Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 ETNK1

Basic gene info.	Gene symbol	ETNK1
	Gene name	ethanolamine kinase 1
	Synonyms	EKI\|EKI 1\|EKI1\|Nbla10396
	Cytomap	UCSC genome browser: 12p12.1
	Genomic location	chr12 :22778075-22797349
	Type of gene	protein-coding
	RefGenes	NM_001039481.1, NM_018638.4,
	Ensembl id	ENSG00000139163
	Description	putative protein product of Nbla10396
	Modification date	20141207
dbXrefs	MIM : 609858
	HGNC : HGNC
	Ensembl : ENSG00000139163
	HPRD : 09934
	Vega : OTTHUMG00000169008
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ETNK1
	BioGPS: 55500
	Gene Expression Atlas: ENSG00000139163
	The Human Protein Atlas: ENSG00000139163
Pathway	NCI Pathway Interaction Database: ETNK1
	KEGG: ETNK1
	REACTOME: ETNK1
	ConsensusPathDB
	Pathway Commons: ETNK1
Metabolism	MetaCyc: ETNK1
	HUMANCyc: ETNK1
Regulation	Ensembl's Regulation: ENSG00000139163
	miRBase: chr12 :22,778,075-22,797,349
	TargetScan: NM_001039481
	cisRED: ENSG00000139163
Context	iHOP: ETNK1
	cancer metabolism search in PubMed: ETNK1
	UCL Cancer Institute: ETNK1
Assigned class in ccmGDB	C

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Phenotypic Information for ETNK1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ETNK1
	Familial Cancer Database: ETNK1

* 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/

Metabolic Pathway Description
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: ETNK1
	MedGen: ETNK1 (Human Medical Genetics with Condition)
	ClinVar: ETNK1
Phenotype	MGI: ETNK1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ETNK1

Mutations for ETNK1

* 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 ETNK1 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
CB306777	ETNK1	18	281	12	22837943	22838206	ETNK1	275	436	12	22837424	22837910
BQ637998	ETNK1	1	349	12	22843240	22843588	ETNK1	342	623	12	22842331	22842612
BE061136	ENPP2	5	80	8	120609938	120610015	ETNK1	73	599	12	22787799	22788325
CV420024	RBBP6	3	75	16	24555953	24556026	ETNK1	71	520	12	22784348	22784797

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=34)	Stat. for Synonymous SNVs (# total SNVs=14)

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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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
chr12:22796734-22796734	p.C154Y	2
chr12:22812085-22812085	p.K274T	2
chr12:22796743-22796743	p.G157V	2
chr12:22778163-22778163	p.L22L	2
chr12:22796809-22796809	p.R179Q	2
chr12:22812050-22812050	p.L262L	2
chr12:22778446-22778446	p.R117G	2
chr12:22837881-22837881	p.P451L	2
chr12:22826447-22826447	p.V355V	2
chr12:22811990-22811990	p.A242A	1

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

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	3		5	1				3			3	3	1			3	2		9
# mutation	1	3		4	1				3			3	4	1			4	2		10
nonsynonymous SNV	1	3		2					2			1	3	1			3	1		8
synonymous SNV				2	1				1			2	1				1	1		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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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
chr12:22796809	p.R167K,ETNK1	2
chr12:22812085	p.K274T	2
chr12:22796773	p.R179Q,ETNK1	2
chr12:22826547	p.E389K	1
chr12:22796805	p.D217N,ETNK1	1
chr12:22812020	p.K440T	1
chr12:22837848	p.C235S	1
chr12:22812025	p.V450M	1
chr12:22837877	p.R5S,ETNK1	1
chr12:22778110	p.T240A	1

Other 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

Copy Number for ETNK1 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 ETNK1

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.

: Open all plots for all cancer types

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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

: Open all plots for all cancer types


AEBP2,AMN1,METTL20,CASC1,CCDC91,CMAS,ETNK1, FGD4,FGFR1OP2,GOLT1B,IPO8,C2CD5,KLHL42,KRAS, LYRM5,MED21,MIB1,MRPS35,PYROXD1,RECQL,TM7SF3	ANGEL2,CD2AP,CREBZF,DCAF17,ETNK1,FAM122B,FAM76B, FAM91A1,G2E3,CEP44,MOB1B,PAN3,PPIP5K2,PTBP3, SCAMP1,SRSF10,SPIN4,TIA1,TRIM33,ZMYM6,ZNF529

ACTR6,AEBP2,ARL1,C12orf29,ETNK1,FAM103A1,GMNN, GOLT1B,MRPL42,NECAP1,PYROXD1,RAP1B,SEC11C,TBC1D15, TDG,TMED2,TMPO,TWF1,VEZT,YEATS4,ZFAND6	ABHD5,CA2,CSTB,MICU2,ETFDH,ETNK1,FAM45A, FDX1,GDPD3,GHITM,C2CD5,LACTB,LOC25845,ME2, NRG4,OASL,PITX2,SLC20A1,TEKT5,UGDH,UGT1A10

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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 ETNK1

There's no related Drug.

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Cross referenced IDs for ETNK1

* 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