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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for HNMT |
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Phenotypic Information for HNMT(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: HNMT |
Familial Cancer Database: HNMT |
* 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/ |
Metabolic Pathway Description | |
KEGG_HISTIDINE_METABOLISM |
Others | |
OMIM | 605238; gene. |
Orphanet | |
Disease | KEGG Disease: HNMT |
MedGen: HNMT (Human Medical Genetics with Condition) | |
ClinVar: HNMT | |
Phenotype | MGI: HNMT (International Mouse Phenotyping Consortium) |
PhenomicDB: HNMT |
Mutations for HNMT |
* 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HNMT 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 |
Other DBs for Structural Variants |
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Copy 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=23) | (# total SNVs=9) |
(# total SNVs=0) | (# total SNVs=1) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr2:138771379-138771379 | p.Y186Y | 3 |
chr2:138762707-138762707 | p.L145L | 2 |
chr2:138771422-138771422 | p.S201P | 2 |
chr2:138762725-138762725 | p.I151I | 2 |
chr2:138771423-138771423 | p.S201L | 2 |
chr2:138759758-138759758 | p.M141I | 2 |
chr2:138771398-138771398 | p.D193N | 2 |
chr2:138762705-138762705 | p.L145L | 2 |
chr2:138722141-138722141 | p.T27M | 2 |
chr2:138722143-138722143 | p.E28K | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   |   | 11 |   |   |   |   | 1 | 1 |   | 3 | 4 | 1 |   |   |   | 2 |   | 5 |
# mutation | 1 |   |   | 9 |   |   |   |   | 1 | 1 |   | 5 | 5 | 1 |   |   |   | 2 |   | 5 |
nonsynonymous SNV | 1 |   |   | 8 |   |   |   |   | 1 | 1 |   | 4 | 4 | 1 |   |   |   | 1 |   | 2 |
synonymous SNV |   |   |   | 1 |   |   |   |   |   |   |   | 1 | 1 |   |   |   |   | 1 |   | 3 |
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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr2:138771422 | p.S201P | 3 |
chr2:138759758 | p.M141I | 2 |
chr2:138771423 | p.L145L | 2 |
chr2:138762705 | p.S201L | 2 |
chr2:138762743 | p.R86H | 1 |
chr2:138771630 | p.S201S | 1 |
chr2:138738851 | p.R99H | 1 |
chr2:138771361 | p.I226I | 1 |
chr2:138771674 | p.R109C | 1 |
chr2:138738852 | p.G233D | 1 |
Other DBs for Point Mutations |
Copy Number for HNMT 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 HNMT |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
ARHGEF38,WBP1L,C10orf32,KIAA0825,CTSO,DCN,DIXDC1, ECM2,GLT8D2,GNG12,HNMT,ITGBL1,ITM2B,MR1, NTN4,OLFML1,OMD,PRICKLE2,RBM43,RNASEL,SH3D19 | ASAH1,ASPH,TMEM230,CAV1,EBF1,ECM2,GPR34, GTDC1,HNMT,MBD2,MGST1,OSTM1,PALM2-AKAP2,PARVA, PDE8A,PGRMC2,RTN3,SEPT11,SH3D19,STX7,VAMP3 | ||||
ANKRA2,COA5,ZBED8,CAMLG,CCDC121,CCDC90B,CIR1, CRBN,FAM200A,GPR160,HBP1,HNMT,KBTBD3,LMBRD1, PHOSPHO2,PUS10,TSPAN6,UBE2B,UNC50,VAV3,YPEL5 | SMIM7,TMEM230,CLNS1A,DPH5,DUSP11,HNMT,IAH1, LIAS,LYRM7,MRPL15,MRPL45,MRPS33,NDUFB5,NUDCD2, RPL34,RPS8,RPSA,SDHD,TATDN1,TMEM69,ZNF627 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for HNMT |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Chemistry | BindingDB | P50135; -. |
Chemistry | ChEMBL | CHEMBL2190; -. |
Organism-specific databases | PharmGKB | PA190; -. |
Organism-specific databases | CTD | 3176; -. |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00613 | histamine N-methyltransferase | approved | Amodiaquine | ||
DB01752 | histamine N-methyltransferase | experimental | S-Adenosyl-L-Homocysteine | ||
DB04655 | histamine N-methyltransferase | experimental | METOPRINE, METHODICHLOROPHEN | ||
DB07106 | histamine N-methyltransferase | experimental | 4-(DIMETHYLAMINO)BUTYL IMIDOTHIOCARBAMATE | ||
DB01454 | histamine N-methyltransferase | illicit; experimental | 3,4-Methylenedioxymethamphetamine | ||
DB00668 | histamine N-methyltransferase | approved | Epinephrine | ||
DB01033 | histamine N-methyltransferase | approved | Mercaptopurine | ||
DB00667 | histamine N-methyltransferase | approved | Histamine Phosphate |
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Cross referenced IDs for HNMT |
* 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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