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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for BHMT |
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Phenotypic Information for BHMT(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: BHMT |
Familial Cancer Database: BHMT |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
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KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM KEGG_CYSTEINE_AND_METHIONINE_METABOLISM REACTOME_SULFUR_AMINO_ACID_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: BHMT |
MedGen: BHMT (Human Medical Genetics with Condition) | |
ClinVar: BHMT | |
Phenotype | MGI: BHMT (International Mouse Phenotyping Consortium) |
PhenomicDB: BHMT |
Mutations for BHMT |
* 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows BHMT related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
EB362708 | GOLIM4 | 1 | 58 | 3 | 167749724 | 167749781 | BHMT | 53 | 288 | 5 | 78427550 | 78427785 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
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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Stat. for Non-Synonymous SNVs (# total SNVs=47) | (# total SNVs=13) |
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(# total SNVs=3) | (# total SNVs=0) |
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* 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 position | Mutation(aa) | Unique sampleID count |
chr5:78415084-78415084 | p.R57C | 3 |
chr5:78421875-78421875 | p.S211Y | 2 |
chr5:78417076-78417076 | p.V171V | 2 |
chr5:78422045-78422045 | p.P268S | 2 |
chr5:78426861-78426861 | p.E381E | 2 |
chr5:78416358-78416359 | p.A158fs*4 | 2 |
chr5:78415085-78415085 | p.R57H | 2 |
chr5:78417157-78417157 | p.P198P | 2 |
chr5:78416209-78416209 | p.R108R | 1 |
chr5:78423623-78423623 | p.A285D | 1 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   | 1 |   | 9 |   |   |   |   | 2 | 3 |   | 7 | 3 | 2 |   | 1 | 8 | 8 |   | 6 |
# mutation |   | 1 |   | 12 |   |   |   |   | 2 | 3 |   | 7 | 3 | 2 |   | 1 | 11 | 8 |   | 6 |
nonsynonymous SNV |   | 1 |   | 8 |   |   |   |   | 2 | 3 |   | 6 | 2 | 2 |   |   | 9 | 6 |   | 4 |
synonymous SNV |   |   |   | 4 |   |   |   |   |   |   |   | 1 | 1 |   |   | 1 | 2 | 2 |   | 2 |
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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* 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 Position | Mutation(aa) | Unique sampleID count |
chr5:78422045 | p.R57C | 2 |
chr5:78415084 | p.S211Y | 2 |
chr5:78421875 | p.P268T | 2 |
chr5:78417047 | p.V56I | 1 |
chr5:78411693 | p.A116T | 1 |
chr5:78422036 | p.P273L | 1 |
chr5:78415191 | p.V56A | 1 |
chr5:78423785 | p.Y128H | 1 |
chr5:78417094 | p.K283I | 1 |
chr5:78411716 | p.T135N | 1 |
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* 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. |
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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 BHMT |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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 |
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AHSG,BHMT,CPB2,F9,G6PC,GALR2,GCNT3, GJB6,GPR12,HRG,KRT4,KRT77,LOC642929,MAL, MORC1,PGLYRP3,PRB2,RHCG,SCTR,SLC2A2,SLC9A3 | ANXA5,BHMT2,BHMT,CAV1,CPPED1,DPT,EHBP1, EPB41L2,EPS8,GCOM1,GLYAT,GNG2,ITGB1BP1,ITIH5, ITSN1,MARK1,PALMD,PICALM,SORBS1,SPTBN1,ZDHHC3 | ||||
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ADAMTS20,BHMT,BSX,CDH20,CFHR4,CHRND,CLDN19, DLX2,GABRG2,HYALP1,KCNH5,LINC00052,OR1L6,PGAM2, PLCZ1,PLEKHG4B,PM20D1,SPANXD,SYN2,TAC3,TP53TG3B | AMPH,BCHE,BHMT2,BHMT,C14orf39,DDIT4L,DGKB, DKK2,DMGDH,GAS1,GAS2L2,GLRB,LOC255167,LOC285548, LPPR5,LSAMP,NKX3-2,NRG3,PDGFC,PENK,PPAPDC1A |
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* 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 |
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Pharmacological Information for BHMT |
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DB Category | DB Name | DB's ID and Url link |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00134 | betaine--homocysteine S-methyltransferase | approved; nutraceutical | L-Methionine | ![]() | ![]() |
DB02337 | betaine--homocysteine S-methyltransferase | experimental | S-(D-Carboxybutyl)-L-Homocysteine | ![]() | ![]() |
DB04272 | betaine--homocysteine S-methyltransferase | experimental | Citric Acid | ![]() | ![]() |
DB00158 | betaine--homocysteine S-methyltransferase | approved; nutraceutical | Folic Acid | ![]() | ![]() |
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Cross referenced IDs for BHMT |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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