotypeMGI: PTGDS (International Mouse Phenotyping Consortium)
PhenomicDB: PTGDS

Mutations for PTGDS
* 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 PTGDS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CB153680PTGDS2909139871956139872044HIP1R8554212123343442123344782
DA811774PTGDS13549139871956139873699HKR1349637193785372237854005
AJ711203PTGDS1679139871977139872044MYL76339374417846644179968
AJ711202PTGDS12789139871977139872044MYL77440474417846644179968
Z17825SRRM221451628133062813449PTGDS1372549139871956139872075
DA262936PTGDS14569139871956139874447DIP2C45355910709466709572
BC094690MYBPC21918195093616050945535PTGDS91616219139872062139876194
BQ950270PTGDS12659139876117139876170PTGDS578299139871961139876144
AW316630PTGDS14029139874404139876196FAM63A3974911150970227150970623
EB387717PTGDS11679139871994139872160SIDT216375811117052160117053256

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
There's no copy number variation information in COSMIC data for this gene.

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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=13)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr9:139872039-139872039p.T3T2
chr9:139874450-139874450p.Y128*2
chr9:139874487-139874487p.E141K2
chr9:139874654-139874654p.R156R1
chr9:139873565-139873565p.L79V1
chr9:139875307-139875307p.*191Y1
chr9:139873680-139873680p.N87S1
chr9:139872048-139872048p.T6T1
chr9:139873688-139873688p.E90K1
chr9:139872093-139872093p.Q21H1

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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
# sample1  2    1  2 1  21 3
# mutation1  2    1  2 1  31 3
nonsynonymous SNV   2    1  2    11 3
synonymous SNV1            1  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
chr9:139873751p.H111N2
chr9:139873732p.F34Y1
chr9:139872093p.K38K1
chr9:139872131p.R42H1
chr9:139874454p.L48L1
chr9:139872144p.L62L1
chr9:139874654p.V69M1
chr9:139873455p.D74N1
chr9:139873474p.N87S1
chr9:139873514p.A99E1

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 PTGDS 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 PTGDS

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

MILR1,CD248,CLEC4GP1,DAZL,DEFB124,FOLR2,GP9,
HES3,LAMC3,LCE3C,LCE3D,LCE3E,LCNL1,MMP9,
LINC00162,PCOLCE,PF4,PTGDS,SPON2,SPRR2G,XPNPEP2
ABI3,CCL19,CD74,CD7,CST7,EBI3,FCGR1A,
FCGR1B,FCGR1C,GNGT2,GRAP,GZMM,IFITM3,LAT2,
PTGDS,RBP5,S1PR4,SLC2A6,SPNS3,IGFLR1,TMIGD2

ABI3BP,ANK2,CCL19,CD37,CYSLTR1,GAPT,GFRA2,
GIMAP7,TP73-AS1,TESPA1,MFNG,MUSK,NAPSB,PPP1R16B,
PRKCB,PTGDS,RBP5,RSPO1,SCN4B,SLC9A9,TDRD10
AADACL4,BPIFB4,C4A,CDH3,CNBD1,CPXM1,CR1,
DEFB124,DPYS,DYDC1,FAM26D,GLYCAM1,IGFN1,LIM2,
MARCO,OR3A4P,PTGDS,SCGB1A1,SCGB3A1,SNORA22,TIMD4
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 PTGDS
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
DB00482prostaglandin D2 synthase 21kDa (brain)approved; investigationalCelecoxib


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Cross referenced IDs for PTGDS
* 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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