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 PTGES

Basic gene info.	Gene symbol	PTGES
	Gene name	prostaglandin E synthase
	Synonyms	MGST-IV\|MGST1-L1\|MGST1L1\|MPGES\|PGES\|PIG12\|PP102\|PP1294\|TP53I12\|mPGES-1
	Cytomap	UCSC genome browser: 9q34.3
	Genomic location	chr9 :132500614-132515344
	Type of gene	protein-coding
	RefGenes	NM_004878.4, NM_198797.1,
	Ensembl id	ENSG00000148344
	Description	MGST1-like 1glutathione S-transferase 1-like 1microsomal glutathione S-transferase 1-like 1microsomal prostaglandin E synthase 1microsomal prostaglandin E synthase-1p53-induced apoptosis protein 12p53-induced gene 12 proteintumor protein p53 induci
	Modification date	20141207
dbXrefs	MIM : 605172
	HGNC : HGNC
	Ensembl : ENSG00000148344
	HPRD : 05528
	Vega : OTTHUMG00000020791
Protein	UniProt: O14684 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PTGES
	BioGPS: 9536
	Gene Expression Atlas: ENSG00000148344
	The Human Protein Atlas: ENSG00000148344
Pathway	NCI Pathway Interaction Database: PTGES
	KEGG: PTGES
	REACTOME: PTGES
	ConsensusPathDB
	Pathway Commons: PTGES
Metabolism	MetaCyc: PTGES
	HUMANCyc: PTGES
Regulation	Ensembl's Regulation: ENSG00000148344
	miRBase: chr9 :132,500,614-132,515,344
	TargetScan: NM_004878
	cisRED: ENSG00000148344
Context	iHOP: PTGES
	cancer metabolism search in PubMed: PTGES
	UCL Cancer Institute: PTGES
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: PTGES
	Familial Cancer Database: PTGES

* 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	605172; gene.
Orphanet
Disease	KEGG Disease: PTGES
	MedGen: PTGES (Human Medical Genetics with Condition)
	ClinVar: PTGES
Phenotype	MGI: PTGES (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PTGES

Mutations for PTGES

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	PTGES	chr9	132501490	132501510	PTGES	chr9	132503537	132503557

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PTGES 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
BM797058	IVD	1	103	15	40711358	40711460	PTGES	99	434	9	132500840	132501175
T03380	PTGES	1	70	9	132500629	132500698	SOX2-OT	67	376	3	181457795	181458101

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

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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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=1

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=7)	Stat. for Synonymous SNVs (# total SNVs=0)
	There's no s-snv.
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
chr9:132501984-132501984	p.R122Q	1
chr9:132502053-132502053	p.A99V	1
chr9:132502069-132502069	p.P94T	1
chr9:132502137-132502137	p.A71V	1
chr9:132510953-132510953	p.D64H	1
chr9:132510954-132510954	p.P63P	1
chr9:132510994-132510994	p.A50V	1
chr9:132511009-132511009	p.A45V	1
chr9:132501928-132501928	p.A141P	1
chr9:132501937-132501937	p.A138T	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=1

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					1				1				1		1	2
# mutation				1					1				1				1		1	2
nonsynonymous SNV				1					1				1						1	2
synonymous SNV																	1

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
chr9:132502051	p.R122Q	1
chr9:132502053	p.W100G	1
chr9:132510953	p.A99V	1
chr9:132510954	p.D64H	1
chr9:132511009	p.P63P	1
chr9:132501975	p.A45V	1
chr9:132501984	p.I125T	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 PTGES 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 PTGES

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


AURKAIP1,UQCC3,C19orf60,C9orf142,C9orf16,RABL6,CCDC124, DOHH,EDF1,GADD45GIP1,NTMT1,NDUFA11,NDUFB7,PMPCA, PTGES2,REXO4,RPL35,RPS19BP1,SSNA1,SURF2,TIMM13	ADRM1,ATP5D,RABL6,ESRRA,EMC9,FAM195A,FASTK, CPTP,MAP2K2,NTMT1,MRPL12,MRPL14,NDUFA13,NDUFV1, NOSIP,PCBP4,PHPT1,PMF1,PTGES2,STK11,TIMM17B

ATP5D,AURKAIP1,UQCC3,C9orf142,COQ4,ENDOG,FPGS, NTMT1,MRPL12,MRPL41,MRPS2,MRPS5,NDUFV1,PMPCA, PTGES2,PTRH1,SLC25A10,TUBB4B,UBAC1,WDR34,ZMYND19	APEH,ASL,AURKAIP1,CDK2AP2,CYBA,DUS1L,SLC52A2, LMAN2,MAEA,MRPL12,MRPS34,NDUFS6,NDUFS7,NDUFV1, PTGES2,SLC25A10,SLC25A39,TIMM13,TLCD1,TUFM,UQCRC1

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 PTGES

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	O14684; -.
Chemistry	ChEMBL	CHEMBL5658; -.
Organism-specific databases	PharmGKB	PA33948; -.
Organism-specific databases	CTD	9536; -.

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
DB00917	prostaglandin E synthase	approved	Dinoprostone
DB01240	prostaglandin E synthase	approved	Epoprostenol
DB00482	prostaglandin E synthase	approved; investigational	Celecoxib

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Cross referenced IDs for PTGES

* 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