TissGeneSummary for BHMT |
Gene summary |
Basic gene information | Gene symbol | BHMT |
Gene name | betaine--homocysteine S-methyltransferase | |
Synonyms | BHMT1|HEL-S-61p | |
Cytomap | UCSC genome browser: 5q14.1 | |
Type of gene | protein-coding | |
RefGenes | NM_001713.2, | |
Description | betaine--homocysteine S-methyltransferase 1epididymis secretory sperm binding protein Li 61p | |
Modification date | 20141211 | |
dbXrefs | MIM : 602888 | |
HGNC : HGNC | ||
Ensembl : ENSG00000145692 | ||
HPRD : 04200 | ||
Vega : OTTHUMG00000108157 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_BHMT | |
BioGPS: 635 | ||
Pathway | NCI Pathway Interaction Database: BHMT | |
KEGG: BHMT | ||
REACTOME: BHMT | ||
Pathway Commons: BHMT | ||
Context | iHOP: BHMT | |
ligand binding site mutation search in PubMed: BHMT | ||
UCL Cancer Institute: BHMT | ||
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) | KidneyLiver | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | KIRC,KIRP,KICHLIHC | |
Reference showing the relevant tissue of BHMT | ||
Description by TissGene annotations |
* 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:0006577 | amino-acid betaine metabolic process | 18230605 | GO:0046500 | S-adenosylmethionine metabolic process | 18230605 | GO:0071267 | L-methionine salvage | 18230605 | GO:0006577 | amino-acid betaine metabolic process | 18230605 | GO:0046500 | S-adenosylmethionine metabolic process | 18230605 | GO:0071267 | L-methionine salvage | 18230605 |
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TissGeneExp for BHMT |
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 |
STAD | -1.674050404 | 0.865630846 | -2.53968125 | 1.99E-07 | 4.71E-06 |
KIRP | 5.429965221 | 9.989562096 | -4.559596875 | 5.06E-08 | 3.30E-07 |
LIHC | 8.557893721 | 11.69067372 | -3.13278 | 1.85E-08 | 1.54E-07 |
KICH | 0.339021721 | 8.491301721 | -8.15228 | 3.00E-17 | 1.22E-15 |
ESCA | -1.445031369 | 1.848177721 | -3.293209091 | 0.00312 | 0.029780601 |
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TissGene-miRNA for BHMT |
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 BHMT |
TissGeneSNV for BHMT |
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.K377E | KIRP | 1 |
p.G188S | SKCM | 1 |
p.V203M | UCEC | 1 |
p.E34V | COAD | 1 |
p.L59P | KIRP | 1 |
p.S211F | SKCM | 1 |
p.Y305H | SKCM | 1 |
p.R57C | SKCM | 1 |
p.L64I | KIRC | 1 |
p.G121E | CESC | 1 |
p.V164I | BLCA | 1 |
p.G27V | ESCA | 1 |
p.I213N | LUAD | 1 |
p.G191E | SKCM | 1 |
p.S130I | SARC | 1 |
p.R57C | UCEC | 1 |
p.L355I | LUAD | 1 |
p.S330N | STAD | 1 |
p.E381* | LUAD | 1 |
p.E113K | LUAD | 1 |
p.I13N | SKCM | 1 |
p.E54K | LUSC | 1 |
p.P268S | SKCM | 1 |
p.P273L | LUSC | 1 |
p.R57H | READ | 1 |
p.A167V | SKCM | 1 |
p.T339S | OV | 1 |
p.S95Y | UCEC | 1 |
p.V56A | KIRP | 1 |
p.P268T | LUAD | 1 |
p.A182T | ESCA | 1 |
p.R204H | PRAD | 1 |
p.P46L | SKCM | 1 |
p.E313K | SKCM | 1 |
p.P265S | SKCM | 1 |
p.T135N | OV | 1 |
p.L33P | UCEC | 1 |
p.R318K | SKCM | 1 |
p.L59V | LUAD | 1 |
p.Q72P | BRCA | 1 |
p.L193F | STAD | 1 |
p.D263N | READ | 1 |
p.E162Q | LUAD | 1 |
p.R361Q | HNSC | 1 |
p.T390A | STAD | 1 |
p.S211F | PRAD | 1 |
p.G5E | KIRC | 1 |
p.R57H | STAD | 1 |
p.S211Y | READ | 1 |
p.E312K | KIRC | 1 |
p.A107V | ESCA | 1 |
