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 MTR
Basic gene info.Gene symbolMTR
Gene name5-methyltetrahydrofolate-homocysteine methyltransferase
SynonymsHMAG|MS|cblG
CytomapUCSC genome browser: 1q43
Genomic locationchr1 :236958580-237067281
Type of geneprotein-coding
RefGenesNM_000254.2,
NM_001291939.1,NM_001291940.1,
Ensembl idENSG00000116984
Description5-methyltetrahydrofolate-homocysteine methyltransferase 1cobalamin-dependent methionine synthasemethionine synthasevitamin-B12 dependent methionine synthase
Modification date20141219
dbXrefs MIM : 156570
HGNC : HGNC
Ensembl : ENSG00000116984
HPRD : 01136
Vega : OTTHUMG00000040060
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MTR
BioGPS: 4548
Gene Expression Atlas: ENSG00000116984
The Human Protein Atlas: ENSG00000116984
PathwayNCI Pathway Interaction Database: MTR
KEGG: MTR
REACTOME: MTR
ConsensusPathDB
Pathway Commons: MTR
MetabolismMetaCyc: MTR
HUMANCyc: MTR
RegulationEnsembl's Regulation: ENSG00000116984
miRBase: chr1 :236,958,580-237,067,281
TargetScan: NM_000254
cisRED: ENSG00000116984
ContextiHOP: MTR
cancer metabolism search in PubMed: MTR
UCL Cancer Institute: MTR
Assigned class in ccmGDBC

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

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

Mutations for MTR
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasMTRchr1237046024237046044MTRchr1237046787237046807
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MTR related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW841012MTR92641237061346237061603CCAR1262485107052566370531012
BE767082MTR121551237064437237064582CC2D2A15035141551175915512966
CV363529MTR11551237052621237054571MTR1474771237057750237060335
BG986763MTR1233581236964888236965122PGM534736697104762771047646
AW841013MTR22551237061350237061603CCAR1253434107052570570531012

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 # sample3                
GAIN (# sample)2                
LOSS (# sample)1                
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=86)		Stat. for Synonymous SNVs
(# total SNVs=35)
Stat. for Deletions
(# total SNVs=4)		Stat. for Insertions
(# total SNVs=4)

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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
chr1:237024474-237024474p.K700fs*85
chr1:237058828-237058828p.L1192L3
chr1:236998969-236998969p.S437S2
chr1:236976058-236976058p.A175T2
chr1:237001790-237001790p.V469A2
chr1:236988699-236988699p.K309N2
chr1:237048500-237048500p.D919G2
chr1:236973825-236973825p.G144G2
chr1:237037139-237037139p.A824A2
chr1:236992548-236992548p.E352V2

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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
# sample3518  2 1  17821 914116
# mutation3619  2 1  18921 917119
nonsynonymous SNV34 7  2 1  147 1 811112
synonymous SNV 212       422  16 7
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
chr1:237057790p.A1036T,MTR2
chr1:236992548p.E48K,MTR2
chr1:236966835p.A1062D,MTR2
chr1:236976058p.E352V,MTR2
chr1:237057711p.S30S,MTR2
chr1:236998969p.V62A,MTR2
chr1:237001790p.A175T,MTR2
chr1:237016305p.S64S,MTR1
chr1:237054505p.N290T,MTR1
chr1:236973863p.G888G,MTR1

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 MTR 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 MTR

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

ABCB10,AHCTF1,ANGEL2,ARID4B,ASH1L,SPRTN,SDE2,
BROX,CEP350,CNST,EXOC8,HEATR1,KLHL20,MTR,
NUP133,RAB3GAP2,TOR1AIP1,TOR1AIP2,TPR,ZNF281,ZNF678		APC,ASXL2,ATE1,ATF7IP,ATG2B,CEP350,DPP8,
AGO4,FAM178A,KIAA1109,KIAA2018,MARCH6,MED13,MTR,
SMG1,TNKS2,TTBK2,UBR2,VPS13A,ZDBF2,ZFX

ABL2,ARHGEF11,ARID4B,ASH1L,PRRC2C,DIEXF,CEP350,
DCAF8,DSTYK,GATAD2B,GON4L,HEATR1,MTR,POGK,
POGZ,RAB3GAP2,RPRD2,SETDB1,TP53BP2,TPR,ZC3H11A		ATF7,ATRX,CHD6,COL5A2,FAM120C,FRMD4A,HIP1,
LAMC1,MCC,MTR,MTX3,NEK1,NEK9,NFIA,
PCDHGB3,PDZD2,REV3L,SLC41A1,TTC28,ZNF37A,ZNF445
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 MTR
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
DB001155-methyltetrahydrofolate-homocysteine methyltransferaseapproved; nutraceuticalCyanocobalamin
DB001165-methyltetrahydrofolate-homocysteine methyltransferaseapproved; nutraceuticalTetrahydrofolic acid
DB001345-methyltetrahydrofolate-homocysteine methyltransferaseapproved; nutraceuticalL-Methionine
DB002005-methyltetrahydrofolate-homocysteine methyltransferaseapprovedHydroxocobalamin
DB036145-methyltetrahydrofolate-homocysteine methyltransferaseexperimentalCo-Methylcobalamin
DB005155-methyltetrahydrofolate-homocysteine methyltransferaseapprovedCisplatin
DB005315-methyltetrahydrofolate-homocysteine methyltransferaseapproved; investigationalCyclophosphamide
DB009705-methyltetrahydrofolate-homocysteine methyltransferaseapprovedDactinomycin
DB009975-methyltetrahydrofolate-homocysteine methyltransferaseapproved; investigationalDoxorubicin
DB005415-methyltetrahydrofolate-homocysteine methyltransferaseapproved; investigationalVincristine
DB016115-methyltetrahydrofolate-homocysteine methyltransferaseapprovedHydroxychloroquine
DB007955-methyltetrahydrofolate-homocysteine methyltransferaseapprovedSulfasalazine
DB008985-methyltetrahydrofolate-homocysteine methyltransferaseapprovedEthanol
DB005445-methyltetrahydrofolate-homocysteine methyltransferaseapprovedFluorouracil
DB006505-methyltetrahydrofolate-homocysteine methyltransferaseapprovedLeucovorin
DB005265-methyltetrahydrofolate-homocysteine methyltransferaseapproved; investigationalOxaliplatin
DB006405-methyltetrahydrofolate-homocysteine methyltransferaseapproved; investigationalAdenosine
DB001585-methyltetrahydrofolate-homocysteine methyltransferaseapproved; nutraceuticalFolic Acid
DB001655-methyltetrahydrofolate-homocysteine methyltransferaseapproved; nutraceuticalPyridoxine
DB005635-methyltetrahydrofolate-homocysteine methyltransferaseapprovedMethotrexate
DB004605-methyltetrahydrofolate-homocysteine methyltransferaseapproved; investigationalVerteporfin


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Cross referenced IDs for MTR
* 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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