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 DGKD

Basic gene info.	Gene symbol	DGKD
	Gene name	diacylglycerol kinase, delta 130kDa
	Synonyms	DGKdelta\|dgkd-2
	Cytomap	UCSC genome browser: 2q37.1
	Genomic location	chr2 :234263152-234380743
	Type of gene	protein-coding
	RefGenes	NM_003648.2, NM_152879.2,
	Ensembl id	ENSG00000077044
	Description	DAG kinase deltaDGK-deltadiacylglycerol kinase deltadiglyceride kinase delta
	Modification date	20141207
dbXrefs	MIM : 601826
	HGNC : HGNC
	Ensembl : ENSG00000077044
	HPRD : 03492
	Vega : OTTHUMG00000133290
Protein	UniProt: Q16760 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DGKD
	BioGPS: 8527
	Gene Expression Atlas: ENSG00000077044
	The Human Protein Atlas: ENSG00000077044
Pathway	NCI Pathway Interaction Database: DGKD
	KEGG: DGKD
	REACTOME: DGKD
	ConsensusPathDB
	Pathway Commons: DGKD
Metabolism	MetaCyc: DGKD
	HUMANCyc: DGKD
Regulation	Ensembl's Regulation: ENSG00000077044
	miRBase: chr2 :234,263,152-234,380,743
	TargetScan: NM_003648
	cisRED: ENSG00000077044
Context	iHOP: DGKD
	cancer metabolism search in PubMed: DGKD
	UCL Cancer Institute: DGKD
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DGKD in cancer cell metabolism	1. Sakai H, Sakane F (2012) Recent progress on type II diacylglycerol kinases: the physiological functions of diacylglycerol kinase delta, eta and kappa and their involvement in disease. J Biochem 152: 397-406. doi: 10.1093/jb/mvs104. go to article 2. Wang H, Xiao L, Kazanietz MG (2011) p23/Tmp21 associates with protein kinase Cdelta (PKCdelta) and modulates its apoptotic function. J Biol Chem 286: 15821-15831. doi: 10.1074/jbc.M111.227991. pmid: 3091192. go to article 3. Crotty TM, Nakano T, Stafforini DM, Topham MK (2013) Diacylglycerol kinase delta modulates Akt phosphorylation through pleckstrin homology domain leucine-rich repeat protein phosphatase 2 (PHLPP2). J Biol Chem 288: 1439-1447. doi: 10.1074/jbc.M112.407379. pmid: 3548457. go to article

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

Cancer Description
Cancer	CGAP: DGKD
	Familial Cancer Database: DGKD

* 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	601826; gene.
Orphanet
Disease	KEGG Disease: DGKD
	MedGen: DGKD (Human Medical Genetics with Condition)
	ClinVar: DGKD
Phenotype	MGI: DGKD (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: DGKD

Mutations for DGKD

* 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
breast	DGKD	chr2	234361403	234361403	LOC285692	chr5	9834538	9834538
ovary	DGKD	chr2	234374735	234374755	DGKD	chr2	234377078	234377098

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 DGKD 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
BE245442	BRD9	1	98	5	863856	863953	DGKD	94	295	2	234373442	234373643
BM151326	BRD9	17	114	5	863856	863953	DGKD	110	309	2	234373444	234373643
BM150804	BRD9	17	114	5	863856	863953	DGKD	110	361	2	234373392	234373643

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=89)	Stat. for Synonymous SNVs (# total SNVs=30)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=2)

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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
chr2:234368926-234368926	p.M972I	3
chr2:234359623-234359623	p.S698S	3
chr2:234343074-234343074	p.E133*	2
chr2:234296985-234296985	p.R80Q	2
chr2:234296986-234296986	p.R80R	2
chr2:234345025-234345025	p.D253N	2
chr2:234371341-234371341	p.R1049H	2
chr2:234377116-234377116	p.S1158C	2
chr2:234355371-234355371	p.A450T	2
chr2:234346077-234346077	p.K292E	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	3	5	1	25	6		1		1	1		8	7	4			13	7		14
# mutation	3	5	1	25	6		1		1	1		8	8	4			15	8		21
nonsynonymous SNV	3	2	1	20	6		1			1		6	5	3			9	4		17
synonymous SNV		3		5					1			2	3	1			6	4		4

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
chr2:234359623	p.S654S,DGKD	3
chr2:234368407	p.R36Q,DGKD	2
chr2:234368410	p.R36R,DGKD	2
chr2:234296985	p.D209N,DGKD	2
chr2:234371341	p.R1005H,DGKD	2
chr2:234296986	p.R856H,DGKD	2
chr2:234345025	p.T857R,DGKD	2
chr2:234296918	p.A1052S,DGKD	1
chr2:234355371	p.T144T,DGKD	1
chr2:234363425	p.R329W,DGKD	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 DGKD 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 DGKD

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


ACIN1,ADCY6,ATG16L1,CASZ1,CRIPAK,D2HGDH,DGKD, EHMT1,FARP2,ING5,KIAA0556,LOC338799,MLPH,MYO15B, PLXNB1,PSD4,RBM5,SEC16A,SRSF5,SGSM2,USP40	VWA7,CEP85,DGKD,DUSP28,GPR157,HIF1AN,LMO7, MAST2,NEU3,P2RY2,PPM1J,PPP2R3B,PTPN3,SBK1, SEMA4D,SIX4,SLC20A2,TADA2B,USP19,USP28,ZNF76

AHSA2,ATAT1,MIR600HG,CAPN10,CBFA2T2,CCDC93,CROCCP2, DGKD,EDC4,FAM168B,ING5,JRK,LOC100129637,LOC91316, LPIN3,MLLT6,NSUN5P1,RBM33,SS18L1,TET3,TUBGCP6	ADCY6,ARHGAP27,ARID3B,CDC42BPG,CLN8,CNNM2,CTDP1, DGKD,DGKQ,DNM2,ELF4,FAM83G,FGFR3,CEP170B, KLF13,LMTK2,LOC100131193,MINK1,RNF152,PPP6R2,SLC26A6

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 DGKD

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL1075120; -.
Organism-specific databases	PharmGKB	PA27312; -.
Organism-specific databases	CTD	8527; -.

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
DB00144	diacylglycerol kinase, delta 130kDa	approved; nutraceutical	Phosphatidylserine

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Cross referenced IDs for DGKD

* 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