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 MTHFD2
Basic gene info.Gene symbolMTHFD2
Gene namemethylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase
SynonymsNMDMC
CytomapUCSC genome browser: 2p13.1
Genomic locationchr2 :74425689-74442424
Type of geneprotein-coding
RefGenesNM_006636.3,
NR_027405.1,NM_001040409.1,
Ensembl idENSG00000065911
DescriptionNAD-dependent methylene tetrahydrofolate dehydrogenase cyclohydrolasebifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
Modification date20141207
dbXrefs MIM : 604887
HGNC : HGNC
HPRD : 05351
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MTHFD2
BioGPS: 10797
Gene Expression Atlas: ENSG00000065911
The Human Protein Atlas: ENSG00000065911
PathwayNCI Pathway Interaction Database: MTHFD2
KEGG: MTHFD2
REACTOME: MTHFD2
ConsensusPathDB
Pathway Commons: MTHFD2
MetabolismMetaCyc: MTHFD2
HUMANCyc: MTHFD2
RegulationEnsembl's Regulation: ENSG00000065911
miRBase: chr2 :74,425,689-74,442,424
TargetScan: NM_006636
cisRED: ENSG00000065911
ContextiHOP: MTHFD2
cancer metabolism search in PubMed: MTHFD2
UCL Cancer Institute: MTHFD2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MTHFD2 in cancer cell metabolism1. Llanos AA, Dumitrescu RG, Brasky TM, Liu Z, Mason JB, et al. (2014) Relationships among Folate, Alcohol Consumption, Gene Variants in One-Carbon Metabolism, and p16INK4a Methylation and Expression in Healthy Breast Tissues. Carcinogenesis: bgu219. go to article

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Phenotypic Information for MTHFD2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MTHFD2
Familial Cancer Database: MTHFD2
* 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_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: MTHFD2
MedGen: MTHFD2 (Human Medical Genetics with Condition)
ClinVar: MTHFD2
PhenotypeMGI: MTHFD2 (International Mouse Phenotyping Consortium)
PhenomicDB: MTHFD2

Mutations for MTHFD2
* 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 MTHFD2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW837123FNDC3A20171134976625149766403MTHFD216418427442758174427601

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 # sample1                
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=16)
Stat. for Synonymous SNVs
(# total SNVs=3)
Stat. for Deletions
(# total SNVs=1)
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
chr2:74441223-74441223p.G201R3
chr2:74434923-74434923p.D25H2
chr2:74438867-74438867p.?2
chr2:74435774-74435774p.G61E2
chr2:74435777-74435777p.R62Q2
chr2:74441241-74441241p.P207A2
chr2:74438352-74438352p.R131*1
chr2:74441263-74441263p.T214I1
chr2:74434890-74434890p.L14V1
chr2:74438395-74438395p.A145V1

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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
# sample21 3  1 11 241  11 5
# mutation21 3  1 11 241  11 5
nonsynonymous SNV1  2  1 11 241  11 3
synonymous SNV11 1               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
chr2:74435777p.R164Q2
chr2:74441263p.T4A1
chr2:74425778p.H280H1
chr2:74435816p.L6L1
chr2:74441282p.P282P1
chr2:74425784p.S8P1
chr2:74437140p.V298I1
chr2:74441326p.V39F1
chr2:74425790p.P309T1
chr2:74437170p.R54W1

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 MTHFD2 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 MTHFD2

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

C11orf71,COA5,FAM200B,GRSF1,DANCR,LOC100303728,LOC147727,
LOC202781,LOC400027,LOC400752,LOC401588,MRPL1,MTHFD2L,RCHY1,
RUFY3,SDAD1,SNHG10,TCTE3,THAP6,THAP9,UTP3
ACTR6,AP1AR,VCPKMT,C5orf28,CAAP1,CLDN12,CSNK1A1,
EEF1E1,KIAA0895,LZTFL1,LAMTOR3,MTHFD2L,NUP35,NUPL2,
ORC4,POT1,PRSS16,SRSF6,SVIP,TMEM161B,ZBED5

ATP5L,C14orf142,COMMD8,COX18,DCK,DANCR,MTHFD2L,
MYEOV2,NDUFB1,NUDCD2,NUP54,ORC4,PACRGL,PHF5A,
RCHY1,SDHD,SNRPG,TIMM8B,TMEM126B,TOMM22,UQCR10
BRIX1,DTD2,KATNBL1,C5orf28,TRAPPC13,CCDC58,TRMT13,
MRPL1,MRPL32,MRPL50,MTERF3,MTHFD2L,NUPL2,OTUD6B,
PAK1IP1,PRMT3,PTRH2,RCN2,TRMT10C,TAF9,TRUB1
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 MTHFD2
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
DB00116methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolaseapproved; nutraceuticalTetrahydrofolic acid
DB00157methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolaseapproved; nutraceuticalNADH
DB00563methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolaseapprovedMethotrexate
DB00158methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolaseapproved; nutraceuticalFolic Acid


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Cross referenced IDs for MTHFD2
* 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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