TissGeneSummary for GNMT |
Gene summary |
Basic gene information | Gene symbol | GNMT |
Gene name | glycine N-methyltransferase | |
Synonyms | - | |
Cytomap | UCSC genome browser: 6p12 | |
Type of gene | protein-coding | |
RefGenes | NM_018960.4, | |
Description | HEL-S-182mPepididymis secretory sperm binding protein Li 182mP | |
Modification date | 20141207 | |
dbXrefs | MIM : 606628 | |
HGNC : HGNC | ||
Ensembl : ENSG00000124713 | ||
HPRD : 05970 | ||
Vega : OTTHUMG00000014712 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GNMT | |
BioGPS: 27232 | ||
Pathway | NCI Pathway Interaction Database: GNMT | |
KEGG: GNMT | ||
REACTOME: GNMT | ||
Pathway Commons: GNMT | ||
Context | iHOP: GNMT | |
ligand binding site mutation search in PubMed: GNMT | ||
UCL Cancer Institute: GNMT | ||
Assigned class in TissGDB* | C | |
Included tissue-specific gene expression resources | TiGER,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 annotations | Cancer 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. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO term | PubMed ID | GO:0046500 | S-adenosylmethionine metabolic process | 15340920 | GO:0046500 | S-adenosylmethionine metabolic process | 15340920 |
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TissGeneExp for GNMT |
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 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 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. |
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) |
- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
KIRC | -2.691991424 | -0.989809479 | -1.702181944 | 1.21E-17 | 7.68E-17 |
KIRP | -1.877090729 | -0.472421979 | -1.40466875 | 1.17E-06 | 5.83E-06 |
LUSC | -2.087908009 | 0.342878266 | -2.430786275 | 2.63E-22 | 4.08E-21 |
LUAD | -1.415898272 | 0.426541383 | -1.842439655 | 2.42E-12 | 1.82E-11 |
THCA | -0.78646075 | 0.292820606 | -1.079281356 | 3.70E-08 | 1.70E-07 |
LIHC | 5.177371521 | 8.122565521 | -2.945194 | 1.92E-08 | 1.59E-07 |
KICH | -1.707028479 | -0.648376479 | -1.058652 | 0.00365 | 0.007094004 |
STAD | -2.106800104 | -0.856846979 | -1.249953125 | 0.00138 | 0.006851258 |
PRAD | 5.43469629 | 4.305013598 | 1.129682692 | 0.00128 | 0.003989541 |
HNSC | -2.224163549 | -1.005424014 | -1.218739535 | 0.00017 | 0.000709647 |
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TissGene-miRNA for GNMT |
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 type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
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TissGeneMut for GNMT |
TissGeneSNV for GNMT |
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. |
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) |
- nsSNVs sorted by frequency. |
AAchange | Cancer type | # samples |
p.L238F | LUAD | 1 |
p.A164V | STAD | 1 |
p.G131D | UCEC | 1 |
p.R242Q | SKCM | 1 |
p.D181N | BLCA | 1 |
p.S128L | CESC | 1 |
p.A230D | LIHC | 1 |
p.R242L | THYM | 1 |
p.A216T | STAD | 1 |
p.A144T | UCEC | 1 |
p.H177P | COAD | 1 |
p.V290M | STAD | 1 |
p.R178C | LUSC | 1 |
p.R157Q | LIHC | 1 |
p.I195M | BLCA | 1 |
p.G79D | COAD | 1 |
p.R103W | UCEC | 1 |
p.A95S | THYM | 1 |
p.D181N | SKCM | 1 |
p.H156Y | STAD | 1 |
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TissGeneCNV for GNMT |
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) |
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TissGeneFusions for GNMT |
Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
TCGAfusionPortal | PRADA | LUAD | TCGA-50-6591-01A | TRERF1-GNMT | 5UTR-CDS | Chr6:42330685 | Chr6:42929950 |
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TissGeneNet for GNMT |
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) |
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TissGeneProg for GNMT |
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. |
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. |
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. |
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. |
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TissGeneClin for GNMT |
TissGeneDrug for GNMT |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
DB04272 | Citric Acid | Small molecule | Nutraceutical|Vet_approved |
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TissGeneDisease for GNMT |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C2239176 | Liver carcinoma | 15 | BeFree,CTD_human,LHGDN,MGD |
umls:C0023903 | Liver neoplasms | 6 | BeFree,CTD_human,LHGDN |
umls:C0279000 | Liver and Intrahepatic Biliary Tract Carcinoma | 4 | BeFree |
umls:C0345904 | Malignant neoplasm of liver | 4 | BeFree |
umls:C0400966 | Non-alcoholic Fatty Liver Disease | 3 | BeFree |
umls:C0019189 | Hepatitis, Chronic | 2 | BeFree,CTD_human |
umls:C0023895 | Liver diseases | 2 | BeFree,LHGDN |
umls:C0033578 | Prostatic Neoplasms | 2 | BeFree,CTD_human |
umls:C0268621 | Hepatic methionine adenosyltransferase deficiency | 2 | CTD_human |
umls:C0376358 | Malignant neoplasm of prostate | 2 | BeFree,GAD |
umls:C0596263 | Carcinogenesis | 2 | BeFree |
umls:C0600139 | Prostate carcinoma | 2 | BeFree |
umls:C1847720 | Glycine N-Methyltransferase Deficiency | 2 | CLINVAR,MGD,ORPHANET,UNIPROT |
umls:C0006142 | Malignant neoplasm of breast | 1 | BeFree |
umls:C0008924 | Cleft Lip | 1 | GAD |
umls:C0008925 | Cleft Palate | 1 | GAD |
umls:C0019158 | Hepatitis | 1 | CTD_human |
umls:C0023467 | Leukemia, Myelocytic, Acute | 1 | BeFree |
umls:C0025202 | melanoma | 1 | BeFree |
umls:C0036341 | Schizophrenia | 1 | BeFree |
umls:C0080178 | Spina Bifida | 1 | GAD |
umls:C0205748 | Dysplastic Nevus | 1 | BeFree |
umls:C0206698 | Cholangiocarcinoma | 1 | LHGDN |
umls:C0281361 | Adenocarcinoma of pancreas | 1 | BeFree |
umls:C0598608 | Hyperhomocysteinemia | 1 | CTD_human |
umls:C0678222 | Breast Carcinoma | 1 | BeFree |
umls:C0936223 | Metastatic Prostate Carcinoma | 1 | BeFree |
umls:C1335302 | Pancreatic Ductal Adenocarcinoma | 1 | BeFree |
umls:C1512409 | Hepatocarcinogenesis | 1 | BeFree |
umls:C1704272 | Benign Prostatic Hyperplasia | 1 | BeFree |