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 HEMK1
Basic gene info.Gene symbolHEMK1
Gene nameHemK methyltransferase family member 1
SynonymsHEMK|MTQ1
CytomapUCSC genome browser: 3p21.3
Genomic locationchr3 :50606908-50622421
Type of geneprotein-coding
RefGenesNM_016173.3,
Ensembl idENSG00000114735
DescriptionHEMK homolog 7kbhemK methyltransferase family member 1m.HsaHemKP
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000114735
HPRD : 13645
Vega : OTTHUMG00000156849
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HEMK1
BioGPS: 51409
Gene Expression Atlas: ENSG00000114735
The Human Protein Atlas: ENSG00000114735
PathwayNCI Pathway Interaction Database: HEMK1
KEGG: HEMK1
REACTOME: HEMK1
ConsensusPathDB
Pathway Commons: HEMK1
MetabolismMetaCyc: HEMK1
HUMANCyc: HEMK1
RegulationEnsembl's Regulation: ENSG00000114735
miRBase: chr3 :50,606,908-50,622,421
TargetScan: NM_016173
cisRED: ENSG00000114735
ContextiHOP: HEMK1
cancer metabolism search in PubMed: HEMK1
UCL Cancer Institute: HEMK1
Assigned class in ccmGDBC

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Phenotypic Information for HEMK1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HEMK1
Familial Cancer Database: HEMK1
* 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
KEGG_TYROSINE_METABOLISM
KEGG_SELENOAMINO_ACID_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: HEMK1
MedGen: HEMK1 (Human Medical Genetics with Condition)
ClinVar: HEMK1
PhenotypeMGI: HEMK1 (International Mouse Phenotyping Consortium)
PhenomicDB: HEMK1

Mutations for HEMK1
* 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 HEMK1 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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=16)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted 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
chr3:50615293-50615293p.L217L2
chr3:50617315-50617315p.M271V2
chr3:50617642-50617642p.R321L1
chr3:50608743-50608743p.H70Y1
chr3:50614942-50614942p.S184S1
chr3:50617645-50617645p.R322K1
chr3:50608747-50608747p.V71A1
chr3:50615261-50615261p.R207W1
chr3:50617817-50617817p.R329Q1
chr3:50609158-50609158p.P82P1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 2  1     1   43 3
# mutation 1 2  1     1   43 3
nonsynonymous SNV 1 1  1         31 2
synonymous SNV   1        1   12 1
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
chr3:50614589p.S184S1
chr3:50614591p.R207W1
chr3:50614942p.L217L1
chr3:50615261p.A262A1
chr3:50615293p.M271V1
chr3:50617290p.R298M1
chr3:50608616p.R329Q1
chr3:50617315p.R334W1
chr3:50608618p.S27S1
chr3:50617573p.S28L1

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 HEMK1 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 HEMK1

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

ACBD4,ADAMTS13,ATRIP,LMNTD2,C3orf18,ARIH2OS,CCDC71,
CYB561D2,HEMK1,MYL5,NAT6,NEIL1,NICN1,NISCH,
NPRL2,RBM5,TEX264,TMEM115,TUSC2,UBXN11,WDR6
ANKZF1,APBB3,CDAN1,CDK5RAP3,FAM193B,GIGYF1,HAUS5,
HEMK1,JMJD7-PLA2G4B,KAT2A,LPIN3,MST1,NEIL1,NISCH,
NSUN5P2,RECQL5,SNRNP70,TUBGCP6,USP20,ZBTB48,ZFYVE27

ARIH2OS,CDK10,DALRD3,HEMK1,IFRD2,IP6K2,LOC440944,
LOC440957,MRPS25,NAT6,NDUFAF3,NICN1,NPRL2,NSUN5P1,
NSUN5P2,RFT1,SLC26A6,SPATA24,TEX264,TMEM42,TUSC2
BCS1L,C16orf58,DFFB,DXO,EIF4EBP1,GTF2H4,HEMK1,
IFT27,INO80E,LGTN,MLST8,PPOX,RPUSD3,SARS2,
SDR39U1,TARBP2,TRMT1,TRMT2A,DPH7,MSS51,ZNF76
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 HEMK1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01752HemK methyltransferase family member 1experimentalS-Adenosyl-L-Homocysteine


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Cross referenced IDs for HEMK1
* 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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