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 MTHFR
Basic gene info.Gene symbolMTHFR
Gene namemethylenetetrahydrofolate reductase (NAD(P)H)
Synonyms-
CytomapUCSC genome browser: 1p36.3
Genomic locationchr1 :11845786-11866160
Type of geneprotein-coding
RefGenesNM_005957.4,
Ensembl idENSG00000177000
Description5,10-methylenetetrahydrofolate reductase (NADPH)methylenetetrahydrofolate reductase
Modification date20141222
dbXrefs MIM : 607093
HGNC : HGNC
Ensembl : ENSG00000177000
HPRD : 06158
Vega : OTTHUMG00000002277
ProteinUniProt: P42898
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MTHFR
BioGPS: 4524
Gene Expression Atlas: ENSG00000177000
The Human Protein Atlas: ENSG00000177000
PathwayNCI Pathway Interaction Database: MTHFR
KEGG: MTHFR
REACTOME: MTHFR
ConsensusPathDB
Pathway Commons: MTHFR
MetabolismMetaCyc: MTHFR
HUMANCyc: MTHFR
RegulationEnsembl's Regulation: ENSG00000177000
miRBase: chr1 :11,845,786-11,866,160
TargetScan: NM_005957
cisRED: ENSG00000177000
ContextiHOP: MTHFR
cancer metabolism search in PubMed: MTHFR
UCL Cancer Institute: MTHFR
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MTHFR in cancer cell metabolism1. Abedinzadeh M, Zare-Shehneh M, Neamatzadeh H, Karami H (2014) Association between MTHFR C677T Polymorphism and Risk of Prostate Cancer: Evidence from 22 Studies with 10,832 Cases and 11,993 Controls. Asian Pacific journal of cancer prevention: APJCP 16: 4525-4530. go to article
2. Kim JW, Jeon YJ, Jang MJ, Kim JO, Chong SY, et al. (2015) Association between folate metabolism-related polymorphisms and colorectal cancer risk. Molecular and Clinical Oncology 3: 639-648. go to article

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Phenotypic Information for MTHFR(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MTHFR
Familial Cancer Database: MTHFR
* 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 236250; phenotype.
601367; phenotype.
601634; phenotype.
603174; phenotype.
607093; gene.
Orphanet 1048; Isolated anencephaly/exencephaly.
240977; Susceptibility to adverse reaction due to methotrexate treatment.
268377; Total spina bifida aperta.
268384; Thoracolumbosacral spina bifida aperta.
268388; Lumbosacral spina bifida aperta.
268392; Cervical spina bifida aperta.
268397; Cervicothoracic spina bifida aperta.
268740; Upper thoracic spina bifida aperta.
268748; Total spina bifida cystica.
268752; Thoracolumbosacral spina bifida cystica.
268758; Lumbosacral spina bifida cystica.
268762; Cervical spina bifida cystica.
268766; Cervicothoracic spina bifida cystica.
268770; Upper thoracic spina bifida cystica.
395; Homocystinuria due to methylene tetrahydrofolate reductase deficiency.
64738; Non rare thrombophilia.
90070; Methotrexate poisoning.
DiseaseKEGG Disease: MTHFR
MedGen: MTHFR (Human Medical Genetics with Condition)
ClinVar: MTHFR
PhenotypeMGI: MTHFR (International Mouse Phenotyping Consortium)
PhenomicDB: MTHFR

Mutations for MTHFR
* 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 MTHFR related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
R09898NUAK116112106459136106459196MTHFR6011411185878511858848

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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=54)		Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=2)		Stat. for Insertions
(# total SNVs=0)
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
chr1:11854476-11854476p.E429A5
chr1:11860307-11860307p.R183Q3
chr1:11854864-11854864p.R363H3
chr1:11854116-11854116p.L460V2
chr1:11856367-11856367p.I226F2
chr1:11856378-11856378p.A222V2
chr1:11863114-11863114p.S20S2
chr1:11861228-11861228p.A155A2
chr1:11851348-11851348p.P556P2
chr1:11856335-11856335p.F236F1

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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
# sample3 3101 2 1  62  249111
# mutation3 3101 2 1  62  2410110
nonsynonymous SNV1 291 1 1  52  21818
synonymous SNV2 11  1    1    32 2
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
chr1:11860307p.R183Q3
chr1:11854026p.G298D2
chr1:11855293p.P556P2
chr1:11851348p.G490R2
chr1:11861293p.P459L1
chr1:11854538p.R357H1
chr1:11854864p.R157W1
chr1:11852386p.W455C1
chr1:11856448p.E326E1
chr1:11861298p.L150P1

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 MTHFR 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 MTHFR

