Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for HNMT
Basic gene info.Gene symbolHNMT
Gene namehistamine N-methyltransferase
SynonymsHMT|HNMT-S1|HNMT-S2
CytomapUCSC genome browser: 2q22.1
Genomic locationchr2 :138721807-138725014
Type of geneprotein-coding
RefGenesNM_001024074.2,
NM_001024075.1,NM_006895.2,
Ensembl idENSG00000150540
Description-
Modification date20141207
dbXrefs MIM : 605238
HGNC : HGNC
Ensembl : ENSG00000150540
HPRD : 05575
Vega : OTTHUMG00000131751
ProteinUniProt: P50135
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HNMT
BioGPS: 3176
Gene Expression Atlas: ENSG00000150540
The Human Protein Atlas: ENSG00000150540
PathwayNCI Pathway Interaction Database: HNMT
KEGG: HNMT
REACTOME: HNMT
ConsensusPathDB
Pathway Commons: HNMT
MetabolismMetaCyc: HNMT
HUMANCyc: HNMT
RegulationEnsembl's Regulation: ENSG00000150540
miRBase: chr2 :138,721,807-138,725,014
TargetScan: NM_001024074
cisRED: ENSG00000150540
ContextiHOP: HNMT
cancer metabolism search in PubMed: HNMT
UCL Cancer Institute: HNMT
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for HNMT(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HNMT
Familial Cancer Database: HNMT
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
KEGG_HISTIDINE_METABOLISM

check002.gifOthers
OMIM 605238; gene.
Orphanet
DiseaseKEGG Disease: HNMT
MedGen: HNMT (Human Medical Genetics with Condition)
ClinVar: HNMT
PhenotypeMGI: 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HNMT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=23)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr2:138771379-138771379p.Y186Y3
chr2:138759758-138759758p.M141I2
chr2:138771398-138771398p.D193N2
chr2:138762705-138762705p.L145L2
chr2:138722141-138722141p.T27M2
chr2:138762707-138762707p.L145L2
chr2:138771422-138771422p.S201P2
chr2:138762725-138762725p.I151I2
chr2:138771423-138771423p.S201L2
chr2:138722087-138722087p.F9S1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=6

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  11    11 341   2 5
# mutation1  9    11 551   2 5
nonsynonymous SNV1  8    11 441   1 2
synonymous SNV   1       11    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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr2:138771422p.S201P3
chr2:138762705p.S201L2
chr2:138759758p.M141I2
chr2:138771423p.L145L2
chr2:138771424p.G13W,HNMT1
chr2:138722098p.K184E1
chr2:138762707p.H25N,HNMT1
chr2:138771499p.Y186Y1
chr2:138722134p.R68L1
chr2:138762712p.Q197R1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

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
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for HNMT
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P50135; -.
ChemistryChEMBL CHEMBL2190; -.
Organism-specific databasesPharmGKB PA190; -.
Organism-specific databasesCTD 3176; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00613histamine N-methyltransferaseapprovedAmodiaquine
DB01752histamine N-methyltransferaseexperimentalS-Adenosyl-L-Homocysteine
DB04655histamine N-methyltransferaseexperimentalMETOPRINE, METHODICHLOROPHEN
DB07106histamine N-methyltransferaseexperimental4-(DIMETHYLAMINO)BUTYL IMIDOTHIOCARBAMATE
DB01454histamine N-methyltransferaseillicit; experimental3,4-Methylenedioxymethamphetamine
DB00668histamine N-methyltransferaseapprovedEpinephrine
DB01033histamine N-methyltransferaseapprovedMercaptopurine
DB00667histamine N-methyltransferaseapprovedHistamine 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

: Open all cross reference information



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