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 FPGS
Basic gene info.Gene symbolFPGS
Gene namefolylpolyglutamate synthase
Synonyms-
CytomapUCSC genome browser: 9q34.1
Genomic locationchr9 :130565507-130576556
Type of geneprotein-coding
RefGenesNM_001018078.2,
NM_001288803.1,NM_004957.5,NR_110170.1,
Ensembl idENSG00000136877
Descriptionfolylpoly-gamma-glutamate synthetasefolylpolyglutamate synthase, mitochondrialtetrahydrofolate synthasetetrahydrofolylpolyglutamate synthase
Modification date20141207
dbXrefs MIM : 136510
HGNC : HGNC
Ensembl : ENSG00000136877
HPRD : 00642
Vega : OTTHUMG00000020716
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FPGS
BioGPS: 2356
Gene Expression Atlas: ENSG00000136877
The Human Protein Atlas: ENSG00000136877
PathwayNCI Pathway Interaction Database: FPGS
KEGG: FPGS
REACTOME: FPGS
ConsensusPathDB
Pathway Commons: FPGS
MetabolismMetaCyc: FPGS
HUMANCyc: FPGS
RegulationEnsembl's Regulation: ENSG00000136877
miRBase: chr9 :130,565,507-130,576,556
TargetScan: NM_001018078
cisRED: ENSG00000136877
ContextiHOP: FPGS
cancer metabolism search in PubMed: FPGS
UCL Cancer Institute: FPGS
Assigned class in ccmGDBC

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

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

Mutations for FPGS
* 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
ovaryFPGSchr9130569321130569341SH2D3Cchr9130537332130537352
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 FPGS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE514681COBL21324475133658151336612FPGS2424819130572003130573276
CN275141FPGS511509130565894130565993FPGS1455819130565673130566264
BF772512FPGS51039130569942130570585FPGS1002709130566642130566979

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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=40)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr9:130565267-130565267p.I22V4
chr9:130566821-130566821p.T104M3
chr9:130566572-130566572p.V49V2
chr9:130575758-130575758p.H547D2
chr9:130569923-130569923p.D234N2
chr9:130569293-130569293p.N143S2
chr9:130575672-130575672p.S518I2
chr9:130566630-130566630p.R69G1
chr9:130572317-130572317p.E407K1
chr9:130575710-130575710p.R531*1

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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
# sample11 5  313  121  22 6
# mutation11 5  313  121  22 6
nonsynonymous SNV11 3  113  121  21 5
synonymous SNV   2  2          1 1
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
chr9:130569923p.D208N,FPGS2
chr9:130569902p.L113M,FPGS1
chr9:130573287p.N449K,FPGS1
chr9:130566616p.P125S,FPGS1
chr9:130569916p.G469S,FPGS1
chr9:130575544p.T132A,FPGS1
chr9:130566689p.S471S,FPGS1
chr9:130575602p.G178D,FPGS1
chr9:130566821p.P514S,FPGS1
chr9:130570856p.D201N,FPGS1

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 FPGS 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 FPGS

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

AK1,C9orf114,CDK9,COQ4,DPM2,EDF1,ENDOG,
FBXW5,FPGS,LRSAM1,NTMT1,NUDT22,PHPT1,PPP2R4,
PTGES2,PTRH1,SLC2A8,SSNA1,TOR2A,UCK1,URM1
BSG,C20orf27,EIF4EBP1,ETFB,F8A1,FPGS,GCDH,
GCHFR,MAPK11,MPST,PCYT2,PMM1,POLR2E,PQLC1,
PSMA7,SLC25A10,SLC25A1,SLC2A4RG,SNX8,TMEM120A,TSPO

ARPC5L,C9orf142,CDK9,NELFB,COQ4,EDF1,ENDOG,
FPGS,NTMT1,MRPL41,PMPCA,PPP2R4,PTGES2,PTRH1,
SH3GLB2,SSNA1,TOR2A,TUBB4B,UBAC1,WDR34,ZDHHC12
C19orf10,DHRS13,FARSA,FPGS,HMBS,METTL1,MRPL4,
MTX1,NUDT8,NUP85,PDF,PMM2,PPIB,PUSL1,
PYCR1,PYCRL,RRP9,RUVBL2,ALYREF,THOC6,TSFM
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 FPGS
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
DB00142folylpolyglutamate synthaseapproved; nutraceuticalL-Glutamic Acid
DB00293folylpolyglutamate synthaseapproved; investigationalRaltitrexed
DB00544folylpolyglutamate synthaseapprovedFluorouracil
DB00650folylpolyglutamate synthaseapprovedLeucovorin
DB00145folylpolyglutamate synthaseapproved; nutraceuticalGlycine
DB00133folylpolyglutamate synthaseapproved; nutraceuticalL-Serine
DB00515folylpolyglutamate synthaseapprovedCisplatin
DB00252folylpolyglutamate synthaseapprovedPhenytoin
DB00563folylpolyglutamate synthaseapprovedMethotrexate
DB00642folylpolyglutamate synthaseapproved; investigationalPemetrexed


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Cross referenced IDs for FPGS
* 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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