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 GGT5

Basic gene info.	Gene symbol	GGT5
	Gene name	gamma-glutamyltransferase 5
	Synonyms	GGL\|GGT 5\|GGT-REL\|GGTLA1
	Cytomap	UCSC genome browser: 22q11.23
	Genomic location	chr22 :24615621-24641110
	Type of gene	protein-coding
	RefGenes	NM_001099781.2, NM_001099782.2,NM_001302464.1,NM_001302465.1,NM_004121.3,
	Ensembl id	ENSG00000099998
	Description	gamma-glutamyl cleaving enzymegamma-glutamyl transpeptidase-related enzymegamma-glutamyl transpeptidase-related proteingamma-glutamyltransferase-like activity 1gamma-glutamyltranspeptidase 5glutathione hydrolase 5leukotriene-C4 hydrolase
	Modification date	20141215
dbXrefs	MIM : 137168
	HGNC : HGNC
	Ensembl : ENSG00000099998
	HPRD : 00666
	Vega : OTTHUMG00000150796
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GGT5
	BioGPS: 2687
	Gene Expression Atlas: ENSG00000099998
	The Human Protein Atlas: ENSG00000099998
Pathway	NCI Pathway Interaction Database: GGT5
	KEGG: GGT5
	REACTOME: GGT5
	ConsensusPathDB
	Pathway Commons: GGT5
Metabolism	MetaCyc: GGT5
	HUMANCyc: GGT5
Regulation	Ensembl's Regulation: ENSG00000099998
	miRBase: chr22 :24,615,621-24,641,110
	TargetScan: NM_001099781
	cisRED: ENSG00000099998
Context	iHOP: GGT5
	cancer metabolism search in PubMed: GGT5
	UCL Cancer Institute: GGT5
Assigned class in ccmGDB	C

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Phenotypic Information for GGT5(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GGT5
	Familial Cancer Database: GGT5

* 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_TAURINE_AND_HYPOTAURINE_METABOLISM KEGG_SELENOAMINO_ACID_METABOLISM KEGG_GLUTATHIONE_METABOLISM KEGG_ARACHIDONIC_ACID_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: GGT5
	MedGen: GGT5 (Human Medical Genetics with Condition)
	ClinVar: GGT5
Phenotype	MGI: GGT5 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GGT5

Mutations for GGT5

* 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 GGT5 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

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=49)	Stat. for Synonymous SNVs (# total SNVs=20)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=1)

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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
chr22:24621549-24621549	p.R434Q	4
chr22:24622608-24622608	p.P343P	3
chr22:24628803-24628803	p.A195V	3
chr22:24621319-24621319	p.R466H	2
chr22:24640618-24640618	p.A26T	2
chr22:24622188-24622188	p.R362H	2
chr22:24628845-24628845	p.S181I	2
chr22:24622189-24622189	p.R362C	2
chr22:24615946-24615946	p.G585S	2
chr22:24621251-24621251	p.G489R	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				14	1		3		2			2	3	2		2	10	3		5
# mutation				12	1		3		2			2	4	2		2	8	3		5
nonsynonymous SNV				10	1		2		2			2	2	2		1	4			3
synonymous SNV				2			1						2			1	4	3		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
chr22:24621549	p.R402Q,GGT5	4
chr22:24628803	p.A163V,GGT5	3
chr22:24615946	p.T293T,GGT5	2
chr22:24622608	p.G553S,GGT5	2
chr22:24622662	p.P311P,GGT5	2
chr22:24622670	p.R434H,GGT5	1
chr22:24640618	p.S407S,GGT5	1
chr22:24621019	p.V291I,GGT5	1
chr22:24622121	p.G282G,GGT5	1
chr22:24622695	p.G389S,GGT5	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 GGT5 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 GGT5

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


ACVRL1,CLDN5,COL18A1,CYGB,EFEMP2,ENG,GGT5, GRASP,HIC1,HSPA12B,IFFO1,KANK3,LTC4S,LYL1, MFRP,NAALADL1,NNMT,PTGIR,TGFB1,TMEM204,USHBP1	AIP,ARHGDIA,ARPC1B,EFHD2,GGT5,GIMAP1,HAUS7, HDAC7,KCTD17,LYL1,MAP3K11,MVP,PLOD3,PPP1R12C, RNH1,RPS6KA4,SHKBP1,SIPA1,SLC39A13,TNIP2,ZNF668

BGN,VSTM4,C1R,C1S,COL6A2,EFEMP2,EVC2, FBLN2,GGT5,LHFP,MRAS,MSC,MXRA8,OLFML1, OLFML2B,PDGFRB,PNMAL2,PRICKLE1,SERPINF1,SERPING1,VIM	ADAM22,ALOX5,BARX1,BMPER,BMX,CCDC129,ENG, GANAB,GGT5,IL1R1,LRRC32,MKL2,OVCH1,PLVAP, PTK7,S1PR2,SCARA5,TAS1R3,TBX2,UTRN,ZNF732

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 GGT5

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
DB00143	gamma-glutamyltransferase 5	approved; nutraceutical	Glutathione
DB00145	gamma-glutamyltransferase 5	approved; nutraceutical	Glycine

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Cross referenced IDs for GGT5

* 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