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 GART
Basic gene info.Gene symbolGART
Gene namephosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase
SynonymsAIRS|GARS|GARTF|PAIS|PGFT|PRGS
CytomapUCSC genome browser: 21q22.11
Genomic locationchr21 :34896315-34914464
Type of geneprotein-coding
RefGenesNM_000819.4,
NM_001136005.1,NM_001136006.1,NM_175085.2,
Ensembl idENSG00000262473
Descriptiontrifunctional purine biosynthetic protein adenosine-3
Modification date20141207
dbXrefs MIM : 138440
HGNC : HGNC
Ensembl : ENSG00000159131
HPRD : 00716
Vega : OTTHUMG00000065628
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GART
BioGPS: 2618
Gene Expression Atlas: ENSG00000262473
The Human Protein Atlas: ENSG00000262473
PathwayNCI Pathway Interaction Database: GART
KEGG: GART
REACTOME: GART
ConsensusPathDB
Pathway Commons: GART
MetabolismMetaCyc: GART
HUMANCyc: GART
RegulationEnsembl's Regulation: ENSG00000262473
miRBase: chr21 :34,896,315-34,914,464
TargetScan: NM_000819
cisRED: ENSG00000262473
ContextiHOP: GART
cancer metabolism search in PubMed: GART
UCL Cancer Institute: GART
Assigned class in ccmGDBC

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

check002.gifMetabolic Pathway Description
KEGG_PURINE_METABOLISM
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PURINE_METABOLISM

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

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryGARTchr213491309934913119LOC349160chr7136721438136721458
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GART related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF763230GART4244213488729034887528FCHO222933057235970472364512
BE147859GART28129213489148634891587VCP12542293507017635070473

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=51)
Stat. for Synonymous SNVs
(# total SNVs=24)
Stat. for Deletions
(# total SNVs=5)
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
chr21:34882122-34882122p.K807fs*77
chr21:34889714-34889714p.S635F3
chr21:34903066-34903066p.Q241R2
chr21:34878352-34878352p.D838N2
chr21:34889728-34889728p.I630I2
chr21:34882121-34882122p.A808fs*262
chr21:34889295-34889295p.?2
chr21:34877961-34877961p.I878V2
chr21:34883613-34883613p.Q754K2
chr21:34894583-34894583p.L435F2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13 6  6  2 11411 10718
# mutation13 6  7  2 11411 97112
nonsynonymous SNV11 3  3  2 5311 74 9
synonymous SNV 2 3  4    61   2313
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
chr21:34878379p.R829R,GART2
chr21:34889714p.Q241R,GART2
chr21:34903066p.S635F,GART2
chr21:34882226p.P143T,GART1
chr21:34903096p.A853A,GART1
chr21:34889728p.S634Y,GART1
chr21:34907023p.Q361E,GART1
chr21:34876803p.C93F,GART1
chr21:34897279p.R829L,GART1
chr21:34883584p.I630I,GART1

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 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

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

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
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 GART
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
DB00642phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetaseapproved; investigationalPemetrexed
DB02236phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetaseexperimentalGlycinamide Ribonucleotide
DB03546phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetaseexperimental10-CF3C(OH)2-DDACTHF
DB00145phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetaseapproved; nutraceuticalGlycine
DB00130phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetaseapproved; nutraceutical; investigationalL-Glutamine
DB00563phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetaseapprovedMethotrexate


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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



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