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

CACNA1D,CASZ1,CLCN6,CYB561D1,TP73-AS1,LOC100129534,MAP3K1,
MFN2,MKNK2,MORN1,MTHFR,NDST1,NISCH,PGPEP1,
RERE,SLC35E2,TBC1D13,TRIM66,UBXN10,VPS13D,ZBTB40		ANKRD52,ATXN7L2,IBA57,DGKD,DNMT3A,EFR3B,GTF3C1,
HCFC1,LARGE,LIMD1,MTHFR,NEU3,OPA3,P2RY2,
PGPEP1,PLEC,RHOBTB2,SBK1,SEMA4D,USP22,WDR37

ATP13A2,GDPGP1,CASZ1,DHDDS,DOCK5,KIF1B,KLF13,
LUZP1,MAP3K6,MBD1,MFN2,MTHFR,MTOR,SH3BP2,
TNRC6B,TXLNA,UBR4,VPS13D,VPS18,WASF2,ZCCHC2		ALX3,AMDHD2,ARHGEF11,CDC42BPB,IQCE,KIAA0556,ZSWIM8,
MED15,MTHFR,PHRF1,PLXNB2,RALGDS,RNF123,PPP6R2,
SBF1,TAOK2,TNS3,USP42,ZMIZ1,ZNF592,ZZEF1
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 MTHFR
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA245; -.
Organism-specific databasesCTD 4524; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB03147methylenetetrahydrofolate reductase (NAD(P)H)experimentalFlavin-Adenine Dinucleotide
DB00115methylenetetrahydrofolate reductase (NAD(P)H)approved; nutraceuticalCyanocobalamin
DB00116methylenetetrahydrofolate reductase (NAD(P)H)approved; nutraceuticalTetrahydrofolic acid
DB01234methylenetetrahydrofolate reductase (NAD(P)H)approved; investigationalDexamethasone
DB00515methylenetetrahydrofolate reductase (NAD(P)H)approvedCisplatin
DB00970methylenetetrahydrofolate reductase (NAD(P)H)approvedDactinomycin
DB00313methylenetetrahydrofolate reductase (NAD(P)H)approved; investigationalValproic Acid
DB00526methylenetetrahydrofolate reductase (NAD(P)H)approved; investigationalOxaliplatin
DB01101methylenetetrahydrofolate reductase (NAD(P)H)approved; investigationalCapecitabine
DB00175methylenetetrahydrofolate reductase (NAD(P)H)approvedPravastatin
DB00145methylenetetrahydrofolate reductase (NAD(P)H)approved; nutraceuticalGlycine
DB00133methylenetetrahydrofolate reductase (NAD(P)H)approved; nutraceuticalL-Serine
DB00165methylenetetrahydrofolate reductase (NAD(P)H)approved; nutraceuticalPyridoxine
DB00531methylenetetrahydrofolate reductase (NAD(P)H)approved; investigationalCyclophosphamide
DB01248methylenetetrahydrofolate reductase (NAD(P)H)approved; investigationalDocetaxel
DB00997methylenetetrahydrofolate reductase (NAD(P)H)approved; investigationalDoxorubicin
DB01229methylenetetrahydrofolate reductase (NAD(P)H)approvedPaclitaxel
DB01030methylenetetrahydrofolate reductase (NAD(P)H)approved; investigationalTopotecan
DB00293methylenetetrahydrofolate reductase (NAD(P)H)approved; investigationalRaltitrexed
DB00795methylenetetrahydrofolate reductase (NAD(P)H)approvedSulfasalazine
DB00987methylenetetrahydrofolate reductase (NAD(P)H)approved; investigationalCytarabine
DB00694methylenetetrahydrofolate reductase (NAD(P)H)approvedDaunorubicin
DB00773methylenetetrahydrofolate reductase (NAD(P)H)approvedEtoposide
DB00650methylenetetrahydrofolate reductase (NAD(P)H)approvedLeucovorin
DB01033methylenetetrahydrofolate reductase (NAD(P)H)approvedMercaptopurine
DB00563methylenetetrahydrofolate reductase (NAD(P)H)approvedMethotrexate
DB00635methylenetetrahydrofolate reductase (NAD(P)H)approvedPrednisone
DB00541methylenetetrahydrofolate reductase (NAD(P)H)approved; investigationalVincristine
DB00158methylenetetrahydrofolate reductase (NAD(P)H)approved; nutraceuticalFolic Acid
DB00460methylenetetrahydrofolate reductase (NAD(P)H)approved; investigationalVerteporfin
DB00544methylenetetrahydrofolate reductase (NAD(P)H)approvedFluorouracil
DB00762methylenetetrahydrofolate reductase (NAD(P)H)approved; investigationalIrinotecan
DB00958methylenetetrahydrofolate reductase (NAD(P)H)approvedCarboplatin
DB00642methylenetetrahydrofolate reductase (NAD(P)H)approved; investigationalPemetrexed


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Cross referenced IDs for MTHFR
* 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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