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 GPT

Basic gene info.	Gene symbol	GPT
	Gene name	glutamic-pyruvate transaminase (alanine aminotransferase)
	Synonyms	AAT1\|ALT1\|GPT1
	Cytomap	UCSC genome browser: 8q24.3
	Genomic location	chr8 :145729464-145732555
	Type of gene	protein-coding
	RefGenes	NM_005309.2,
	Ensembl id	ENSG00000167701
	Description	GPT 1alanine aminotransferase 1glutamate pyruvate transaminase 1glutamic--alanine transaminase 1glutamic--pyruvic transaminase 1glutamic-alanine transaminase 1
	Modification date	20141218
dbXrefs	MIM : 138200
	HGNC : HGNC
	Ensembl : ENSG00000167701
	HPRD : 00689
	Vega : OTTHUMG00000165176
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GPT
	BioGPS: 2875
	Gene Expression Atlas: ENSG00000167701
	The Human Protein Atlas: ENSG00000167701
Pathway	NCI Pathway Interaction Database: GPT
	KEGG: GPT
	REACTOME: GPT
	ConsensusPathDB
	Pathway Commons: GPT
Metabolism	MetaCyc: GPT
	HUMANCyc: GPT
Regulation	Ensembl's Regulation: ENSG00000167701
	miRBase: chr8 :145,729,464-145,732,555
	TargetScan: NM_005309
	cisRED: ENSG00000167701
Context	iHOP: GPT
	cancer metabolism search in PubMed: GPT
	UCL Cancer Institute: GPT
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: GPT
	Familial Cancer Database: GPT

* 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_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

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

Mutations for GPT

* 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 GPT 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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=29)	Stat. for Synonymous SNVs (# total SNVs=5)

Stat. for Deletions (# total SNVs=1)	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
chr8:145730404-145730404	p.I129V	2
chr8:145729727-145729727	p.H14N	2
chr8:145729729-145729729	p.H14Q	1
chr8:145731945-145731945	p.N398S	1
chr8:145730399-145730399	p.S127C	1
chr8:145731256-145731256	p.I255I	1
chr8:145729780-145729780	p.R31R	1
chr8:145731954-145731954	p.P401H	1
chr8:145731400-145731400	p.A281V	1
chr8:145729849-145729849	p.Q54H	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	3	4		7					1	1		1	1				2	3	3	3
# mutation	3	4		7					1	1		1	1				2	3	3	3
nonsynonymous SNV		3		6					1	1			1				2	3	1	2
synonymous SNV	3	1		1								1							2	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
chr8:145730220	p.G145R	1
chr8:145731400	p.R427R	1
chr8:145732224	p.E175K	1
chr8:145730243	p.G448S	1
chr8:145731402	p.I186T	1
chr8:145732325	p.F466F	1
chr8:145730399	p.A215A	1
chr8:145731462	p.R478P	1
chr8:145732328	p.D217D	1
chr8:145730424	p.L479R	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 GPT 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 GPT

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


ASNS,CMC2,CFAP20,C16orf87,AUNIP,CDCA8,EMC8, GPT2,KARS,TLDC1,NAE1,NIP7,NUP93,ORC6, PAK1IP1,PSAT1,RANBP1,RBM17,RGMA,SHCBP1,SNRPD1	ACAT1,ADHFE1,CS,DLD,DLST,ETFA,ETFDH, GPT2,HSPB6,KIAA0408,NDUFV3,PDHA1,PDK2,GATB, PFKFB1,PGM1,PHYH,PLIN5,RNF157,SLC2A4,SLC6A8

AARS,SAPCD2,CCDC86,GARS,GFPT1,GGCT,GOT2, GPT2,HNRNPAB,LONP1,ORC6,PDF,PGP,PHGDH, PKMYT1,PSAT1,SAC3D1,SLC19A1,SLC29A2,STC2,ZNF598	ANLN,AURKA,CCNB1,CDC20,CDCA8,CENPA,CENPO, CEP55,CLDN14,GPT2,GSDMB,KIF18A,KPNA2,MUC1, MYEOV,NFE2L3,PDIA4,PLK1,POC1A,PSAT1,TMEM214

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 GPT

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
DB00114	glutamic-pyruvate transaminase (alanine aminotransferase)	nutraceutical	Pyridoxal Phosphate
DB00142	glutamic-pyruvate transaminase (alanine aminotransferase)	approved; nutraceutical	L-Glutamic Acid
DB00160	glutamic-pyruvate transaminase (alanine aminotransferase)	approved; nutraceutical	L-Alanine
DB00780	glutamic-pyruvate transaminase (alanine aminotransferase)	approved	Phenelzine
DB04898	glutamic-pyruvate transaminase (alanine aminotransferase)	approved; withdrawn; investigational	Ximelagatran

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Cross referenced IDs for GPT

* 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