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 DGKZ

Basic gene info.	Gene symbol	DGKZ
	Gene name	diacylglycerol kinase, zeta
	Synonyms	DAGK5\|DAGK6\|DGK-ZETA\|hDGKzeta
	Cytomap	UCSC genome browser: 11p11.2
	Genomic location	chr11 :46354454-46402104
	Type of gene	protein-coding
	RefGenes	NM_001105540.1, NM_001199266.1,NM_001199267.1,NM_003646.3,NM_201532.2, NM_201533.3,NM_001199268.1,
	Ensembl id	ENSG00000149091
	Description	DAG kinase zetadiacylglycerol kinase zetadiacylglycerol kinase, zeta 104kDadiglyceride kinase zeta
	Modification date	20141207
dbXrefs	MIM : 601441
	HGNC : HGNC
	Ensembl : ENSG00000149091
	HPRD : 03260
	Vega : OTTHUMG00000166437
Protein	UniProt: Q13574 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DGKZ
	BioGPS: 8525
	Gene Expression Atlas: ENSG00000149091
	The Human Protein Atlas: ENSG00000149091
Pathway	NCI Pathway Interaction Database: DGKZ
	KEGG: DGKZ
	REACTOME: DGKZ
	ConsensusPathDB
	Pathway Commons: DGKZ
Metabolism	MetaCyc: DGKZ
	HUMANCyc: DGKZ
Regulation	Ensembl's Regulation: ENSG00000149091
	miRBase: chr11 :46,354,454-46,402,104
	TargetScan: NM_001105540
	cisRED: ENSG00000149091
Context	iHOP: DGKZ
	cancer metabolism search in PubMed: DGKZ
	UCL Cancer Institute: DGKZ
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DGKZ in cancer cell metabolism	1. Vrba L, Junk DJ, Novak P, Futscher BW (2008) p53 induces distinct epigenetic states at its direct target promoters. BMC Genomics 9: 486. doi: 10.1186/1471-2164-9-486. pmid: 2585595. go to article

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

Cancer Description
Cancer	CGAP: DGKZ
	Familial Cancer Database: DGKZ

* 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_GLYCEROLIPID_METABOLISM KEGG_GLYCEROPHOSPHOLIPID_METABOLISM

Others
OMIM	601441; gene. 601441; gene.
Orphanet
Disease	KEGG Disease: DGKZ
	MedGen: DGKZ (Human Medical Genetics with Condition)
	ClinVar: DGKZ
Phenotype	MGI: DGKZ (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: DGKZ

Mutations for DGKZ

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	DGKZ	chr11	46380853	46380873	DGKZ	chr11	46394630	46394650

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DGKZ 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
AW889506	DGKZ	41	240	11	46397727	46397926	DGKZ	234	382	11	46396812	46396960
AI638821	DGKZ	2	108	11	46401998	46402104	RAB6B	105	527	3	133545158	133545580
BI032998	MEG3	40	357	14	101314669	101314990	DGKZ	347	526	11	46389528	46389707
BG945849	DGKZ	1	185	11	46398738	46398926	PCSK7	182	307	11	117096141	117096734
AI656073	DGKZ	2	108	11	46401998	46402104	RAB6B	105	495	3	133545158	133545548

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

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

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=52)	Stat. for Synonymous SNVs (# total SNVs=12)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr11:46389258-46389258	p.F126L	2
chr11:46389292-46389292	p.M138L	2
chr11:46397143-46397143	p.Q640Q	2
chr11:46398102-46398102	p.I746I	2
chr11:46397158-46397158	p.R645R	2
chr11:46391092-46391092	p.V181I	1
chr11:46395999-46395999	p.A502T	1
chr11:46400643-46400643	p.R857C	1
chr11:46388861-46388861	p.G78A	1
chr11:46393125-46393125	p.T260I	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	4	1		11	5		3		3			5	4			1	11	7	1	11
# mutation	6	1		12	5		3		3			5	4			1	11	7	1	13
nonsynonymous SNV	3			8	4		2		2			4	4			1	7	5	1	11
synonymous SNV	3	1		4	1		1		1			1					4	2		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
chr11:46397884	p.D677N,DGKZ	2
chr11:46393049	p.T756M,DGKZ	1
chr11:46398102	p.E102Q,DGKZ	1
chr11:46387912	p.E205K,DGKZ	1
chr11:46393685	p.S454S,DGKZ	1
chr11:46400643	p.R758W,DGKZ	1
chr11:46389250	p.S106A,DGKZ	1
chr11:46396525	p.G211V,DGKZ	1
chr11:46393057	p.A463T,DGKZ	1
chr11:46398650	p.A764S,DGKZ	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 DGKZ 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 DGKZ

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


AGAP3,ATAD3A,C1orf159,CDC34,CSK,CSNK1G2,DAZAP1, DGKZ,DOHH,ESRRA,GRK6,LRWD1,MIIP,PEX16, PSMC3,RNF166,SAFB,SH2B2,TAF6L,TSC22D4,ZNF408	APBA3,ARMC6,ASPSCR1,ATAD3A,RABL6,CSNK1G2,CTBP1, DGKZ,LRWD1,MAP2K2,MBD3,NCLN,NUBP2,POLRMT, PTCD1,RPS6KB2,SCAF1,SCRIB,STK11,TAF6L,TELO2

ADRM1,ANO9,BRAT1,CLCN7,DGKZ,DUS1L,GIT1, GMEB2,INTS1,KAT2A,LRRC45,PEX16,PKP3,RALY, RECQL4,SCRIB,TBL3,TELO2,TOMM34,TRMT61A,ZGPAT	ACOT12,ASPDH,LINC00479,CD82,CIDEB,DGKZ,DSG3, RMDN3,GGN,KDM8,MT1B,MYH7,NLRP6,OSBPL6, PLCB3,PRSS1,SLC2A5,SLC5A1,SLC5A2,SLC6A6,TTC36

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 DGKZ

There's no related Drug.

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Cross referenced IDs for DGKZ

* 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