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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PFAS |
Basic gene info. | Gene symbol | PFAS |
Gene name | phosphoribosylformylglycinamidine synthase | |
Synonyms | FGAMS|FGAR-AT|FGARAT|PURL | |
Cytomap | UCSC genome browser: 17p13.1 | |
Genomic location | chr17 :8152595-8173809 | |
Type of gene | protein-coding | |
RefGenes | NM_012393.2, | |
Ensembl id | ENSG00000178921 | |
Description | FGAM synthaseFGAR amidotransferaseformylglycinamide ribonucleotide amidotransferaseformylglycinamide ribotide amidotransferaseformylglycinamide ribotide synthetase | |
Modification date | 20141207 | |
dbXrefs | MIM : 602133 | |
HGNC : HGNC | ||
Ensembl : ENSG00000178921 | ||
HPRD : 09072 | ||
Vega : OTTHUMG00000108188 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PFAS | |
BioGPS: 5198 | ||
Gene Expression Atlas: ENSG00000178921 | ||
The Human Protein Atlas: ENSG00000178921 | ||
Pathway | NCI Pathway Interaction Database: PFAS | |
KEGG: PFAS | ||
REACTOME: PFAS | ||
ConsensusPathDB | ||
Pathway Commons: PFAS | ||
Metabolism | MetaCyc: PFAS | |
HUMANCyc: PFAS | ||
Regulation | Ensembl's Regulation: ENSG00000178921 | |
miRBase: chr17 :8,152,595-8,173,809 | ||
TargetScan: NM_012393 | ||
cisRED: ENSG00000178921 | ||
Context | iHOP: PFAS | |
cancer metabolism search in PubMed: PFAS | ||
UCL Cancer Institute: PFAS | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PFAS(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PFAS |
Familial Cancer Database: PFAS |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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: PFAS |
MedGen: PFAS (Human Medical Genetics with Condition) | |
ClinVar: PFAS | |
Phenotype | MGI: 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PFAS 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 |
BF985017 | AGBL5 | 10 | 101 | 2 | 27293376 | 27293467 | PFAS | 90 | 179 | 17 | 8157319 | 8157494 | |
AK292402 | PFAS | 6 | 4245 | 17 | 8152607 | 8172675 | RNF141 | 4240 | 4352 | 11 | 10533870 | 10533982 |
Other DBs for Structural Variants |
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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 |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=74) | (# total SNVs=27) |
(# total SNVs=3) | (# 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 |
chr17:8172316-8172316 | p.A1251S | 3 |
chr17:8172502-8172502 | p.P1313A | 2 |
chr17:8167875-8167875 | p.L669L | 2 |
chr17:8160243-8160243 | p.G346D | 2 |
chr17:8168224-8168224 | p.S687S | 2 |
chr17:8168866-8168866 | p.? | 2 |
chr17:8167608-8167608 | p.P624A | 2 |
chr17:8169275-8169275 | p.D881Y | 2 |
chr17:8158833-8158833 | p.P133L | 2 |
chr17:8159164-8159164 | p.R206C | 2 |
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SNV Counts per Each Loci in TCGA data |
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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 | 1 | 1 | 9 | 1 |   | 12 |   | 2 | 1 |   | 7 | 6 | 3 |   |   | 11 | 8 |   | 15 |
# mutation | 1 | 1 | 1 | 8 | 1 |   | 14 |   | 2 | 1 |   | 7 | 6 | 3 |   |   | 14 | 9 |   | 17 |
nonsynonymous SNV |   | 1 | 1 | 6 |   |   | 12 |   | 1 | 1 |   | 7 | 6 | 2 |   |   | 8 | 7 |   | 10 |
synonymous SNV | 1 |   |   | 2 | 1 |   | 2 |   | 1 |   |   |   |   | 1 |   |   | 6 | 2 |   | 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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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 |
chr17:8166274 | p.R458M | 2 |
chr17:8158833 | p.P133L | 2 |
chr17:8157323 | p.R23L | 2 |
chr17:8159900 | p.Q277Q | 1 |
chr17:8168914 | p.T749S | 1 |
chr17:8157504 | p.R1008Q | 1 |
chr17:8161517 | p.P1278T | 1 |
chr17:8170199 | p.A74V | 1 |
chr17:8158879 | p.V281V | 1 |
chr17:8167625 | p.S468Y | 1 |
Other DBs for Point Mutations |
Copy 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 |
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. |
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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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for PFAS |
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 |
DB00142 | phosphoribosylformylglycinamidine synthase | approved; nutraceutical | L-Glutamic Acid | ||
DB03431 | phosphoribosylformylglycinamidine synthase | experimental | Adenosine-5'-Diphosphate | ||
DB00145 | phosphoribosylformylglycinamidine synthase | approved; nutraceutical | Glycine | ||
DB00130 | phosphoribosylformylglycinamidine synthase | approved; nutraceutical; investigational | L-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 |
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