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 GART

Basic gene info.	Gene symbol	GART
	Gene name	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase
	Synonyms	AIRS\|GARS\|GARTF\|PAIS\|PGFT\|PRGS
	Cytomap	UCSC genome browser: 21q22.11
	Genomic location	chr21 :34896315-34914464
	Type of gene	protein-coding
	RefGenes	NM_000819.4, NM_001136005.1,NM_001136006.1,NM_175085.2,
	Ensembl id	ENSG00000262473
	Description	trifunctional purine biosynthetic protein adenosine-3
	Modification date	20141207
dbXrefs	MIM : 138440
	HGNC : HGNC
	Ensembl : ENSG00000159131
	HPRD : 00716
	Vega : OTTHUMG00000065628
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GART
	BioGPS: 2618
	Gene Expression Atlas: ENSG00000262473
	The Human Protein Atlas: ENSG00000262473
Pathway	NCI Pathway Interaction Database: GART
	KEGG: GART
	REACTOME: GART
	ConsensusPathDB
	Pathway Commons: GART
Metabolism	MetaCyc: GART
	HUMANCyc: GART
Regulation	Ensembl's Regulation: ENSG00000262473
	miRBase: chr21 :34,896,315-34,914,464
	TargetScan: NM_000819
	cisRED: ENSG00000262473
Context	iHOP: GART
	cancer metabolism search in PubMed: GART
	UCL Cancer Institute: GART
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: GART
	Familial Cancer Database: GART

* 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_PURINE_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PURINE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: GART
	MedGen: GART (Human Medical Genetics with Condition)
	ClinVar: GART
Phenotype	MGI: GART (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GART

Mutations for GART

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	GART	chr21	34913099	34913119	LOC349160	chr7	136721438	136721458

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GART related fusion information.

ID	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
BF763230	GART	4	244	21	34887290	34887528	FCHO2	229	330	5	72359704	72364512
BE147859	GART	28	129	21	34891486	34891587	VCP	125	422	9	35070176	35070473

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=51)	Stat. for Synonymous SNVs (# total SNVs=24)

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

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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
chr21:34882122-34882122	p.K807fs*7	7
chr21:34889714-34889714	p.S635F	3
chr21:34878352-34878352	p.D838N	2
chr21:34889728-34889728	p.I630I	2
chr21:34882121-34882122	p.A808fs*26	2
chr21:34889295-34889295	p.?	2
chr21:34877961-34877961	p.I878V	2
chr21:34883613-34883613	p.Q754K	2
chr21:34894583-34894583	p.L435F	2
chr21:34903066-34903066	p.Q241R	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=2

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	1	3		6			6			2		11	4	1	1		10	7	1	8
# mutation	1	3		6			7			2		11	4	1	1		9	7	1	12
nonsynonymous SNV	1	1		3			3			2		5	3	1	1		7	4		9
synonymous SNV		2		3			4					6	1				2	3	1	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
chr21:34878379	p.R829R,GART	2
chr21:34889714	p.Q241R,GART	2
chr21:34903066	p.S635F,GART	2
chr21:34876803	p.A853A,GART	1
chr21:34897279	p.S634Y,GART	1
chr21:34883584	p.Q361E,GART	1
chr21:34903121	p.P143T,GART	1
chr21:34876442	p.R829L,GART	1
chr21:34889792	p.I630I,GART	1
chr21:34907045	p.S315F,GART	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 GART 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 GART

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


COA7,CHAF1B,CHEK1,DONSON,EXO1,GART,GMPS, GSG2,GTPBP4,MSH2,NUP205,ORC1,RRP1B,SCAF4, SRPK1,STIL,SUV39H2,TEX10,TTK,URB1,WDR43	AK3___AK4,ANKEF1,BAZ1B,MIS18BP1,CDK8,DARS2,DHTKD1, EIF3A,GART,GMCL1,KIF2A,KPNB1,LARP1,MPHOSPH9, NCBP1,RAD50,RPE,TRIM44,TXLNG,ZC3H15,ZNF664

PARPBP,CCDC138,CCT8,CENPL,GART,LIN9,MARS2, MRPL39,MRS2,NOC3L,PUS7L,RACGAP1,RAD54B,RRP1B, SUV39H2,TFAM,TFB2M,UMPS,URB1,WDR12,WDR3	DDIAS,ASUN,CCT2,GART,GINS1,GINS3,H2AFZ, ILF2,MCM6,MRPL3,NUP85,POLE2,RAN,RFC3, RQCD1,SNRPD1,SUV39H2,TFDP1,UTP6,VRK1,WDR77

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 GART

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB00642	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	approved; investigational	Pemetrexed
DB02236	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	experimental	Glycinamide Ribonucleotide
DB03546	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	experimental	10-CF3C(OH)2-DDACTHF
DB00145	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	approved; nutraceutical	Glycine
DB00130	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	approved; nutraceutical; investigational	L-Glutamine
DB00563	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	approved	Methotrexate

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Cross referenced IDs for GART

* 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