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 symbolGPT
Gene nameglutamic-pyruvate transaminase (alanine aminotransferase)
SynonymsAAT1|ALT1|GPT1
CytomapUCSC genome browser: 8q24.3
Genomic locationchr8 :145729464-145732555
Type of geneprotein-coding
RefGenesNM_005309.2,
Ensembl idENSG00000167701
DescriptionGPT 1alanine aminotransferase 1glutamate pyruvate transaminase 1glutamic--alanine transaminase 1glutamic--pyruvic transaminase 1glutamic-alanine transaminase 1
Modification date20141218
dbXrefs MIM : 138200
HGNC : HGNC
Ensembl : ENSG00000167701
HPRD : 00689
Vega : OTTHUMG00000165176
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPT
BioGPS: 2875
Gene Expression Atlas: ENSG00000167701
The Human Protein Atlas: ENSG00000167701
PathwayNCI Pathway Interaction Database: GPT
KEGG: GPT
REACTOME: GPT
ConsensusPathDB
Pathway Commons: GPT
MetabolismMetaCyc: GPT
HUMANCyc: GPT
RegulationEnsembl's Regulation: ENSG00000167701
miRBase: chr8 :145,729,464-145,732,555
TargetScan: NM_005309
cisRED: ENSG00000167701
ContextiHOP: GPT
cancer metabolism search in PubMed: GPT
UCL Cancer Institute: GPT
Assigned class in ccmGDBC

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Phenotypic Information for GPT(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GPT
MedGen: GPT (Human Medical Genetics with Condition)
ClinVar: GPT
PhenotypeMGI: GPT (International Mouse Phenotyping Consortium)
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.

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 GPT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=29)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr8:145730404-145730404p.I129V2
chr8:145729727-145729727p.H14N2
chr8:145729729-145729729p.H14Q1
chr8:145731945-145731945p.N398S1
chr8:145730399-145730399p.S127C1
chr8:145731256-145731256p.I255I1
chr8:145729780-145729780p.R31R1
chr8:145731954-145731954p.P401H1
chr8:145731400-145731400p.A281V1
chr8:145729849-145729849p.Q54H1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample34 7    11 11   2333
# mutation34 7    11 11   2333
nonsynonymous SNV 3 6    11  1   2312
synonymous SNV31 1       1      21
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
chr8:145730220p.G145R1
chr8:145731400p.R427R1
chr8:145732224p.E175K1
chr8:145730243p.G448S1
chr8:145731402p.I186T1
chr8:145732325p.F466F1
chr8:145730399p.A215A1
chr8:145731462p.R478P1
chr8:145732328p.D217D1
chr8:145730424p.L479R1

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 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

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

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
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 GPT
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00114glutamic-pyruvate transaminase (alanine aminotransferase)nutraceuticalPyridoxal Phosphate
DB00142glutamic-pyruvate transaminase (alanine aminotransferase)approved; nutraceuticalL-Glutamic Acid
DB00160glutamic-pyruvate transaminase (alanine aminotransferase)approved; nutraceuticalL-Alanine
DB00780glutamic-pyruvate transaminase (alanine aminotransferase)approvedPhenelzine
DB04898glutamic-pyruvate transaminase (alanine aminotransferase)approved; withdrawn; investigationalXimelagatran


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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



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