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 GNMT
Basic gene info.Gene symbolGNMT
Gene nameglycine N-methyltransferase
Synonyms-
CytomapUCSC genome browser: 6p12
Genomic locationchr6 :42928499-42931618
Type of geneprotein-coding
RefGenesNM_018960.4,
Ensembl idENSG00000124713
DescriptionHEL-S-182mPepididymis secretory sperm binding protein Li 182mP
Modification date20141207
dbXrefs MIM : 606628
HGNC : HGNC
Ensembl : ENSG00000124713
HPRD : 05970
Vega : OTTHUMG00000014712
ProteinUniProt: Q14749
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GNMT
BioGPS: 27232
Gene Expression Atlas: ENSG00000124713
The Human Protein Atlas: ENSG00000124713
PathwayNCI Pathway Interaction Database: GNMT
KEGG: GNMT
REACTOME: GNMT
ConsensusPathDB
Pathway Commons: GNMT
MetabolismMetaCyc: GNMT
HUMANCyc: GNMT
RegulationEnsembl's Regulation: ENSG00000124713
miRBase: chr6 :42,928,499-42,931,618
TargetScan: NM_018960
cisRED: ENSG00000124713
ContextiHOP: GNMT
cancer metabolism search in PubMed: GNMT
UCL Cancer Institute: GNMT
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GNMT in cancer cell metabolism1. Huidobro C, Fernandez AF, Fraga MF (2013) The role of genetics in the establishment and maintenance of the epigenome. Cell Mol Life Sci 70: 1543-1573. doi: 10.1007/s00018-013-1296-2. go to article
2. Khan AP, Rajendiran TM, Ateeq B, Asangani IA, Athanikar JN, et al. (2013) The role of sarcosine metabolism in prostate cancer progression. Neoplasia 15: 491-501. pmid: 3638352. go to article

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

check002.gifOthers
OMIM 606628; gene.
606664; phenotype.
Orphanet 289891; Hypermethioninemia due to glycine N-methyltransferase deficiency.
DiseaseKEGG Disease: GNMT
MedGen: GNMT (Human Medical Genetics with Condition)
ClinVar: GNMT
PhenotypeMGI: GNMT (International Mouse Phenotyping Consortium)
PhenomicDB: GNMT

Mutations for GNMT
* 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 GNMT 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
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=13)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr6:42930890-42930890p.R178C2
chr6:42930899-42930899p.D181N2
chr6:42928565-42928565p.D20E1
chr6:42930850-42930850p.A164A1
chr6:42931364-42931364p.L270L1
chr6:42929951-42929951p.V70M1
chr6:42930888-42930888p.H177P1
chr6:42931381-42931381p.P275P1
chr6:42929979-42929979p.G79D1
chr6:42931424-42931424p.V290M1

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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
# sample11 2    3  21   33 3
# mutation11 2    3  21   33 4
nonsynonymous SNV   2    2  11   12 3
synonymous SNV11      1  1    21 1
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
chr6:42929979p.G79D1
chr6:42930898p.G263D1
chr6:42930003p.A87V1
chr6:42931107p.L270L1
chr6:42930028p.A95A1
chr6:42931185p.P275P1
chr6:42930050p.R103W1
chr6:42931281p.V290M1
chr6:42930557p.G131D1
chr6:42931339p.G132G1

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 GNMT 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 GNMT

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

ACY1,AFMID,AKR1D1,CLPSL1,C6orf223,CCDC57,CHRNA2,
DHRS4,GGT1,GGT3P,GGTLC1,GGTLC2,GNMT,HPD,
KCTD4,LDHD,SERHL2,SERHL,SPINK8,SULT1C3,UCN3
ABCC11,ABCC12,ACSL3,ADCY10,ALOX15B,C15orf43,CHRNA2,
DMRTC2,EPS8L3,FMO5,GGT1,GGTLC2,GNMT,HIST1H3D,
IYD,NSUN2,SERHL,SLC12A3,SLC26A6,SPINK8,TMEM62

ACTN2,ERICH3,CACNG3,CNTNAP4,CT45A2,CUX2,FAM57B,
FLJ36000,FOXR2,GIP,GNMT,KIRREL2,MAGEA10,NECAB2,
OR2H1,P2RX2,RP1-177G6.2,SHISA7,SYT6,THSD7B,XAGE5
ACCS,ALOX15B,AZU1,C17orf99,CABP4,CD70,FBXW12,
GAB3,GNMT,GPR149,HIST1H1A,ITGA10,LBX2,LOC283999,
LOC729668,LOC731789,OR10G7,OTOF,POU6F2,SLC26A11,ZNF750
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 GNMT
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA28794; -.
Organism-specific databasesCTD 27232; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00118glycine N-methyltransferaseapproved; nutraceuticalS-Adenosylmethionine
DB00145glycine N-methyltransferaseapproved; nutraceuticalGlycine
DB01752glycine N-methyltransferaseexperimentalS-Adenosyl-L-Homocysteine
DB04272glycine N-methyltransferaseexperimentalCitric Acid


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Cross referenced IDs for GNMT
* 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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