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 AGXT

Basic gene info.	Gene symbol	AGXT
	Gene name	alanine-glyoxylate aminotransferase
	Synonyms	AGT\|AGT1\|AGXT1\|PH1\|SPAT\|SPT\|TLH6
	Cytomap	UCSC genome browser: 2q37.3
	Genomic location	chr2 :241808161-241818536
	Type of gene	protein-coding
	RefGenes	NM_000030.2,
	Ensembl id	ENSG00000172482
	Description	L-alanine: glyoxylate aminotransferase 1alanine--glyoxylate aminotransferasehepatic peroxisomal alanine:glyoxylate aminotransferaseserine--pyruvate aminotransferaseserine-pyruvate aminotransferaseserine:pyruvate aminotransferase
	Modification date	20141222
dbXrefs	MIM : 604285
	HGNC : HGNC
	Ensembl : ENSG00000172482
	HPRD : 05048
	Vega : OTTHUMG00000133354
Protein	UniProt: P21549 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_AGXT
	BioGPS: 189
	Gene Expression Atlas: ENSG00000172482
	The Human Protein Atlas: ENSG00000172482
Pathway	NCI Pathway Interaction Database: AGXT
	KEGG: AGXT
	REACTOME: AGXT
	ConsensusPathDB
	Pathway Commons: AGXT
Metabolism	MetaCyc: AGXT
	HUMANCyc: AGXT
Regulation	Ensembl's Regulation: ENSG00000172482
	miRBase: chr2 :241,808,161-241,818,536
	TargetScan: NM_000030
	cisRED: ENSG00000172482
Context	iHOP: AGXT
	cancer metabolism search in PubMed: AGXT
	UCL Cancer Institute: AGXT
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of AGXT in cancer cell metabolism	1. 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

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

Cancer 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/

Metabolic Pathway Description
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM	259900; phenotype. 604285; gene.
Orphanet	93598; Primary hyperoxaluria type 1.
Disease	KEGG Disease: AGXT
	MedGen: AGXT (Human Medical Genetics with Condition)
	ClinVar: AGXT
Phenotype	MGI: AGXT (International Mouse Phenotyping Consortium)
Phenotype	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.

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 AGXT 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

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=30)	Stat. for Synonymous SNVs (# total SNVs=12)

Stat. for Deletions (# total SNVs=4)	Stat. for Insertions (# total SNVs=5)

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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
chr2:241808307-241808308	p.K12fs*156	5
chr2:241812428-241812428	p.A186V	3
chr2:241808308-241808308	p.K12fs*34	3
chr2:241815350-241815350	p.?	2
chr2:241808652-241808652	p.V77V	2
chr2:241815373-241815373	p.V266V	2
chr2:241817554-241817554	p.P353L	2
chr2:241813456-241813456	p.L219L	2
chr2:241812439-241812439	p.G190R	2
chr2:241816988-241816988	p.A294V	2

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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		2		3	1				1	1		6	1	1		1	15	4		6
# mutation		2		3	1				1	1		6	1	1		1	19	4		8
nonsynonymous SNV		1		1					1	1		5	1	1		1	9	1		5
synonymous SNV		1		2	1							1					10	3		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])

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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
chr2:241808652	p.V266V	2
chr2:241812439	p.G190R	2
chr2:241815373	p.V77V	2
chr2:241810793	p.V91V	1
chr2:241814527	p.S221S	1
chr2:241808596	p.T369N	1
chr2:241817501	p.G103R	1
chr2:241810813	p.K228Q	1
chr2:241814543	p.R370R	1
chr2:241808602	p.G103E	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 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]

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Gene Expression for AGXT

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


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

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 AGXT

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA24633; -.
Organism-specific databases	CTD	189; -.

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	alanine-glyoxylate aminotransferase	nutraceutical	Pyridoxal Phosphate
DB00133	alanine-glyoxylate aminotransferase	approved; nutraceutical	L-Serine
DB00145	alanine-glyoxylate aminotransferase	approved; nutraceutical	Glycine
DB00160	alanine-glyoxylate aminotransferase	approved; nutraceutical	L-Alanine
DB02079	alanine-glyoxylate aminotransferase	experimental	(Aminooxy)Acetic Acid
DB04083	alanine-glyoxylate aminotransferase	experimental	N'-Pyridoxyl-Lysine-5'-Monophosphate
DB08060	alanine-glyoxylate aminotransferase	experimental	4-(2-AMINOPHENYL)-4-OXOBUTANOIC ACID

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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