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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for GNMT
check button Gene summary
Basic gene informationGene symbolGNMT
Gene nameglycine N-methyltransferase
Synonyms-
CytomapUCSC genome browser: 6p12
Type of geneprotein-coding
RefGenesNM_018960.4,
DescriptionHEL-S-182mPepididymis secretory sperm binding protein Li 182mP
Modification date20141207
dbXrefs MIM : 606628
HGNC : HGNC
Ensembl : ENSG00000124713
HPRD : 05970
Vega : OTTHUMG00000014712
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GNMT
BioGPS: 27232
PathwayNCI Pathway Interaction Database: GNMT
KEGG: GNMT
REACTOME: GNMT
Pathway Commons: GNMT
ContextiHOP: GNMT
ligand binding site mutation search in PubMed: GNMT
UCL Cancer Institute: GNMT
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)LiverPancreas
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LIHCPAAD
Reference showing the relevant tissue of GNMT
Description by TissGene annotationsCancer gene
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID
GO:0046500S-adenosylmethionine metabolic process15340920
GO:0046500S-adenosylmethionine metabolic process15340920


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TissGeneExp for GNMT

check button Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
gene exp


check button Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)
gene isoform exp


check button Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.
normal gene exp


check button Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
KIRC-2.691991424-0.989809479-1.7021819441.21E-177.68E-17
KIRP-1.877090729-0.472421979-1.404668751.17E-065.83E-06
LUSC-2.0879080090.342878266-2.4307862752.63E-224.08E-21
LUAD-1.4158982720.426541383-1.8424396552.42E-121.82E-11
THCA-0.786460750.292820606-1.0792813563.70E-081.70E-07
LIHC5.1773715218.122565521-2.9451941.92E-081.59E-07
KICH-1.707028479-0.648376479-1.0586520.003650.007094004
STAD-2.106800104-0.856846979-1.2499531250.001380.006851258
PRAD5.434696294.3050135981.1296826920.001280.003989541
HNSC-2.224163549-1.005424014-1.2187395350.000170.000709647


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TissGene-miRNA for GNMT

check button Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))
Cancer typemiRNA idmiRNA accessionP-val.Coeff.# samples


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TissGeneMut for GNMT
TissGeneSNV for GNMT

check button nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)

* Click on the image to enlarge it in a new window.
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check button Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.L238FLUAD1
p.A164VSTAD1
p.G131DUCEC1
p.R242QSKCM1
p.D181NBLCA1
p.S128LCESC1
p.A230DLIHC1
p.R242LTHYM1
p.A216TSTAD1
p.A144TUCEC1
p.H177PCOAD1
p.V290MSTAD1
p.R178CLUSC1
p.R157QLIHC1
p.I195MBLCA1
p.G79DCOAD1
p.R103WUCEC1
p.A95STHYM1
p.D181NSKCM1
p.H156YSTAD1


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TissGeneCNV for GNMT

check button Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)
CNV


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TissGeneFusions for GNMT

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
TCGAfusionPortalPRADALUADTCGA-50-6591-01ATRERF1-GNMT5UTR-CDSChr6:42330685Chr6:42929950


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TissGeneNet for GNMT

check button Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)
BRCA (tumor)BRCA (normal)
GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (tumor)GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (normal)
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COAD (tumor)COAD (normal)
GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (tumor)GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (normal)
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HNSC (tumor)HNSC (normal)
GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (tumor)GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (normal)
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KICH (tumor)KICH (normal)
GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (tumor)GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (normal)
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KIRC (tumor)KIRC (normal)
GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (tumor)GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (normal)
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KIRP (tumor)KIRP (normal)
GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (tumor)GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (normal)
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LIHC (tumor)LIHC (normal)
GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (tumor)GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (normal)
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LUAD (tumor)LUAD (normal)
GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (tumor)GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (normal)
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LUSC (tumor)LUSC (normal)
GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (tumor)GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (normal)
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PRAD (tumor)PRAD (normal)
GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (tumor)GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (normal)
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STAD (tumor)STAD (normal)
GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (tumor)GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (normal)
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THCA (tumor)THCA (normal)
GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (tumor)GNMT, TINF2, S100A9, POT1, TERF2, NUDT18, PRKACA, RPSA, ARRB1, ARR3, TERF2IP, NIF3L1, PLEKHF2 (normal)
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TissGeneProg for GNMT

check button Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image to enlarge it in a new window.
survival 1

check button Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 2

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 3

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 4

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TissGeneClin for GNMT
TissGeneDrug for GNMT

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status
DB04272Citric AcidSmall moleculeNutraceutical|Vet_approved


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TissGeneDisease for GNMT

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C2239176Liver carcinoma15BeFree,CTD_human,LHGDN,MGD
umls:C0023903Liver neoplasms6BeFree,CTD_human,LHGDN
umls:C0279000Liver and Intrahepatic Biliary Tract Carcinoma4BeFree
umls:C0345904Malignant neoplasm of liver4BeFree
umls:C0400966Non-alcoholic Fatty Liver Disease3BeFree
umls:C0019189Hepatitis, Chronic2BeFree,CTD_human
umls:C0023895Liver diseases2BeFree,LHGDN
umls:C0033578Prostatic Neoplasms2BeFree,CTD_human
umls:C0268621Hepatic methionine adenosyltransferase deficiency2CTD_human
umls:C0376358Malignant neoplasm of prostate2BeFree,GAD
umls:C0596263Carcinogenesis2BeFree
umls:C0600139Prostate carcinoma2BeFree
umls:C1847720Glycine N-Methyltransferase Deficiency2CLINVAR,MGD,ORPHANET,UNIPROT
umls:C0006142Malignant neoplasm of breast1BeFree
umls:C0008924Cleft Lip1GAD
umls:C0008925Cleft Palate1GAD
umls:C0019158Hepatitis1CTD_human
umls:C0023467Leukemia, Myelocytic, Acute1BeFree
umls:C0025202melanoma1BeFree
umls:C0036341Schizophrenia1BeFree
umls:C0080178Spina Bifida1GAD
umls:C0205748Dysplastic Nevus1BeFree
umls:C0206698Cholangiocarcinoma1LHGDN
umls:C0281361Adenocarcinoma of pancreas1BeFree
umls:C0598608Hyperhomocysteinemia1CTD_human
umls:C0678222Breast Carcinoma1BeFree
umls:C0936223Metastatic Prostate Carcinoma1BeFree
umls:C1335302Pancreatic Ductal Adenocarcinoma1BeFree
umls:C1512409Hepatocarcinogenesis1BeFree
umls:C1704272Benign Prostatic Hyperplasia1BeFree