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 DGKA

Basic gene info.	Gene symbol	DGKA
	Gene name	diacylglycerol kinase, alpha 80kDa
	Synonyms	DAGK\|DAGK1\|DGK-alpha
	Cytomap	UCSC genome browser: 12q13.3
	Genomic location	chr12 :56324945-56347807
	Type of gene	protein-coding
	RefGenes	NM_001345.4, NM_201444.2,NM_201445.1,NM_201554.1,
	Ensembl id	ENSG00000065357
	Description	80 kDa diacylglycerol kinaseDAG kinase alphadiacylglycerol kinase alphadiglyceride kinase alpha
	Modification date	20141207
dbXrefs	MIM : 125855
	HGNC : HGNC
	Ensembl : ENSG00000065357
	HPRD : 00517
	Vega : OTTHUMG00000170109
Protein	UniProt: P23743 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DGKA
	BioGPS: 1606
	Gene Expression Atlas: ENSG00000065357
	The Human Protein Atlas: ENSG00000065357
Pathway	NCI Pathway Interaction Database: DGKA
	KEGG: DGKA
	REACTOME: DGKA
	ConsensusPathDB
	Pathway Commons: DGKA
Metabolism	MetaCyc: DGKA
	HUMANCyc: DGKA
Regulation	Ensembl's Regulation: ENSG00000065357
	miRBase: chr12 :56,324,945-56,347,807
	TargetScan: NM_001345
	cisRED: ENSG00000065357
Context	iHOP: DGKA
	cancer metabolism search in PubMed: DGKA
	UCL Cancer Institute: DGKA
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DGKA in cancer cell metabolism	1. Dominguez CL, Floyd DH, Xiao A, Mullins GR, Kefas BA, et al. (2013) Diacylglycerol kinase alpha is a critical signaling node and novel therapeutic target in glioblastoma and other cancers. Cancer Discov 3: 782-797. doi: 10.1158/2159-8290.CD-12-0215. pmid: 3710531. go to article 2. Chauveau A, Le Floc'h A, Bantilan NS, Koretzky GA, Huse M (2014) Diacylglycerol kinase alpha establishes T cell polarity by shaping diacylglycerol accumulation at the immunological synapse. Sci Signal 7: ra82. doi: 10.1126/scisignal.2005287. go to article 3. Torres-Ayuso P, Daza-Martin M, Martin-Perez J, Avila-Flores A, Merida I (2014) Diacylglycerol kinase alpha promotes 3D cancer cell growth and limits drug sensitivity through functional interaction with Src. Oncotarget 5: 9710-9726. pmid: 4259432. go to article

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

Cancer Description
Cancer	CGAP: DGKA
	Familial Cancer Database: DGKA

* 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	125855; gene.
Orphanet
Disease	KEGG Disease: DGKA
	MedGen: DGKA (Human Medical Genetics with Condition)
	ClinVar: DGKA
Phenotype	MGI: DGKA (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: DGKA

Mutations for DGKA

* 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 DGKA 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
AW340041	DGKA	22	123	12	56347681	56347782	RGS22	124	509	8	101051221	101059795
AI653235	EML3	1	166	11	62369691	62369856	DGKA	163	391	12	56324991	56325219
BU948429	NDUFB5	8	430	3	179341970	179342392	DGKA	426	511	12	56347720	56347805
AI203264	EML3	1	166	11	62369691	62369856	DGKA	163	391	12	56324991	56325219
BE717774	NAV2	21	263	11	19841944	19842188	DGKA	259	493	12	56346920	56347616

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=55)	Stat. for Synonymous SNVs (# total SNVs=20)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=0)
	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
chr12:56345564-56345564	p.G528G	2
chr12:56347164-56347164	p.D698D	2
chr12:56334722-56334722	p.K353K	2
chr12:56330872-56330872	p.D46N	2
chr12:56334729-56334729	p.D356Y	2
chr12:56346633-56346633	p.G620E	2
chr12:56347487-56347487	p.N715Y	2
chr12:56346661-56346661	p.L629L	2
chr12:56336007-56336007	p.G462G	2
chr12:56347514-56347514	p.R726fs*9	2

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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	2		10	1		1	1		1		9	4	4			6	9		10
# mutation	4	2		10	1		1	1		1		9	4	4			7	10		16
nonsynonymous SNV	1	2		7			1	1		1		8	3	3			3	3		9
synonymous SNV	3			3	1							1	1	1			4	7		7

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
chr12:56346661	p.F730L,DGKA	2
chr12:56347534	p.L629L,DGKA	2
chr12:56345564	p.G528G,DGKA	2
chr12:56346939	p.F559L,DGKA	1
chr12:56334764	p.E664E,DGKA	1
chr12:56331219	p.S132T,DGKA	1
chr12:56345838	p.K349R,DGKA	1
chr12:56334110	p.E560K,DGKA	1
chr12:56346620	p.I668M,DGKA	1
chr12:56347147	p.I167I,DGKA	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 DGKA 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 DGKA

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


ACAP1,BTLA,CARD11,CD19,CD37,CD40LG,CD79B, DGKA,FAM159A,FCRL3,FCRLA,GPR18,HVCN1,IL16, TESPA1,LY9,MS4A1,PARP15,RAC2,RASGRP2,TMC8	APOBEC3G,BTN2A2,CARD11,CD3D,CD3E,CXCR3,DEF6, DGKA,GPR114,HLA-DOB,JAK3,LAT2,LCK,RASAL3, RASSF5,RHBDF2,SEPT1,TAPBP,TCF7,TRAF3IP3,WNT10A

ABCB11,CAPN8,COL17A1,CYTH1,DENND3,DGKA,DHRS9, EPS8L1,GDPD3,GIPR,FAM214B,LIMA1,LYST,MMP28, PCSK7,PLCD3,RAPGEF3,RHOF,VILL,VSIG2,ZFYVE28	SH3D21,C2CD2L,DAPK2,DGKA,DHRS11,EPS8L2,EPS8L3, EZR,FLVCR2,GCOM1,GRTP1,HECTD3,IFNLR1,KIAA0247, NR1I2,PDXP,PTK2B,RAB8A,RHOU,SLC9A3R1,SULT1A2

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 DGKA

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA27310; -.
Organism-specific databases	CTD	1606; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00163	diacylglycerol kinase, alpha 80kDa	approved; nutraceutical	Vitamin E

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Cross referenced IDs for DGKA

* 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