Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 PTGDS

Basic gene info.	Gene symbol	PTGDS
	Gene name	prostaglandin D2 synthase 21kDa (brain)
	Synonyms	L-PGDS\|LPGDS\|PDS\|PGD2\|PGDS\|PGDS2
	Cytomap	UCSC genome browser: 9q34.2-q34.3
	Genomic location	chr9 :139871955-139876194
	Type of gene	protein-coding
	RefGenes	NM_000954.5,
	Ensembl id	ENSG00000107317
	Description	PGD2 synthasebeta-trace proteincerebrin-28glutathione-independent PGD synthaseglutathione-independent PGD synthetaselipocalin-type prostaglandin D synthaselipocalin-type prostaglandin-D synthaseprostaglandin D synthaseprostaglandin-D2 synthasepro
	Modification date	20141207
dbXrefs	MIM : 176803
	HGNC : HGNC
	Ensembl : ENSG00000107317
	HPRD : 08904
	Vega : OTTHUMG00000020957
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PTGDS
	BioGPS: 5730
	Gene Expression Atlas: ENSG00000107317
	The Human Protein Atlas: ENSG00000107317
Pathway	NCI Pathway Interaction Database: PTGDS
	KEGG: PTGDS
	REACTOME: PTGDS
	ConsensusPathDB
	Pathway Commons: PTGDS
Metabolism	MetaCyc: PTGDS
	HUMANCyc: PTGDS
Regulation	Ensembl's Regulation: ENSG00000107317
	miRBase: chr9 :139,871,955-139,876,194
	TargetScan: NM_000954
	cisRED: ENSG00000107317
Context	iHOP: PTGDS
	cancer metabolism search in PubMed: PTGDS
	UCL Cancer Institute: PTGDS
Assigned class in ccmGDB	C

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Phenotypic Information for PTGDS(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_ARACHIDONIC_ACID_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: PTGDS
	MedGen: PTGDS (Human Medical Genetics with Condition)
	ClinVar: PTGDS
Phenotype	MGI: PTGDS (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PTGDS related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
CB153680	PTGDS	2	90	9	139871956	139872044	HIP1R	85	542	12	123343442	123344782
DA811774	PTGDS	1	354	9	139871956	139873699	HKR1	349	637	19	37853722	37854005
AJ711203	PTGDS	1	67	9	139871977	139872044	MYL7	63	393	7	44178466	44179968
AJ711202	PTGDS	12	78	9	139871977	139872044	MYL7	74	404	7	44178466	44179968
Z17825	SRRM2	2	145	16	2813306	2813449	PTGDS	137	254	9	139871956	139872075
DA262936	PTGDS	1	456	9	139871956	139874447	DIP2C	453	559	10	709466	709572
BC094690	MYBPC2	1	918	19	50936160	50945535	PTGDS	916	1621	9	139872062	139876194
BQ950270	PTGDS	12	65	9	139876117	139876170	PTGDS	57	829	9	139871961	139876144
AW316630	PTGDS	1	402	9	139874404	139876196	FAM63A	397	491	1	150970227	150970623
EB387717	PTGDS	1	167	9	139871994	139872160	SIDT2	163	758	11	117052160	117053256

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr9:139874450-139874450	p.Y128*	2
chr9:139874487-139874487	p.E141K	2
chr9:139872039-139872039	p.T3T	2
chr9:139872131-139872131	p.F34Y	1
chr9:139873751-139873751	p.H111Y	1
chr9:139872144-139872144	p.K38K	1
chr9:139873455-139873455	p.R42H	1
chr9:139874454-139874454	p.L130M	1
chr9:139873474-139873474	p.L48L	1
chr9:139873535-139873535	p.V69M	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1			2					1			2		1			2	1		3
# mutation	1			2					1			2		1			3	1		3
nonsynonymous SNV				2					1			2					1	1		3
synonymous SNV	1													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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr9:139873751	p.H111N	2
chr9:139874454	p.R42H	1
chr9:139872144	p.L48L	1
chr9:139874654	p.L62L	1
chr9:139873455	p.V69M	1
chr9:139873474	p.D74N	1
chr9:139873514	p.N87S	1
chr9:139873535	p.A99E	1
chr9:139873550	p.S104S	1
chr9:139873680	p.L130M	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00482	prostaglandin D2 synthase 21kDa (brain)	approved; investigational	Celecoxib

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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