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 PFAS
Basic gene info.Gene symbolPFAS
Gene namephosphoribosylformylglycinamidine synthase
SynonymsFGAMS|FGAR-AT|FGARAT|PURL
CytomapUCSC genome browser: 17p13.1
Genomic locationchr17 :8152595-8173809
Type of geneprotein-coding
RefGenesNM_012393.2,
Ensembl idENSG00000178921
DescriptionFGAM synthaseFGAR amidotransferaseformylglycinamide ribonucleotide amidotransferaseformylglycinamide ribotide amidotransferaseformylglycinamide ribotide synthetase
Modification date20141207
dbXrefs MIM : 602133
HGNC : HGNC
Ensembl : ENSG00000178921
HPRD : 09072
Vega : OTTHUMG00000108188
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PFAS
BioGPS: 5198
Gene Expression Atlas: ENSG00000178921
The Human Protein Atlas: ENSG00000178921
PathwayNCI Pathway Interaction Database: PFAS
KEGG: PFAS
REACTOME: PFAS
ConsensusPathDB
Pathway Commons: PFAS
MetabolismMetaCyc: PFAS
HUMANCyc: PFAS
RegulationEnsembl's Regulation: ENSG00000178921
miRBase: chr17 :8,152,595-8,173,809
TargetScan: NM_012393
cisRED: ENSG00000178921
ContextiHOP: PFAS
cancer metabolism search in PubMed: PFAS
UCL Cancer Institute: PFAS
Assigned class in ccmGDBC

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Phenotypic Information for PFAS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PFAS
Familial Cancer Database: PFAS
* 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: PFAS
MedGen: PFAS (Human Medical Genetics with Condition)
ClinVar: PFAS
PhenotypeMGI: PFAS (International Mouse Phenotyping Consortium)
PhenomicDB: PFAS

Mutations for PFAS
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PFAS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF985017AGBL51010122729337627293467PFAS901791781573198157494
AK292402PFAS642451781526078172675RNF14142404352111053387010533982

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=74)
Stat. for Synonymous SNVs
(# total SNVs=27)
Stat. for Deletions
(# total SNVs=3)
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
chr17:8172316-8172316p.A1251S3
chr17:8158845-8158845p.V137G2
chr17:8159199-8159199p.V217V2
chr17:8167544-8167544p.D602D2
chr17:8159200-8159200p.E218*2
chr17:8168442-8168442p.R760Q2
chr17:8158398-8158398p.T111S2
chr17:8172502-8172502p.P1313A2
chr17:8167875-8167875p.L669L2
chr17:8160243-8160243p.G346D2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11191 12 21 763  118 15
# mutation11181 14 21 763  149 17
nonsynonymous SNV 116  12 11 762  87 10
synonymous SNV1  21 2 1    1  62 7
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
chr17:8158833p.R23L2
chr17:8157323p.R458M2
chr17:8166274p.P133L2
chr17:8158437p.Q1186Q1
chr17:8167098p.S2F1
chr17:8170745p.A183V1
chr17:8159851p.P413S1
chr17:8168408p.R638Q1
chr17:8172397p.R969G1
chr17:8157260p.Y1202Y1

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 PFAS 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 PFAS

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

CTC1,CHD3,CNTROB,CYB5D1,DPH1,DVL2,ELAC2,
FXR2,KIAA0753,KRBA2,MNT,MYBBP1A,MYH10,NEURL4,
PFAS,RAI1,SENP3,SGSM2,SMG6,SMYD4,ZNF594
AARS2,PRRC2A,C10orf2,CAD,COL27A1,CRACR2A,ICOSLG,
ILF3,KDM5C,MYBBP1A,PACSIN2,PDCD11,PFAS,RAI1,
TTC22,UBE2O,URB1,WDR4,ZBTB12,ZNF324B,ZNF512B

C17orf85,CAMKK1,CNTROB,COX10,DHX33,DPH1,ELAC2,
GEMIN4,GSG2,CLUH,KIAA0753,MINK1,MYBBP1A,NEURL4,
PELP1,PFAS,PRPF8,SCO1,TOP3A,TSR1,USP43
BMS1,CAD,CKAP5,DNMT1,GCN1L1,ILF3,KHSRP,
MDC1,MYBBP1A,NAT10,NUP188,NUP205,PDCD11,PFAS,
POLR1A,PRKDC,RBM14,RBM19,TMEM201,URB1,ZC3H18
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 PFAS
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
DB00142phosphoribosylformylglycinamidine synthaseapproved; nutraceuticalL-Glutamic Acid
DB03431phosphoribosylformylglycinamidine synthaseexperimentalAdenosine-5'-Diphosphate
DB00145phosphoribosylformylglycinamidine synthaseapproved; nutraceuticalGlycine
DB00130phosphoribosylformylglycinamidine synthaseapproved; nutraceutical; investigationalL-Glutamine


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Cross referenced IDs for PFAS
* 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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