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 GOT1

Basic gene info.	Gene symbol	GOT1
	Gene name	glutamic-oxaloacetic transaminase 1, soluble
	Synonyms	ASTQTL1\|GIG18\|cAspAT\|cCAT
	Cytomap	UCSC genome browser: 10q24.1-q25.1
	Genomic location	chr10 :101156626-101190530
	Type of gene	protein-coding
	RefGenes	NM_002079.2,
	Ensembl id	ENSG00000120053
	Description	aspartate aminotransferase 1aspartate aminotransferase, cytoplasmicaspartate transaminase 1cysteine aminotransferase, cytoplasmiccysteine transaminase, cytoplasmicglutamate oxaloacetate transaminase 1growth-inhibiting protein 18transaminase A
	Modification date	20141207
dbXrefs	MIM : 138180
	HGNC : HGNC
	Ensembl : ENSG00000120053
	HPRD : 00687
	Vega : OTTHUMG00000018882
Protein	UniProt: P17174 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GOT1
	BioGPS: 2805
	Gene Expression Atlas: ENSG00000120053
	The Human Protein Atlas: ENSG00000120053
Pathway	NCI Pathway Interaction Database: GOT1
	KEGG: GOT1
	REACTOME: GOT1
	ConsensusPathDB
	Pathway Commons: GOT1
Metabolism	MetaCyc: GOT1
	HUMANCyc: GOT1
Regulation	Ensembl's Regulation: ENSG00000120053
	miRBase: chr10 :101,156,626-101,190,530
	TargetScan: NM_002079
	cisRED: ENSG00000120053
Context	iHOP: GOT1
	cancer metabolism search in PubMed: GOT1
	UCL Cancer Institute: GOT1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GOT1 in cancer cell metabolism	1. Jiang X, Chang H, Zhou Y (2015) Expression, purification and preliminary crystallographic studies of human glutamate oxaloacetate transaminase 1 (GOT1). Protein Expr Purif 113: 102-106. doi: 10.1016/j.pep.2015.05.010. go to article 2. Chakrabarti G (2015) Mutant KRAS associated malic enzyme 1 expression is a predictive marker for radiation therapy response in non-small cell lung cancer. Radiat Oncol 10: 145. doi: 10.1186/s13014-015-0457-x. pmid: 4502640. go to article

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Phenotypic Information for GOT1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GOT1
	Familial Cancer Database: GOT1

* 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 CRC ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
7Therapeutic 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_SULFUR_AMINO_ACID_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_POLYAMINES REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM	138180; gene. 614419; phenotype.
Orphanet
Disease	KEGG Disease: GOT1
	MedGen: GOT1 (Human Medical Genetics with Condition)
	ClinVar: GOT1
Phenotype	MGI: GOT1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GOT1

Mutations for GOT1

* 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 GOT1 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

AI114691

GOT1

319

101180445

101190377

FABP1

304

643

88424050

88427579

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=32)	Stat. for Synonymous SNVs (# total SNVs=8)

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
chr10:101180424-101180424	p.R86H	2
chr10:101163500-101163501	p.S258F	2
chr10:101163552-101163552	p.I241S	2
chr10:101163327-101163327	p.S286S	2
chr10:101163586-101163586	p.A230T	2
chr10:101157386-101157386	p.R387Q	2
chr10:101163356-101163356	p.E277*	2
chr10:101163595-101163595	p.Q227*	2
chr10:101180382-101180382	p.R100Q	1
chr10:101162397-101162397	p.P348S	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=3

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				8			3					3	2			1	6	4		6
# mutation				9			3					4	2			1	6	4		10
nonsynonymous SNV				5			1					3	1			1	4	3		9
synonymous SNV				4			2					1	1				2	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
chr10:101180424	p.R86H	2
chr10:101163586	p.G262W	2
chr10:101163490	p.A230T	2
chr10:101162431	p.A344A	1
chr10:101163546	p.Q227E	1
chr10:101163312	p.S336S	1
chr10:101163585	p.K214T	1
chr10:101180428	p.I291I	1
chr10:101163320	p.Q208H	1
chr10:101180532	p.E289K	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 GOT1 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 GOT1

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


ATP5B,ATP5G3,ATP5O,BOLA3,CCNB1,COX5A,COX7B, CWF19L1,DDT,GOT1,MDH1,MRPS22,NDUFA6,PGAM1, PTTG1,RFC2,SHMT2,SLC25A5,SUCLG1,UFD1L,USMG5	ASB4,BEST3,PERM1,CTXN3,EEF1A2,FEM1A,FHL3, GOT1,IP6K3,JPH1,MYADML2,MYOM2,MYOZ2,PEBP4, PFKM,PGPEP1L,SLC25A4,SRPK3,SYNPO2L,TRIM54,WDR62

ATP5B,ATP5G3,ATP5O,CHCHD10,COX7C,COX8A,ECHS1, FH,GHITM,GOT1,MRPS5,NDUFB8,NDUFS3,NDUFV1, PGAM1,SDHB,TMX2,UBAC1,UQCRC1,UQCRH,USMG5	APEH,ATP5A1,ATP5B,DARS2,DLAT,FAR2,FASTKD1, FH,GOT1,GSS,MIPEP,MRRF,PDHA1,PDSS2, RTN4IP1,SLC25A10,SLC35A4,SUPV3L1,TBRG4,TTLL12,TUFM

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 GOT1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL2189139; -.
Organism-specific databases	PharmGKB	PA28817; -.
Organism-specific databases	CTD	2805; -.

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 1, soluble	nutraceutical	Pyridoxal Phosphate
DB00128	glutamic-oxaloacetic transaminase 1, soluble	approved; nutraceutical	L-Aspartic Acid
DB00142	glutamic-oxaloacetic transaminase 1, soluble	approved; nutraceutical	L-Glutamic Acid
DB00151	glutamic-oxaloacetic transaminase 1, soluble	approved; nutraceutical	L-Cysteine
DB04299	glutamic-oxaloacetic transaminase 1, soluble	experimental	Maleic Acid
DB00121	glutamic-oxaloacetic transaminase 1, soluble	approved; nutraceutical	Biotin
DB00130	glutamic-oxaloacetic transaminase 1, soluble	approved; nutraceutical; investigational	L-Glutamine

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Cross referenced IDs for GOT1

* 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