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 PTGS2

Basic gene info.	Gene symbol	PTGS2
	Gene name	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)
	Synonyms	COX-2\|COX2\|GRIPGHS\|PGG/HS\|PGHS-2\|PHS-2\|hCox-2
	Cytomap	UCSC genome browser: 1q25.2-q25.3
	Genomic location	chr1 :186640943-186649559
	Type of gene	protein-coding
	RefGenes	NM_000963.3,
	Ensembl id	ENSG00000073756
	Description	PGH synthase 2PHS IIcyclooxygenase 2bprostaglandin G/H synthase 2prostaglandin H2 synthase 2
	Modification date	20141222
dbXrefs	MIM : 600262
	HGNC : HGNC
	Ensembl : ENSG00000073756
	HPRD : 02599
	Vega : OTTHUMG00000035473
Protein	UniProt: P35354 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PTGS2
	BioGPS: 5743
	Gene Expression Atlas: ENSG00000073756
	The Human Protein Atlas: ENSG00000073756
Pathway	NCI Pathway Interaction Database: PTGS2
	KEGG: PTGS2
	REACTOME: PTGS2
	ConsensusPathDB
	Pathway Commons: PTGS2
Metabolism	MetaCyc: PTGS2
	HUMANCyc: PTGS2
Regulation	Ensembl's Regulation: ENSG00000073756
	miRBase: chr1 :186,640,943-186,649,559
	TargetScan: NM_000963
	cisRED: ENSG00000073756
Context	iHOP: PTGS2
	cancer metabolism search in PubMed: PTGS2
	UCL Cancer Institute: PTGS2
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PTGS2 in cancer cell metabolism	1. Habermann N, Ulrich CM, Lundgreen A, Makar KW, Poole EM, et al. (2013) PTGS1, PTGS2, ALOX5, ALOX12, ALOX15, and FLAP SNPs: interaction with fatty acids in colon cancer and rectal cancer. Genes & nutrition 8: 115-126. go to article

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Phenotypic Information for PTGS2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PTGS2
	Familial Cancer Database: PTGS2

* 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	600262; gene.
Orphanet
Disease	KEGG Disease: PTGS2
	MedGen: PTGS2 (Human Medical Genetics with Condition)
	ClinVar: PTGS2
Phenotype	MGI: PTGS2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PTGS2

Mutations for PTGS2

* 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 PTGS2 related fusion information.

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

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=75)	Stat. for Synonymous SNVs (# total SNVs=17)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr1:186643865-186643865	p.A479S	3
chr1:186648219-186648219	p.R95Q	2
chr1:186645968-186645968	p.Y240*	2
chr1:186645691-186645691	p.R293Q	2
chr1:186643498-186643498	p.S601*	2
chr1:186645692-186645692	p.R293W	2
chr1:186643501-186643501	p.R600H	2
chr1:186645242-186645242	p.P349T	2
chr1:186648497-186648497	p.C42C	2
chr1:186648237-186648237	p.N89S	2

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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=4

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	3		11			2		4			8	2	2			10	5		10
# mutation	1	3		11			2		4			10	2	2			11	5		12
nonsynonymous SNV	1	2		8			1		3			8	1	1			10	4		10
synonymous SNV		1		3			1		1			2	1	1			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
chr1:186643808	p.P498S	2
chr1:186648497	p.C42C	2
chr1:186645691	p.R293L	2
chr1:186645692	p.R293W	2
chr1:186645721	p.R170T	1
chr1:186643703	p.A288T	1
chr1:186646828	p.G283D	1
chr1:186648296	p.K155N	1
chr1:186645168	p.A486T	1
chr1:186645722	p.G283S	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 PTGS2 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 PTGS2

