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 AGXT2
Basic gene info.Gene symbolAGXT2
Gene namealanine--glyoxylate aminotransferase 2
SynonymsAGT2|DAIBAT
CytomapUCSC genome browser: 5p13
Genomic locationchr5 :34998205-35048240
Type of geneprotein-coding
RefGenesNM_031900.3,
Ensembl idENSG00000113492
Description(R)-3-amino-2-methylpropionate--pyruvate transaminasealanine--glyoxylate aminotransferase 2, mitochondrialbeta-ALAAT IIbeta-alanine-pyruvate aminotransferase
Modification date20141207
dbXrefs MIM : 612471
HGNC : HGNC
Ensembl : ENSG00000113492
HPRD : 10638
Vega : OTTHUMG00000090788
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AGXT2
BioGPS: 64902
Gene Expression Atlas: ENSG00000113492
The Human Protein Atlas: ENSG00000113492
PathwayNCI Pathway Interaction Database: AGXT2
KEGG: AGXT2
REACTOME: AGXT2
ConsensusPathDB
Pathway Commons: AGXT2
MetabolismMetaCyc: AGXT2
HUMANCyc: AGXT2
RegulationEnsembl's Regulation: ENSG00000113492
miRBase: chr5 :34,998,205-35,048,240
TargetScan: NM_031900
cisRED: ENSG00000113492
ContextiHOP: AGXT2
cancer metabolism search in PubMed: AGXT2
UCL Cancer Institute: AGXT2
Assigned class in ccmGDBC

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Phenotypic Information for AGXT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AGXT2
Familial Cancer Database: AGXT2
* 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
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PYRIMIDINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: AGXT2
MedGen: AGXT2 (Human Medical Genetics with Condition)
ClinVar: AGXT2
PhenotypeMGI: AGXT2 (International Mouse Phenotyping Consortium)
PhenomicDB: AGXT2

Mutations for AGXT2
* 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 AGXT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AF121182SERPINA1156149484898094849230AGXT25535953501307235025960

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample          1  3  1
GAIN (# sample)          1  3  1
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=70)
Stat. for Synonymous SNVs
(# total SNVs=21)
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
chr5:34998865-34998865p.R502C6
chr5:35039555-35039555p.T79M4
chr5:34998924-34998924p.R482H3
chr5:35047956-35047956p.L14L3
chr5:35032909-35032909p.R233C3
chr5:35013131-35013131p.A372A3
chr5:35014173-35014173p.H339Y2
chr5:35010122-35010122p.E441*2
chr5:35003913-35003913p.C464C2
chr5:35039462-35039462p.G110E2

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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=7

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2 15  3 111824  1910 14
# mutation 2 15  3 1111224  1812 14
nonsynonymous SNV 1 9  1 1111113  159 10
synonymous SNV 1 6  2    111  33 4
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
chr5:34998865p.R502C6
chr5:35037140p.L131L3
chr5:35047956p.L14L3
chr5:34998837p.R511K2
chr5:35010173p.G62G2
chr5:35014170p.D340N2
chr5:35037072p.A154D2
chr5:35039605p.E424K2
chr5:35025869p.E321G2
chr5:35040730p.I191N1

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 AGXT2 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 AGXT2

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

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

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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 AGXT2
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
DB00114alanine--glyoxylate aminotransferase 2nutraceuticalPyridoxal Phosphate
DB00119alanine--glyoxylate aminotransferase 2approved; nutraceuticalPyruvic acid
DB00145alanine--glyoxylate aminotransferase 2approved; nutraceuticalGlycine
DB00160alanine--glyoxylate aminotransferase 2approved; nutraceuticalL-Alanine


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Cross referenced IDs for AGXT2
* 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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