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 GFPT2
Basic gene info.Gene symbolGFPT2
Gene nameglutamine-fructose-6-phosphate transaminase 2
SynonymsGFAT2
CytomapUCSC genome browser: 5q34-q35
Genomic locationchr5 :179727699-179780315
Type of geneprotein-coding
RefGenesNM_005110.2,
Ensembl idENSG00000131459
DescriptionD-fructose-6-phosphate amidotransferase 2GFAT 2glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2glutamine--fructose-6-phosphate aminotransferase [isomerizing] 2glutamine: fructose-6-phosphate aminotransferase 2glutamine:fructose 6 ph
Modification date20141207
dbXrefs MIM : 603865
HGNC : HGNC
Ensembl : ENSG00000131459
HPRD : 04842
Vega : OTTHUMG00000163442
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GFPT2
BioGPS: 9945
Gene Expression Atlas: ENSG00000131459
The Human Protein Atlas: ENSG00000131459
PathwayNCI Pathway Interaction Database: GFPT2
KEGG: GFPT2
REACTOME: GFPT2
ConsensusPathDB
Pathway Commons: GFPT2
MetabolismMetaCyc: GFPT2
HUMANCyc: GFPT2
RegulationEnsembl's Regulation: ENSG00000131459
miRBase: chr5 :179,727,699-179,780,315
TargetScan: NM_005110
cisRED: ENSG00000131459
ContextiHOP: GFPT2
cancer metabolism search in PubMed: GFPT2
UCL Cancer Institute: GFPT2
Assigned class in ccmGDBC

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Phenotypic Information for GFPT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GFPT2
Familial Cancer Database: GFPT2
* 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_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GFPT2
MedGen: GFPT2 (Human Medical Genetics with Condition)
ClinVar: GFPT2
PhenotypeMGI: GFPT2 (International Mouse Phenotyping Consortium)
PhenomicDB: GFPT2

Mutations for GFPT2
* 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
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasGFPT2chr5179751827179751847GFPT2chr5179755052179755072
pancreasGFPT2chr5179762681179762701chr5179805364179805384
pancreasGFPT2chr5179763363179763383chr5179638056179638076
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 GFPT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW867731GFPT2372215179727919179728102GFPT22203635179727749179727892
BE841311GFPT221755179727929179728102GFPT21743175179727749179727892
BE841297GFPT2151605179727749179727892GFPT21593485179727913179728102
AW867686GFPT2181535179727758179727892GFPT21523415179727913179728102

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    1          
GAIN (# sample)      1          
LOSS (# sample) 1               
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=58)
Stat. for Synonymous SNVs
(# total SNVs=27)
Stat. for Deletions
(# total SNVs=2)
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
chr5:179740827-179740827p.I471V3
chr5:179763551-179763551p.E48K2
chr5:179751178-179751178p.?2
chr5:179731922-179731922p.T564T2
chr5:179751867-179751867p.R209W2
chr5:179734200-179734200p.Y550Y2
chr5:179731781-179731781p.T611T2
chr5:179765502-179765502p.D36N2
chr5:179731784-179731784p.V610V2
chr5:179745905-179745905p.I282I2

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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
# sample251151 4 21 104  1127 10
# mutation251152 4 21 104  1147 12
nonsynonymous SNV1319  2 2  83  154 10
synonymous SNV12 62 2  1 21   93 2
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
chr5:179743769p.I282I2
chr5:179745905p.V383M2
chr5:179763551p.E48K2
chr5:179743988p.V590I1
chr5:179765502p.T450T1
chr5:179729580p.V285L1
chr5:179734239p.T146I1
chr5:179745956p.R673I1
chr5:179740888p.P589P1
chr5:179757797p.V447I1

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 GFPT2 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 GFPT2

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

ADAM12,AXL,MEDAG,C1R,C1S,COL6A3,CRISPLD2,
DSE,FAP,FSTL1,GAS1,GFPT2,ITGA5,ITPRIP,
MMP2,PDPN,PRRX1,SERPINF1,SERPING1,TIMP2,TSHZ3
AXL,MEDAG,CILP,ACKR3,DNM1,FBN1,FSTL1,
GAS7,GFPT2,GPR1,GPR133,HRH1,ITGB3,LMX1A,
MFAP5,PROCR,PTGIS,SCARA5,SPSB4,WNT10B,XPNPEP2

ADAM12,CLMP,COL15A1,COL1A1,COL3A1,COL5A2,COL8A1,
FBN1,GAS1,GFPT2,GPR176,HHIPL1,HRH2,HTR2A,
IL1R1,ITGA5,LOX,PCDHGA12,PXDN,WISP1,ZNF469
ADAMTSL4,ARHGAP29,MEDAG,C1orf198,CADM3,CD248,CD34,
CREB5,DDX19A,FAM43B,FBLN1,FSTL3,GFPT2,HTRA3,
LATS2,MSX1,NPR1,RBMS1,STK32B,TIMP3,WTIP
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 GFPT2


There's no related Drug.
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Cross referenced IDs for GFPT2
* 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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