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 DGKG

Basic gene info.	Gene symbol	DGKG
	Gene name	diacylglycerol kinase, gamma 90kDa
	Synonyms	DAGK3\|DGK-GAMMA
	Cytomap	UCSC genome browser: 3q27.2-q27.3
	Genomic location	chr3 :185864989-186080023
	Type of gene	protein-coding
	RefGenes	NM_001080744.1, NM_001080745.1,NM_001346.2,
	Ensembl id	ENSG00000058866
	Description	DAG kinase gammadiacylglycerol kinase gammadiacylglyerol kinase gammadiglyceride kinase gamma
	Modification date	20141207
dbXrefs	MIM : 601854
	HGNC : HGNC
	Ensembl : ENSG00000058866
	HPRD : 03510
	Vega : OTTHUMG00000156617
Protein	UniProt: P49619 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DGKG
	BioGPS: 1608
	Gene Expression Atlas: ENSG00000058866
	The Human Protein Atlas: ENSG00000058866
Pathway	NCI Pathway Interaction Database: DGKG
	KEGG: DGKG
	REACTOME: DGKG
	ConsensusPathDB
	Pathway Commons: DGKG
Metabolism	MetaCyc: DGKG
	HUMANCyc: DGKG
Regulation	Ensembl's Regulation: ENSG00000058866
	miRBase: chr3 :185,864,989-186,080,023
	TargetScan: NM_001080744
	cisRED: ENSG00000058866
Context	iHOP: DGKG
	cancer metabolism search in PubMed: DGKG
	UCL Cancer Institute: DGKG
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DGKG in cancer cell metabolism	1. Vahtola E, Storvik M, Louhelainen M, Merasto S, Lakkisto P, et al. (2011) Effects of levosimendan on cardiac gene expression profile and post-infarct cardiac remodelling in diabetic Goto-Kakizaki rats. Basic Clin Pharmacol Toxicol 109: 387-397. doi: 10.1111/j.1742-7843.2011.00743.x. go to article

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

Cancer Description
Cancer	CGAP: DGKG
	Familial Cancer Database: DGKG

* 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 BRCA ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
KEGG_GLYCEROLIPID_METABOLISM KEGG_GLYCEROPHOSPHOLIPID_METABOLISM

Others
OMIM	601854; gene.
Orphanet
Disease	KEGG Disease: DGKG
	MedGen: DGKG (Human Medical Genetics with Condition)
	ClinVar: DGKG
Phenotype	MGI: DGKG (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: DGKG

Mutations for DGKG

* 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	DGKG	chr3	185870654	185870674		chr3	186094451	186094471
ovary	DGKG	chr3	185903150	185903170	DGKG	chr3	185899362	185899382
ovary	DGKG	chr3	185947388	185947408	ZC3H18	chr16	88644360	88644380
ovary	DGKG	chr3	186040698	186040718	DGKG	chr3	186039491	186039511
ovary	DGKG	chr3	186068824	186068844	NSMCE2	chr8	126267459	126267479
pancreas	DGKG	chr3	185960886	185960906	AGPAT3	chr21	45356569	45356589

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 DGKG 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
BF921517	DGKG	28	312	3	185996755	185997040	PCDH9	308	480	13	67661420	67661592
AA322377	FAM107B	177	211	10	14716854	14717034	DGKG	204	277	3	185969588	185969661
BI020438	DGKG	2	278	3	185905959	185906234	RUNX1	272	423	21	36289624	36289775
BF732626	GRINA	1	220	8	145064317	145065536	DGKG	216	517	3	185910768	185911069
BF902754	DGKG	1	83	3	185882770	185906035	TECPR2	78	248	14	102846004	102846174

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=84)	Stat. for Synonymous SNVs (# total SNVs=26)

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
chr3:186024722-186024722	p.G38S	2
chr3:185986618-185986618	p.A363V	2
chr3:185882787-185882787	p.E706K	2
chr3:185969700-185969700	p.G537W	2
chr3:186015231-186015231	p.E118K	2
chr3:186006581-186006581	p.S154S	2
chr3:186015248-186015248	p.N112T	2
chr3:185993374-185993374	p.M291T	2
chr3:185960291-185960291	p.?	2
chr3:186006591-186006591	p.S151F	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	6	7		9	2		3		2	1		14	5				20	3		12
# mutation	6	6		10	2		3		2	1		16	5				22	3		14
nonsynonymous SNV	4	4		4	2				2	1		15	4				16	2		10
synonymous SNV	2	2		6			3					1	1				6	1		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
chr3:185867951	p.A743A,DGKG	2
chr3:186006591	p.S151F,DGKG	2
chr3:186006599	p.V148V,DGKG	2
chr3:185986591	p.T372M,DGKG	2
chr3:186015231	p.E118K,DGKG	2
chr3:185969598	p.P402H,DGKG	1
chr3:185993363	p.D349Y,DGKG	1
chr3:186024720	p.Q177P,DGKG	1
chr3:185979515	p.H74H,DGKG	1
chr3:186006513	p.G617E,DGKG	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 DGKG 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 DGKG

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


ADPRH,ANKRD45,B3GNT5,BCL11A,CTSC,DDX26B,DGKG, EML4,ETV5,FAM136A,IGF2BP2,LAMP3,LOC286467,LYN, MLKL,MSN,PRKD3,RAP2B,SEL1L3,TXNL4B,YEATS2	ACAN,ALDH1B1,MAP3K7CL,DGKG,FHL5,GPR20,HTR1B, INPP5A,ITGA8,ITIH3,KCNA5,LOC401093,MYOCD,NOV, OR51E2,PDE4C,PPP1R12B,RCAN2,SUSD5,TGM2,TYRP1

ABCD1,ACSL4,AIM2,APOBEC3G,CMPK2,DGKG,DYNLT3, ELK1,EMR1,G6PD,HERC6,IFIT2,IFIT3,IFIT5, LAMP3,LOC550643,PJA1,PRKCQ,PRPS1,SLC9A7,SNX10	ACTG2,BVES,CCDC136,CNN1,CSRP1,CTNNA3,DACT3, DES,DGKG,DMPK,DNAJB5,FAM46B,KCNE1,KCTD8, LDB3,MCAM,PCP4L1,PCYT1B,PDLIM7,REEP2,ST6GALNAC5

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 DGKG

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL1075157; -.
Organism-specific databases	PharmGKB	PA27314; -.
Organism-specific databases	CTD	1608; -.

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, gamma 90kDa	approved; nutraceutical	Phosphatidylserine

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Cross referenced IDs for DGKG

* 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