Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolGOT1
Gene nameglutamic-oxaloacetic transaminase 1, soluble
SynonymsASTQTL1|GIG18|cAspAT|cCAT
CytomapUCSC genome browser: 10q24.1-q25.1
Genomic locationchr10 :101156626-101190530
Type of geneprotein-coding
RefGenesNM_002079.2,
Ensembl idENSG00000120053
Descriptionaspartate aminotransferase 1aspartate aminotransferase, cytoplasmicaspartate transaminase 1cysteine aminotransferase, cytoplasmiccysteine transaminase, cytoplasmicglutamate oxaloacetate transaminase 1growth-inhibiting protein 18transaminase A
Modification date20141207
dbXrefs MIM : 138180
HGNC : HGNC
Ensembl : ENSG00000120053
HPRD : 00687
Vega : OTTHUMG00000018882
ProteinUniProt: P17174
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GOT1
BioGPS: 2805
Gene Expression Atlas: ENSG00000120053
The Human Protein Atlas: ENSG00000120053
PathwayNCI Pathway Interaction Database: GOT1
KEGG: GOT1
REACTOME: GOT1
ConsensusPathDB
Pathway Commons: GOT1
MetabolismMetaCyc: GOT1
HUMANCyc: GOT1
RegulationEnsembl's Regulation: ENSG00000120053
miRBase: chr10 :101,156,626-101,190,530
TargetScan: NM_002079
cisRED: ENSG00000120053
ContextiHOP: GOT1
cancer metabolism search in PubMed: GOT1
UCL Cancer Institute: GOT1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GOT1 in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic 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

check002.gifOthers
OMIM 138180; gene.
614419; phenotype.
Orphanet
DiseaseKEGG Disease: GOT1
MedGen: GOT1 (Human Medical Genetics with Condition)
ClinVar: GOT1
PhenotypeMGI: GOT1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GOT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI114691GOT13031910101180445101190377FABP130464328842405088427579

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr10:101180424-101180424p.R86H2
chr10:101163500-101163501p.S258F2
chr10:101163552-101163552p.I241S2
chr10:101163327-101163327p.S286S2
chr10:101163586-101163586p.A230T2
chr10:101157386-101157386p.R387Q2
chr10:101163356-101163356p.E277*2
chr10:101163595-101163595p.Q227*2
chr10:101165531-101165531p.Q208H1
chr10:101162407-101162407p.A344A1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample   8  3    32  164 6
# mutation   9  3    42  164 10
nonsynonymous SNV   5  1    31  143 9
synonymous SNV   4  2    11   21 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr10:101180424p.R86H2
chr10:101163586p.G262W2
chr10:101163490p.A230T2
chr10:101163312p.G269W1
chr10:101163585p.R100Q1
chr10:101180428p.R267K1
chr10:101163320p.S85A1
chr10:101157324p.A408T1
chr10:101180532p.F261F1
chr10:101163324p.V50A1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL2189139; -.
Organism-specific databasesPharmGKB PA28817; -.
Organism-specific databasesCTD 2805; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00114glutamic-oxaloacetic transaminase 1, solublenutraceuticalPyridoxal Phosphate
DB00128glutamic-oxaloacetic transaminase 1, solubleapproved; nutraceuticalL-Aspartic Acid
DB00142glutamic-oxaloacetic transaminase 1, solubleapproved; nutraceuticalL-Glutamic Acid
DB00151glutamic-oxaloacetic transaminase 1, solubleapproved; nutraceuticalL-Cysteine
DB04299glutamic-oxaloacetic transaminase 1, solubleexperimentalMaleic Acid
DB00121glutamic-oxaloacetic transaminase 1, solubleapproved; nutraceuticalBiotin
DB00130glutamic-oxaloacetic transaminase 1, solubleapproved; nutraceutical; investigationalL-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



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