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TissGeneCNV for BHMT |
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 BHMT |
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 |
Chimerdb3.0 | ChiTaRs | NA | EB362708 | GOLIM4-BHMT | chr3:167749781 | chr5:78427550 |
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TissGeneNet for BHMT |
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 BHMT |
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 BHMT |
TissGeneDrug for BHMT |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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TissGeneDisease for BHMT |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0080178 | Spina Bifida | 5 | BeFree,GAD |
umls:C0010068 | Coronary heart disease | 4 | BeFree,GAD |
umls:C0018798 | Congenital Heart Defects | 4 | BeFree,GAD |
umls:C2239176 | Liver carcinoma | 4 | BeFree |
umls:C0006142 | Malignant neoplasm of breast | 3 | BeFree,GAD |
umls:C0013080 | Down Syndrome | 3 | BeFree |
umls:C0598608 | Hyperhomocysteinemia | 3 | BeFree,GAD,LHGDN |
umls:C0678222 | Breast Carcinoma | 3 | BeFree |
umls:C0008924 | Cleft Lip | 2 | GAD |
umls:C0008925 | Cleft Palate | 2 | GAD |
umls:C0010054 | Coronary Arteriosclerosis | 2 | BeFree,GAD |
umls:C0027794 | Neural Tube Defects | 2 | CTD_human,GAD |
umls:C0028754 | Obesity | 2 | BeFree,GAD |
umls:C0038454 | Cerebrovascular accident | 2 | BeFree,GAD |
umls:C0158646 | Cleft palate with cleft lip | 2 | BeFree |
umls:C0278996 | Cancer of Head and Neck | 2 | BeFree |
umls:C1512409 | Hepatocarcinogenesis | 2 | BeFree |
umls:C1956346 | Coronary Artery Disease | 2 | BeFree,GAD |
umls:C3495426 | Homocysteinemia | 2 | BeFree |
umls:C0000832 | Abruptio Placentae | 1 | CTD_human,GAD,LHGDN |
umls:C0004153 | Atherosclerosis | 1 | GAD |
umls:C0005684 | Malignant neoplasm of urinary bladder | 1 | GAD |
umls:C0007131 | Non-Small Cell Lung Carcinoma | 1 | GAD |
umls:C0007222 | Cardiovascular Diseases | 1 | BeFree |
umls:C0007786 | Brain Ischemia | 1 | GAD |
umls:C0008312 | Primary biliary cirrhosis | 1 | BeFree |
umls:C0011860 | Diabetes Mellitus, Non-Insulin-Dependent | 1 | CTD_human |
umls:C0015695 | Fatty Liver | 1 | BeFree,LHGDN |
umls:C0019202 | Hepatolenticular Degeneration | 1 | CTD_human |
umls:C0023452 | Leukemia, Lymphocytic, Acute, L1 | 1 | BeFree |
umls:C0023890 | Liver Cirrhosis | 1 | GAD |
umls:C0024117 | Chronic Obstructive Airway Disease | 1 | GAD |
umls:C0024121 | Lung Neoplasms | 1 | GAD |
umls:C0024301 | Lymphoma, Follicular | 1 | GAD |
umls:C0024305 | Lymphoma, Non-Hodgkin | 1 | CTD_human,GAD |
umls:C0032963 | Pregnancy Complications, Cardiovascular | 1 | GAD |
umls:C0042373 | Vascular Diseases | 1 | BeFree |
umls:C0079744 | Diffuse Large B-Cell Lymphoma | 1 | GAD |
umls:C0151526 | Premature Birth | 1 | GAD |
umls:C0162871 | Aortic Aneurysm, Abdominal | 1 | GAD |
umls:C0242379 | Malignant neoplasm of lung | 1 | GAD |
umls:C0596263 | Carcinogenesis | 1 | BeFree |
umls:C0600452 | Hepatopulmonary Syndrome | 1 | GAD |
umls:C0741916 | Cardiac defects | 1 | GAD |
umls:C0795690 | Congenital omphalocele | 1 | BeFree |
umls:C0948008 | Ischemic stroke | 1 | BeFree |
umls:C1302401 | Adenoma of large intestine | 1 | BeFree |
umls:C1527249 | Colorectal Cancer | 1 | GAD |
umls:C2711227 | Steatohepatitis | 1 | BeFree |