Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 AGXT
Basic gene info.Gene symbolAGXT
Gene namealanine-glyoxylate aminotransferase
SynonymsAGT|AGT1|AGXT1|PH1|SPAT|SPT|TLH6
CytomapUCSC genome browser: 2q37.3
Genomic locationchr2 :241808161-241818536
Type of geneprotein-coding
RefGenesNM_000030.2,
Ensembl idENSG00000172482
DescriptionL-alanine: glyoxylate aminotransferase 1alanine--glyoxylate aminotransferasehepatic peroxisomal alanine:glyoxylate aminotransferaseserine--pyruvate aminotransferaseserine-pyruvate aminotransferaseserine:pyruvate aminotransferase
Modification date20141222
dbXrefs MIM : 604285
HGNC : HGNC
Ensembl : ENSG00000172482
HPRD : 05048
Vega : OTTHUMG00000133354
ProteinUniProt: P21549
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AGXT
BioGPS: 189
Gene Expression Atlas: ENSG00000172482
The Human Protein Atlas: ENSG00000172482
PathwayNCI Pathway Interaction Database: AGXT
KEGG: AGXT
REACTOME: AGXT
ConsensusPathDB
Pathway Commons: AGXT
MetabolismMetaCyc: AGXT
HUMANCyc: AGXT
RegulationEnsembl's Regulation: ENSG00000172482
miRBase: chr2 :241,808,161-241,818,536
TargetScan: NM_000030
cisRED: ENSG00000172482
ContextiHOP: AGXT
cancer metabolism search in PubMed: AGXT
UCL Cancer Institute: AGXT
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of AGXT in cancer cell metabolism1. Oh HR, An CH, Yoo NJ, Lee SH (2014) Somatic mutations of amino acid metabolism-related genes in gastric and colorectal cancers and their regional heterogeneity--a short report. Cell Oncol (Dordr) 37: 455-461. doi: 10.1007/s13402-014-0209-1. go to article

Top
Phenotypic Information for AGXT(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AGXT
Familial Cancer Database: AGXT
* 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
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM 259900; phenotype.
604285; gene.
Orphanet 93598; Primary hyperoxaluria type 1.
DiseaseKEGG Disease: AGXT
MedGen: AGXT (Human Medical Genetics with Condition)
ClinVar: AGXT
PhenotypeMGI: AGXT (International Mouse Phenotyping Consortium)
PhenomicDB: AGXT

Mutations for AGXT
* 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 AGXT 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

Top
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.

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=30)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=4)
Stat. for Insertions
(# total SNVs=5)

Top
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
chr2:241808307-241808308p.K12fs*1565
chr2:241808308-241808308p.K12fs*343
chr2:241812428-241812428p.A186V3
chr2:241812439-241812439p.G190R2
chr2:241816988-241816988p.A294V2
chr2:241817502-241817502p.V336I2
chr2:241815350-241815350p.?2
chr2:241808652-241808652p.V77V2
chr2:241815373-241815373p.V266V2
chr2:241817554-241817554p.P353L2

Top
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 2 31   11 611 1154 6
# mutation 2 31   11 611 1194 8
nonsynonymous SNV 1 1    11 511 191 5
synonymous SNV 1 21      1    103 3
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])

Top
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
chr2:241812439p.V266V2
chr2:241815373p.G190R2
chr2:241808652p.V77V2
chr2:241808356p.L25P1
chr2:241808694p.E117K1
chr2:241818165p.L25L1
chr2:241813423p.L151L1
chr2:241808357p.S268G1
chr2:241815377p.P30L1
chr2:241808728p.E157E1

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 AGXT 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]

Top
Gene Expression for AGXT

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

AFM,AGXT2,APCS,APOA2,APOA4,APOC3,C8A,
C9,CREB3L3,CRP,F2,F9,FABP1,FGF23,
HP,ITIH1,LEAP2,MT1B,PLG,SERPINA7,TM4SF5
AGXT2,AOX2P,ATP11AUN,CGB2,DEFB125,GH2,GNG8,
HDGFL1,HELT,IAPP,KRTAP13-2,LHX9,NKX6-3,OR10J5,
OR2M3,PSG8,SLC17A3,SLC6A19,TP53TG5,WFDC8,ZNF645

AGXT2,LINC00488,CLGN,GPX6,LYZL2,NOL4,OR2J2,
OR2J3,OR2W1,OR5B2,PAX2,PCDHA5,POM121L2,EPPIN,
TAS2R41,ULBP1,UPK1A,WFDC6,ZDHHC8P1,ZNF534,ZNF761
AADAC,AGXT2,APOA1,APOA4,APOB,APOC3,CRISP1,
FAM99A,FAM99B,GSTA5,KCNJ13,LCE3E,LOC388428,MOS,
ONECUT3,OR10H1,OR10H5,OR4N5,PWAR4___F2RL3___PAWR,SLC2A2,SPANXN3
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for AGXT
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA24633; -.
Organism-specific databasesCTD 189; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00114alanine-glyoxylate aminotransferasenutraceuticalPyridoxal Phosphate
DB00133alanine-glyoxylate aminotransferaseapproved; nutraceuticalL-Serine
DB00145alanine-glyoxylate aminotransferaseapproved; nutraceuticalGlycine
DB00160alanine-glyoxylate aminotransferaseapproved; nutraceuticalL-Alanine
DB02079alanine-glyoxylate aminotransferaseexperimental(Aminooxy)Acetic Acid
DB04083alanine-glyoxylate aminotransferaseexperimentalN'-Pyridoxyl-Lysine-5'-Monophosphate
DB08060alanine-glyoxylate aminotransferaseexperimental4-(2-AMINOPHENYL)-4-OXOBUTANOIC ACID


Top
Cross referenced IDs for AGXT
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas