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 FAH
Basic gene info.Gene symbolFAH
Gene namefumarylacetoacetate hydrolase (fumarylacetoacetase)
Synonyms-
CytomapUCSC genome browser: 15q25.1
Genomic locationchr15 :80445232-80478924
Type of geneprotein-coding
RefGenesNM_000137.2,
Ensembl idENSG00000103876
DescriptionFAAbeta-diketonasefumarylacetoacetase
Modification date20141222
dbXrefs MIM : 613871
HGNC : HGNC
Ensembl : ENSG00000103876
HPRD : 02040
Vega : OTTHUMG00000144187
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FAH
BioGPS: 2184
Gene Expression Atlas: ENSG00000103876
The Human Protein Atlas: ENSG00000103876
PathwayNCI Pathway Interaction Database: FAH
KEGG: FAH
REACTOME: FAH
ConsensusPathDB
Pathway Commons: FAH
MetabolismMetaCyc: FAH
HUMANCyc: FAH
RegulationEnsembl's Regulation: ENSG00000103876
miRBase: chr15 :80,445,232-80,478,924
TargetScan: NM_000137
cisRED: ENSG00000103876
ContextiHOP: FAH
cancer metabolism search in PubMed: FAH
UCL Cancer Institute: FAH
Assigned class in ccmGDBC

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

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

Mutations for FAH
* 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 FAH related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU734913CRYBB219180222562767525627836FAH176468158046454380469916
BU956000MIR548N12152179315154179315368FAH215840158046062080473502
CN263730TPM2149893568267635683173FAH491628158045044480452166
BU955820MIR548N392552179315154179315370FAH255875158046062080473494
BU856741MIR548N12152179315154179315368FAH215712158046062080472564

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=23)
Stat. for Synonymous SNVs
(# total SNVs=13)
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
chr15:80454663-80454663p.A147V3
chr15:80467429-80467429p.L303L3
chr15:80465390-80465390p.L247L2
chr15:80450394-80450394p.?2
chr15:80478545-80478545p.P418P2
chr15:80450470-80450470p.F50F2
chr15:80452769-80452769p.A111G2
chr15:80454614-80454614p.R131W2
chr15:80469898-80469898p.A311A1
chr15:80452167-80452167p.L88L1

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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
# sample22 7  1 1  43  175 5
# mutation22 7  1 1  53  175 5
nonsynonymous SNV 1 4  1    2    44 5
synonymous SNV21 3    1  33  131  
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
chr15:80454614p.R131W2
chr15:80454663p.A147V2
chr15:80472567p.D183E1
chr15:80450417p.P354P1
chr15:80465456p.G33S1
chr15:80473403p.P188L1
chr15:80450431p.S361F1
chr15:80454634p.G37G1
chr15:80465464p.P188P1
chr15:80473405p.M362V1

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 FAH 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 FAH

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

ACAA1,ACY1,BLVRB,CCDC57,CYB561D2,CYB5A,DCXR,
DHRS4,DHRS4L2,FAH,GAMT,MFSD7,MMAB,MPV17L,
REEP6,SDSL,SIL1,SPINK8,TTC36,UQCRQ,ZFAND6
ABHD15,ACO1,ACOT1,AOC3,AQP7,BOK,CIDEC,
DGAT1,ESYT1,FAH,GPD1,GYG2,HEPACAM,HEPN1,
LIPE,MARC1,PLA2G16,PLIN1,PNPLA2,RBP4,TYRO3

HYKK,ATIC,BCS1L,CCNE1,CHCHD6,DKC1,FAH,
HDAC8,HSD17B10,LAGE3,NAA10,NECAB3,PDHA1,RBBP7,
SCML1,SLC22A12,SLC5A6,TIMM17B,TIMM8A,TOMM34,UTP14A
AKR1A1,C9orf41,CA9,DDC,DEGS2,DHRS4L2,FAH,
GCHFR,GPR89A,HACL1,NPY6R,OTC,PEBP1,PNPO,
SHMT1,SLC16A10,SLC25A15,SLC2A9,TMEM41A,TMEM52,ZDHHC9
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 FAH
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
DB00143fumarylacetoacetate hydrolase (fumarylacetoacetase)approved; nutraceuticalGlutathione
DB00120fumarylacetoacetate hydrolase (fumarylacetoacetase)approved; nutraceuticalL-Phenylalanine
DB00135fumarylacetoacetate hydrolase (fumarylacetoacetase)approved; nutraceuticalL-Tyrosine
DB00360fumarylacetoacetate hydrolase (fumarylacetoacetase)approved; investigationalTetrahydrobiopterin


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Cross referenced IDs for FAH
* 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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