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 FH
Basic gene info.Gene symbolFH
Gene namefumarate hydratase
SynonymsHLRCC|LRCC|MCL|MCUL1
CytomapUCSC genome browser: 1q42.1
Genomic locationchr1 :241660856-241683085
Type of geneprotein-coding
RefGenesNM_000143.3,
Ensembl idENSG00000091483
Descriptionfumarasefumarate hydratase, mitochondrial
Modification date20141222
dbXrefs MIM : 136850
HGNC : HGNC
Ensembl : ENSG00000091483
HPRD : 00652
Vega : OTTHUMG00000039597
ProteinUniProt: P07954
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FH
BioGPS: 2271
Gene Expression Atlas: ENSG00000091483
The Human Protein Atlas: ENSG00000091483
PathwayNCI Pathway Interaction Database: FH
KEGG: FH
REACTOME: FH
ConsensusPathDB
Pathway Commons: FH
MetabolismMetaCyc: FH
HUMANCyc: FH
RegulationEnsembl's Regulation: ENSG00000091483
miRBase: chr1 :241,660,856-241,683,085
TargetScan: NM_000143
cisRED: ENSG00000091483
ContextiHOP: FH
cancer metabolism search in PubMed: FH
UCL Cancer Institute: FH
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of FH in cancer cell metabolism1. Zecchini V, Madhu B, Russell R, Pertega-Gomes N, Warren A, et al. (2014) Nuclear ARRB1 induces pseudohypoxia and cellular metabolism reprogramming in prostate cancer. EMBO J 33: 1365-1382. doi: 10.15252/embj.201386874. pmid: 4194125. go to article
2. Morin A, Letouze E, Gimenez-Roqueplo AP, Favier J (2014) Oncometabolites-driven tumorigenesis: From genetics to targeted therapy. Int J Cancer 135: 2237-2248. doi: 10.1002/ijc.29080. go to article
3. Nowicki S, Gottlieb E (2015) Oncometabolites: tailoring our genes. FEBS J. doi: 10.1111/febs.13295. go to article
4. Sourbier C, Ricketts CJ, Matsumoto S, Crooks DR, Liao PJ, et al. (2014) Targeting ABL1-mediated oxidative stress adaptation in fumarate hydratase-deficient cancer. Cancer Cell 26: 840-850. doi: 10.1016/j.ccell.2014.10.005. pmid: 4386283. go to article
5. Kaelin WG, Jr. (2014) DisABLing kidney cancers caused by fumarate hydratase mutations. Cancer Cell 26: 779-780. doi: 10.1016/j.ccell.2014.11.022. go to article

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

check002.gifOthers
OMIM 136850; gene.
150800; phenotype.
606812; phenotype.
Orphanet 24; Fumaric aciduria.
29072; Hereditary pheochromocytoma-paraganglioma.
523; Hereditary leiomyomatosis and renal cell cancer.
DiseaseKEGG Disease: FH
MedGen: FH (Human Medical Genetics with Condition)
ClinVar: FH
PhenotypeMGI: FH (International Mouse Phenotyping Consortium)
PhenomicDB: FH

Mutations for FH
* 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 FH related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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        
GAIN (# sample)        1        
LOSS (# sample)                 
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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=44)
Stat. for Synonymous SNVs
(# total SNVs=18)
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
chr1:241663758-241663758p.T457A3
chr1:241665814-241665814p.G389W2
chr1:241661270-241661270p.G464V2
chr1:241675287-241675287p.D179N2
chr1:241663756-241663756p.T457T2
chr1:241680472-241680472p.?2
chr1:241663880-241663880p.V416A2
chr1:241680522-241680522p.T76M2
chr1:241663881-241663881p.V416L2
chr1:241665791-241665791p.V396V1

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample4  17  2 1  831  2319
# mutation4  15  2 1  931  23111
nonsynonymous SNV3  8  2 1  711  2318
synonymous SNV1  7       22      3
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
chr1:241663758p.T457A3
chr1:241663880p.V416A2
chr1:241667497p.A123V1
chr1:241661252p.L453V1
chr1:241675321p.A320T1
chr1:241663871p.I120K1
chr1:241680496p.T442T1
chr1:241667508p.H318R1
chr1:241663756p.A103T1
chr1:241675354p.T442R1

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 FH 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 FH

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

ATP10A,CLIC5,CLIC6,DOK7,EIF4E1B,FHL2,GADD45A,
GPR26,ITPRIPL2,AJUBA,KCNS3,PGR,PLCD3,RAB31,
RBBP8,SEMA3B,SUSD3,TMEM26,TUBA3D,UGDH,WT1
PIFO,FHL2,GPR87,KIF9,KLK5,KLK7,KRT14,
KRT17,KRT5,KRT9,MGP,NXT1,PDLIM1,PDLIM4,
SF3B4,SFN,TACSTD2,TES,TMEM51,ZNF165,ZYX

AGR2,ANG,B3GNT5,SMCO4,GSKIP,CYSTM1,MCU,
DDB2,EGLN3,FHL2,FOXA3,FUT8,GMDS,FFAR4,
LIMA1,MLPH,MRAP2,SEMA4B,TC2N,TRIM16,TSPAN15
ADRM1,AKIRIN2,BCL10,LURAP1L,CASP5,CD55,DGCR11,
FHL2,PLAUR,PSMC4,PSMD12,RAB35,RND1,RNF19B,
SEMA4B,SERPINB8,SERTAD1,TNFRSF1A,TRIM15,TRIM40,TTC39B
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 FH


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