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 ETNK2
Basic gene info.Gene symbolETNK2
Gene nameethanolamine kinase 2
SynonymsEKI2|HMFT1716
CytomapUCSC genome browser: 1q32.1
Genomic locationchr1 :204100189-204121307
Type of geneprotein-coding
RefGenesNM_001297760.1,
NM_001297761.1,NM_001297762.1,NM_018208.3,
Ensembl idENSG00000143845
Descriptionethanolamine kinase-like protein
Modification date20141207
dbXrefs MIM : 609859
HGNC : HGNC
Ensembl : ENSG00000143845
HPRD : 13283
Vega : OTTHUMG00000036061
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ETNK2
BioGPS: 55224
Gene Expression Atlas: ENSG00000143845
The Human Protein Atlas: ENSG00000143845
PathwayNCI Pathway Interaction Database: ETNK2
KEGG: ETNK2
REACTOME: ETNK2
ConsensusPathDB
Pathway Commons: ETNK2
MetabolismMetaCyc: ETNK2
HUMANCyc: ETNK2
RegulationEnsembl's Regulation: ENSG00000143845
miRBase: chr1 :204,100,189-204,121,307
TargetScan: NM_001297760
cisRED: ENSG00000143845
ContextiHOP: ETNK2
cancer metabolism search in PubMed: ETNK2
UCL Cancer Institute: ETNK2
Assigned class in ccmGDBC

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Phenotypic Information for ETNK2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ETNK2
Familial Cancer Database: ETNK2
* 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_GLYCEROPHOSPHOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ETNK2
MedGen: ETNK2 (Human Medical Genetics with Condition)
ClinVar: ETNK2
PhenotypeMGI: ETNK2 (International Mouse Phenotyping Consortium)
PhenomicDB: ETNK2

Mutations for ETNK2
* 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 ETNK2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU624180ETNK2182451204100190204100544MMP14240594142331575523316109
BF933482MBP11112187469151674691618ETNK2983381204110463204110703

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2                
GAIN (# sample)2                
LOSS (# sample)                 
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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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=14

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=30)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr1:204120952-204120952p.P10Q14
chr1:204115853-204115853p.H186H2
chr1:204115879-204115879p.E178*2
chr1:204110547-204110547p.R227Q2
chr1:204115797-204115797p.T205M2
chr1:204106375-204106375p.V291M2
chr1:204109170-204109170p.E287E1
chr1:204109238-204109238p.R265W1
chr1:204118842-204118842p.P169P1
chr1:204103675-204103675p.P388A1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 3  1 1  1 2   212
# mutation 1 3  1 1  1 2   212
nonsynonymous SNV 1 2  1 1  1 2   2 2
synonymous SNV   1              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
chr1:204115797p.T205M3
chr1:204115773p.A176T1
chr1:204115784p.V58M1
chr1:204101382p.Y364C1
chr1:204115852p.L349I1
chr1:204103686p.F343L1
chr1:204115853p.H310R1
chr1:204103702p.V291M1
chr1:204115885p.E287E1
chr1:204106317p.E287G1

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 ETNK2 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 ETNK2

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

ANXA9,CCDC57,DALRD3,DCXR,DNALI1,EBF4,ETNK2,
FASN,GAMT,GATSL3,KCNJ11,MRFAP1,ECI2,REEP5,
SEMA3F,SLC39A11,SORD,SOX13,SPDEF,TP53TG1,TTC39A
AP1M2,ASTN2,BATF,DNAAF3,CLPSL2,C9orf116,ETNK2,
HOXC10,LEO1,MARVELD3,MIPEP,PAFAH2,S100A14,SEC14L2,
SERPINA5,SLC39A11,SMPDL3B,TBC1D8,TSPAN1,WNT4,ZNF689

APBB1,BCAM,CCDC136,CHST10,CPNE1,ETNK2,GGT7,
GPSM1,KCNIP3,KIF3C,LARP6,CERS4,LDLRAD3,LTBP3,
MPP2,ORAI2,PIP4K2B,SHISA4,SLC45A1,SMO,ZNF853
A4GALT,ARMCX1,CLIP4,CRTAP,EFEMP2,ELOVL4,ETNK2,
GALNT16,HSPB2,ISLR,LARP6,LDOC1,LRRN4CL,MITF,
NAP1L3,NUDT10,RADIL,RAI2,RECK,SHISA4,SYNGR1
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 ETNK2


There's no related Drug.
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Cross referenced IDs for ETNK2
* 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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