Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	MTHFD2
	Gene name	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase
	Synonyms	NMDMC
	Cytomap	UCSC genome browser: 2p13.1
	Genomic location	chr2 :74425689-74442424
	Type of gene	protein-coding
	RefGenes	NM_006636.3, NR_027405.1,NM_001040409.1,
	Ensembl id	ENSG00000065911
	Description	NAD-dependent methylene tetrahydrofolate dehydrogenase cyclohydrolasebifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
	Modification date	20141207
dbXrefs	MIM : 604887
	HGNC : HGNC
	HPRD : 05351
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MTHFD2
	BioGPS: 10797
	Gene Expression Atlas: ENSG00000065911
	The Human Protein Atlas: ENSG00000065911
Pathway	NCI Pathway Interaction Database: MTHFD2
	KEGG: MTHFD2
	REACTOME: MTHFD2
	ConsensusPathDB
	Pathway Commons: MTHFD2
Metabolism	MetaCyc: MTHFD2
	HUMANCyc: MTHFD2
Regulation	Ensembl's Regulation: ENSG00000065911
	miRBase: chr2 :74,425,689-74,442,424
	TargetScan: NM_006636
	cisRED: ENSG00000065911
Context	iHOP: MTHFD2
	cancer metabolism search in PubMed: MTHFD2
	UCL Cancer Institute: MTHFD2
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MTHFD2 in cancer cell metabolism	1. 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

Top

Phenotypic Information for MTHFD2(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: MTHFD2
	MedGen: MTHFD2 (Human Medical Genetics with Condition)
	ClinVar: MTHFD2
Phenotype	MGI: MTHFD2 (International Mouse Phenotyping Consortium)
Phenotype	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.

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 MTHFD2 related fusion information.

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

AW837123

FNDC3A

171

49766251

49766403

MTHFD2

164

184

74427581

74427601

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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)

Top

SNV 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

Top

Somatic 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.

Top

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
chr2:74441223-74441223	p.G201R	3
chr2:74441241-74441241	p.P207A	2
chr2:74434923-74434923	p.D25H	2
chr2:74438867-74438867	p.?	2
chr2:74435774-74435774	p.G61E	2
chr2:74435777-74435777	p.R62Q	2
chr2:74437140-74437140	p.L110L	1
chr2:74437170-74437170	p.P120S	1
chr2:74441254-74441254	p.G211D	1
chr2:74438352-74438352	p.R131*	1

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	2	1		3			1		1	1		2	4	1			1	1		5
# mutation	2	1		3			1		1	1		2	4	1			1	1		5
nonsynonymous SNV	1			2			1		1	1		2	4	1			1	1		3
synonymous SNV	1	1		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])

Top

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
chr2:74435777	p.R164Q	2
chr2:74441208	p.P177L	1
chr2:74435758	p.L212L	1
chr2:74441241	p.P222S	1
chr2:74435765	p.A247V	1
chr2:74441254	p.R278T	1
chr2:74441263	p.T4A	1
chr2:74425778	p.H280H	1
chr2:74435816	p.L6L	1
chr2:74441282	p.P282P	1

Other 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

Copy 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]

Top

Gene Expression for MTHFD2

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for MTHFD2

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
DB00116	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase	approved; nutraceutical	Tetrahydrofolic acid
DB00157	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase	approved; nutraceutical	NADH
DB00563	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase	approved	Methotrexate
DB00158	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase	approved; nutraceutical	Folic Acid

Top

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