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


ACTR3B,ADH4,ARID5A,C6orf15,CCND2,DGKI,HOXA11, HOXA11-AS,IRX1,NRG1,OR2T1,PDC,PLA2G4A,PTGS2, QRICH2,SPHK1,SYN3,TAC4,TFAP2D,TMEM132E,TMEM14E	ATF3,B3GNT5,BTG2,CXCL2,CYR61,DUSP1,DUSP5, EGR1,EGR2,FOS,FOSB,IL1B,MAP3K8,NCOA7, NFKBIZ,NR4A2,PTGS2,RGS16,TRIB1,ZFP36,ZFP36L1

A2ML1,ACTBL2,ARHGAP29,C8orf86,CAV2,CP,CST6, DAPK1,F3,IGFBP3,IL1RAPL1,ITGA3,LIPK,LOC285830, NKX3-1,PODXL,PRAMEF6,PSG6,PSG9,PTGES,PTGS2	ATP6V0E2,CCDC160,CCL3,CH25H,EGR1,EGR2,IL9, INTU,KLF11,KLHL20,LOC221710,MSLNL,NALCN,PAGE2, PTGS2,RNU4ATAC,SIK1,SNORA9,TNF,UBE2G2,ZSCAN12P1

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 PTGS2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P35354; -.
Chemistry	ChEMBL	CHEMBL2094253; -.
Chemistry	GuidetoPHARMACOLOGY	1376; -.
Organism-specific databases	PharmGKB	PA293; -.
Organism-specific databases	CTD	5743; -.

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
DB00154	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; nutraceutical	gamma-Homolinolenic acid
DB00159	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; nutraceutical	Icosapent
DB00233	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Aminosalicylic Acid
DB00244	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Mesalazine
DB00316	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Acetaminophen
DB00328	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; investigational	Indomethacin
DB00461	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Nabumetone
DB00465	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Ketorolac
DB00469	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Tenoxicam
DB00480	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; investigational	Lenalidomide
DB00482	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; investigational	Celecoxib
DB00500	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Tolmetin
DB00533	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	withdrawn; investigational	Rofecoxib
DB00554	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; investigational	Piroxicam
DB00573	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Fenoprofen
DB00580	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	withdrawn; investigational	Valdecoxib
DB00586	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Diclofenac
DB00605	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Sulindac
DB00712	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Flurbiprofen
DB00749	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; investigational	Etodolac
DB00784	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Mefenamic acid
DB00788	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Naproxen
DB00795	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Sulfasalazine
DB00812	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Phenylbutazone
DB00814	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Meloxicam
DB00821	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Carprofen
DB00861	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Diflunisal
DB00870	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Suprofen
DB00936	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Salicyclic acid
DB00939	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Meclofenamic acid
DB00945	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Acetylsalicylic acid
DB00963	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Bromfenac
DB00991	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Oxaprozin
DB01009	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Ketoprofen
DB01014	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; investigational	Balsalazide
DB01041	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; withdrawn; investigational	Thalidomide
DB01050	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Ibuprofen
DB01283	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; investigational	Lumiracoxib
DB01294	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Bismuth Subsalicylate
DB01397	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Magnesium salicylate
DB01398	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Salicylate-sodium
DB01399	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Salsalate
DB01401	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Trisalicylate-choline
DB01419	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Antrafenine
DB01435	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Antipyrine
DB01600	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Tiaprofenic acid
DB01628	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; investigational	Etoricoxib
DB02266	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	experimental	Flufenamic Acid
DB02709	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	experimental; investigational	Resveratrol
DB03014	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	experimental	Heme
DB03477	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	experimental	1-Phenylsulfonamide-3-Trifluoromethyl-5-Parabromophenylpyrazole
DB03866	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	experimental	Prostaglandin G2
DB04552	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Niflumic Acid
DB04743	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	experimental	Nimesulide
DB06725	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Lornoxicam
DB06802	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Nepafenac
DB00317	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; investigational	Gefitinib
DB01234	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; investigational	Dexamethasone
DB00864	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; investigational	Tacrolimus
DB01242	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved	Clomipramine
DB01101	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; investigational	Capecitabine
DB00526	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	approved; investigational	Oxaliplatin

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Cross referenced IDs for PTGS2

* 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