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 GOT2

Basic gene info.	Gene symbol	GOT2
	Gene name	glutamic-oxaloacetic transaminase 2, mitochondrial
	Synonyms	KAT4\|KATIV\|mitAAT
	Cytomap	UCSC genome browser: 16q21
	Genomic location	chr16 :58741034-58768246
	Type of gene	protein-coding
	RefGenes	NM_001286220.1, NM_002080.3,
	Ensembl id	ENSG00000125166
	Description	FABP-1FABPpmaspartate aminotransferase 2aspartate aminotransferase, mitochondrialaspartate transaminase 2fatty acid-binding proteinglutamate oxaloacetate transaminase 2glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2
	Modification date	20141211
dbXrefs	MIM : 138150
	HGNC : HGNC
	Ensembl : ENSG00000125166
	HPRD : 00684
	Vega : OTTHUMG00000133769
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GOT2
	BioGPS: 2806
	Gene Expression Atlas: ENSG00000125166
	The Human Protein Atlas: ENSG00000125166
Pathway	NCI Pathway Interaction Database: GOT2
	KEGG: GOT2
	REACTOME: GOT2
	ConsensusPathDB
	Pathway Commons: GOT2
Metabolism	MetaCyc: GOT2
	HUMANCyc: GOT2
Regulation	Ensembl's Regulation: ENSG00000125166
	miRBase: chr16 :58,741,034-58,768,246
	TargetScan: NM_001286220
	cisRED: ENSG00000125166
Context	iHOP: GOT2
	cancer metabolism search in PubMed: GOT2
	UCL Cancer Institute: GOT2
Assigned class in ccmGDB	C

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Phenotypic Information for GOT2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GOT2
	Familial Cancer Database: GOT2

* 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 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM KEGG_ARGININE_AND_PROLINE_METABOLISM KEGG_TYROSINE_METABOLISM KEGG_PHENYLALANINE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: GOT2
	MedGen: GOT2 (Human Medical Genetics with Condition)
	ClinVar: GOT2
Phenotype	MGI: GOT2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GOT2

Mutations for GOT2

* 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 GOT2 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
BQ337855	GOT2	34	282	16	58752121	58752593	HTT	277	449	4	3209030	3210617
AK129856	MIR548N	1	937	2	179437433	179438369	GOT2	933	1696	16	58741037	58741800
DA873777	SLC38A7	1	278	16	58717859	58718674	GOT2	276	565	16	58752140	58753162
BF365549	EML2	1	153	19	46121740	46121892	GOT2	150	362	16	58753187	58753399

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=31)	Stat. for Synonymous SNVs (# total SNVs=7)

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
chr16:58752192-58752192	p.Q204K	5
chr16:58743428-58743428	p.R355G	5
chr16:58768129-58768129	p.A2S	3
chr16:58749996-58749996	p.P314L	3
chr16:58750604-58750604	p.C272C	2
chr16:58750636-58750636	p.R262C	2
chr16:58757668-58757668	p.V76V	2
chr16:58749989-58749989	p.Y316Y	2
chr16:58742142-58742142	p.S409F	2
chr16:58756164-58756164	p.A89T	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=6

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	4	1		3		4	1		6	3			2	6	3	1	3
# mutation			2	4	1		3		4	1		6	3			2	7	3	1	3
nonsynonymous SNV			1	2	1		3		3	1		5	3			1	6	2	1	3
synonymous SNV			1	2					1			1				1	1	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
chr16:58743428	p.R312W,GOT2	7
chr16:58750636	p.R219C,GOT2	2
chr16:58757714	p.N91D	1
chr16:58749996	p.R270R,GOT2	1
chr16:58752174	p.A89S	1
chr16:58757719	p.K236E,GOT2	1
chr16:58749998	p.R81S,GOT2	1
chr16:58752189	p.C229C,GOT2	1
chr16:58757769	p.V80I,GOT2	1
chr16:58750585	p.I222I,GOT2	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 GOT2 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 GOT2

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


AMFR,AP1G1,C16orf70,CCDC113,CDH1,CES2,COQ9, CYB5B,ESRP2,FAM192A,GABARAPL2,GOT2,HSBP1,HSDL1, IST1,GSE1,OGFOD1,POLR2C,SETD6,SLC38A7,TERF2IP	PERM1,CACNB1,CEP85,DUSP28,EEF1A2,FEM1A,FHL3, GAMT,GOT1,GOT2,HSPA2,MYL6B,OBSCN,PDLIM3, PFKM,PHKA1,RTN2,SH3BGR,SMYD1,TPM1,TUBA4A

FOPNL,C2orf47,CIAPIN1,COQ9,CXorf66,EARS2,EEF2KMT, GINS3,GOT2,KATNB1,LOC146481,MRPL38,NDUFAB1,NUBP1, NUP93,OGFOD1,PDF,RTN4IP1,TRAP1,TUFM,UQCRC2	CS,DARS2,DNAJC11,E2F2,EFTUD2,ELAVL1,FAM81A, FARSA,GOT1,GOT2,HSPA9,MTA2,NARS,NOP14, PDHA1,PIGU,PPIF,PROM2,SCFD2,SLC35A4,VARS

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 GOT2

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-oxaloacetic transaminase 2, mitochondrial	nutraceutical	Pyridoxal Phosphate
DB00128	glutamic-oxaloacetic transaminase 2, mitochondrial	approved; nutraceutical	L-Aspartic Acid
DB00142	glutamic-oxaloacetic transaminase 2, mitochondrial	approved; nutraceutical	L-Glutamic Acid
DB02783	glutamic-oxaloacetic transaminase 2, mitochondrial	experimental	4'-Deoxy-4'-Acetylyamino-Pyridoxal-5'-Phosphate
DB00121	glutamic-oxaloacetic transaminase 2, mitochondrial	approved; nutraceutical	Biotin
DB00130	glutamic-oxaloacetic transaminase 2, mitochondrial	approved; nutraceutical; investigational	L-Glutamine

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Cross referenced IDs for GOT2

* 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