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 GGT7

Basic gene info.	Gene symbol	GGT7
	Gene name	gamma-glutamyltransferase 7
	Synonyms	D20S101\|GGT4\|GGTL3\|GGTL5\|dJ18C9.2
	Cytomap	UCSC genome browser: 20q11.22
	Genomic location	chr20 :33432522-33460661
	Type of gene	protein-coding
	RefGenes	NM_178026.2,
	Ensembl id	ENSG00000131067
	Description	GGT 7gamma-glutamyltransferase 4gamma-glutamyltransferase-like 3gamma-glutamyltransferase-like 5gamma-glutamyltranspeptidase 7gamma-glutamyltranspeptidase-like 3glutathione hydrolase 7
	Modification date	20141207
dbXrefs	MIM : 612342
	HGNC : HGNC
	Ensembl : ENSG00000131067
	HPRD : 07488
	Vega : OTTHUMG00000032314
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GGT7
	BioGPS: 2686
	Gene Expression Atlas: ENSG00000131067
	The Human Protein Atlas: ENSG00000131067
Pathway	NCI Pathway Interaction Database: GGT7
	KEGG: GGT7
	REACTOME: GGT7
	ConsensusPathDB
	Pathway Commons: GGT7
Metabolism	MetaCyc: GGT7
	HUMANCyc: GGT7
Regulation	Ensembl's Regulation: ENSG00000131067
	miRBase: chr20 :33,432,522-33,460,661
	TargetScan: NM_178026
	cisRED: ENSG00000131067
Context	iHOP: GGT7
	cancer metabolism search in PubMed: GGT7
	UCL Cancer Institute: GGT7
Assigned class in ccmGDB	C

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Phenotypic Information for GGT7(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GGT7
	Familial Cancer Database: GGT7

* 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: GGT7
	MedGen: GGT7 (Human Medical Genetics with Condition)
	ClinVar: GGT7
Phenotype	MGI: GGT7 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GGT7

Mutations for GGT7

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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
ovary	GGT7	chr20	33456102	33456122	ZNF341	chr20	32371859	32371879

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 GGT7 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
H19810	GGT7	1	182	20	33433152	33437803	CREBBP	183	441	16	3776978	3777235
BI043619	GGT7	27	285	20	33444053	33444310	PIGC	278	394	1	172411581	172411697
BE501149	GGT7	1	376	20	33432967	33437811	SPEG	372	484	2	220344398	220344510

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=25)	Stat. for Synonymous SNVs (# total SNVs=13)

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
chr20:33451148-33451148	p.L125L	3
chr20:33450711-33450711	p.E155*	2
chr20:33433205-33433205	p.R639*	2
chr20:33437795-33437795	p.P598P	2
chr20:33449360-33449360	p.G188V	2
chr20:33451191-33451191	p.I110I	2
chr20:33449261-33449261	p.S221F	2
chr20:33440318-33440318	p.R448Q	1
chr20:33433180-33433180	p.A647V	1
chr20:33447323-33447323	p.V313M	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	2			6			3		4			3	3	2			9	5		3
# mutation	3			6			3		4			3	3	2			11	5		4
nonsynonymous SNV	3			4					3			3	2				6	4		2
synonymous SNV				2			3		1				1	2			5	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
chr20:33437795	p.P598P	2
chr20:33444618	p.V365M	2
chr20:33451191	p.I110I	2
chr20:33449261	p.S221F	2
chr20:33442668	p.L439L	1
chr20:33433180	p.A209T	1
chr20:33449295	p.H597Q	1
chr20:33440071	p.P425P	1
chr20:33442705	p.R197Q	1
chr20:33449298	p.D589N	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 GGT7 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 GGT7

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


CEP250,DYNLRB1,EDEM2,EEF1A2,EIF6,ERGIC3,GGT7, GSS,MAP1LC3A,MMP24,MYH7B,NEURL4,NPEPL1,PIGU, RBMY1E,ROMO1,SCAND1,SSTR1,TRPC4AP,U	CADM4,CNTROB,DDR1,DGCR2,DNAL4,DVL2,ELMO3, EPS8L2,FBXO44,FZR1,GGT7,PHLDB3,PRKCZ,SFI1, SGSM2,SH2D3A,SH3GLB2,SLC4A3,SSH3,SYTL1,ZNF324

ASXL1,ATP9A,AAR2,RTFDC1,CHMP4B,DDX27,DIDO1, ERGIC3,GGT7,GPR56,LOC647979,NCOA6,PCIF1,PCMTD2, POFUT1,PRPF6,RNF43,SNHG11,TM9SF4,TRPC4AP,ZSWIM3	ARHGAP36,ATP2C2,ERICH5,CLDN8,CPA6,FRZB,GGT7, GP2,HEPACAM2,HPCA,IL1R2,KIAA1324,LOC100130872,NRAP, RIMS4,RXFP4,SCGB2A1,STARD10,TMEM38A,WNK4,ZNF774

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 GGT7

There's no related Drug.

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Cross referenced IDs for GGT7

* 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