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 HPGDS
Basic gene info.Gene symbolHPGDS
Gene namehematopoietic prostaglandin D synthase
SynonymsGSTS|GSTS1-1|PGD2|PGDS
CytomapUCSC genome browser: 4q22.3
Genomic locationchr4 :95219706-95264027
Type of geneprotein-coding
RefGenesNM_014485.2,
Ensembl idENSG00000163106
DescriptionGST class-sigmaglutathione S-transferase sigmaglutathione-dependent PGD synthaseglutathione-dependent PGD synthetaseglutathione-requiring prostaglandin D synthasehematopoietic prostaglandin D2 synthaseprostaglandin-H2 D-isomerase
Modification date20141207
dbXrefs MIM : 602598
HGNC : HGNC
Ensembl : ENSG00000163106
HPRD : 04001
Vega : OTTHUMG00000130974
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HPGDS
BioGPS: 27306
Gene Expression Atlas: ENSG00000163106
The Human Protein Atlas: ENSG00000163106
PathwayNCI Pathway Interaction Database: HPGDS
KEGG: HPGDS
REACTOME: HPGDS
ConsensusPathDB
Pathway Commons: HPGDS
MetabolismMetaCyc: HPGDS
HUMANCyc: HPGDS
RegulationEnsembl's Regulation: ENSG00000163106
miRBase: chr4 :95,219,706-95,264,027
TargetScan: NM_014485
cisRED: ENSG00000163106
ContextiHOP: HPGDS
cancer metabolism search in PubMed: HPGDS
UCL Cancer Institute: HPGDS
Assigned class in ccmGDBC

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

Mutations for HPGDS
* 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 HPGDS 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
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=3)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr4:95220653-95220653p.R193Q2
chr4:95223325-95223325p.G136V1
chr4:95239059-95239059p.S64I1
chr4:95223334-95223334p.T133K1
chr4:95239087-95239087p.E55K1
chr4:95223336-95223336p.D132D1
chr4:95239089-95239089p.L54fs*121
chr4:95220654-95220654p.R193*1
chr4:95223384-95223384p.F116F1
chr4:95239101-95239101p.K50R1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1211  1 1  21   51 2
# mutation1211  1 1  21   51 2
nonsynonymous SNV12 1    1  1    31 2
synonymous SNV  1   1    11   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
chr4:95255745p.G79E1
chr4:95223375p.A78V1
chr4:95223384p.I67K1
chr4:95229885p.S64I1
chr4:95220653p.E55K1
chr4:95229888p.K50R1
chr4:95220656p.R193L1
chr4:95239050p.D38N1
chr4:95220697p.K192R1
chr4:95239059p.Y29H1

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 HPGDS 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 HPGDS

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

ALOX5AP,GCSAML,CDK15,CNRIP1,COPZ2,CPA3,CX3CR1,
DCN,GATA1,GPR34,HPGDS,HTRA1,LILRA2,LY86,
MMP2,MS4A2,PDGFRL,RASGRP4,SIGLEC6,SIGLEC17P,TREM2
BCAT1,C3AR1,CD209,CD33,CTSC,DAB2,FCER1G,
FCGR2B,FOLR2,HPGDS,HRH1,LGMN,LOC283070,MRC1,
MS4A4A,MS4A6A,RASGRP4,RNASE1,S100A10,SLC24A4,TLR8

A2M,ARHGAP20,C1orf186,C1S,CCR8,CD1C,CD1E,
CPA3,CTSG,FAM180A,FCER1A,GAS7,HPGDS,MS4A2,
PLD4,RELN,SIGLEC17P,SLC18A2,TIMP3,TM6SF1,VCAM1
AVIL,AZGP1,BMX,C10orf67,C11orf53,APMAP,CCDC129,
GNG13,HMX2,HPGDS,HTR3C,HTR3E,KCNV1,KIFAP3,
KLK13,POU2F3,PSTPIP2,PTGER2,SH2D6,SH2D7,TRPM5
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 HPGDS
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
DB00143hematopoietic prostaglandin D synthaseapproved; nutraceuticalGlutathione
DB01897hematopoietic prostaglandin D synthaseexperimental2-(2f-Benzothiazolyl)-5-Styryl-3-(4f-Phthalhydrazidyl)Tetrazolium Chloride
DB04077hematopoietic prostaglandin D synthaseexperimentalGlycerol
DB07613hematopoietic prostaglandin D synthaseexperimental3-phenyl-5-(1H-pyrazol-3-yl)isoxazole
DB07614hematopoietic prostaglandin D synthaseexperimentalPHENYL-5-(1H-PYRAZOL-3-YL)-1,3-THIAZOLE
DB07615hematopoietic prostaglandin D synthaseexperimental2-{[(2E)-3-(3,4-dimethoxyphenyl)prop-2-enoyl]amino}benzoic acid
DB07616hematopoietic prostaglandin D synthaseexperimental4-{[4-(4-fluoro-3-methylphenyl)-1,3-thiazol-2-yl]amino}-2-hydroxybenzoic acid
DB07917hematopoietic prostaglandin D synthaseexperimental4-(BENZHYDRYLOXY)-1-[3-(1H-TETRAAZOL-5-YL)PROPYL]PIPERIDINE
DB08313hematopoietic prostaglandin D synthaseexperimentalnocodazole
DB08695hematopoietic prostaglandin D synthaseexperimental3-(4-nitrophenyl)-1H-pyrazole
DB08790hematopoietic prostaglandin D synthaseexperimental1-PHENYL-1H-PYRAZOLE-4-CARBOXYLIC ACID


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Cross referenced IDs for HPGDS
* 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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