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 DGKH

Basic gene info.	Gene symbol	DGKH
	Gene name	diacylglycerol kinase, eta
	Synonyms	DGKeta
	Cytomap	UCSC genome browser: 13q14.11
	Genomic location	chr13 :42614171-42803891
	Type of gene	protein-coding
	RefGenes	NM_001204504.2, NM_001204505.2,NM_001204506.2,NM_001297429.1,NM_152910.5, NM_178009.4,NR_123714.1,NR_123715.1,
	Ensembl id	ENSG00000102780
	Description	DAG kinase etadiacylglycerol kinase etadiglyceride kinase eta
	Modification date	20141207
dbXrefs	MIM : 604071
	HGNC : HGNC
	Ensembl : ENSG00000102780
	HPRD : 07237
	Vega : OTTHUMG00000016804
Protein	UniProt: Q86XP1 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DGKH
	BioGPS: 160851
	Gene Expression Atlas: ENSG00000102780
	The Human Protein Atlas: ENSG00000102780
Pathway	NCI Pathway Interaction Database: DGKH
	KEGG: DGKH
	REACTOME: DGKH
	ConsensusPathDB
	Pathway Commons: DGKH
Metabolism	MetaCyc: DGKH
	HUMANCyc: DGKH
Regulation	Ensembl's Regulation: ENSG00000102780
	miRBase: chr13 :42,614,171-42,803,891
	TargetScan: NM_001204504
	cisRED: ENSG00000102780
Context	iHOP: DGKH
	cancer metabolism search in PubMed: DGKH
	UCL Cancer Institute: DGKH
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: DGKH
	Familial Cancer Database: DGKH

* 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	604071; gene. 604071; gene.
Orphanet
Disease	KEGG Disease: DGKH
	MedGen: DGKH (Human Medical Genetics with Condition)
	ClinVar: DGKH
Phenotype	MGI: DGKH (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: DGKH

Mutations for DGKH

* 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	DGKH	chr13	42739494	42739514	C17orf96	chr17	36830559	36830579
pancreas	DGKH	chr13	42728046	42728246		chr13	37058756	37058956
pancreas	DGKH	chr13	42747629	42747649	ENOX1	chr13	44022771	44022791
prostate	DGKH	chr13	42647252	42647252		chr13	47092439	47092439

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 DGKH 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
BF373800	DGKH	1	67	13	42742071	42742138	DGKH	58	140	13	42741978	42742060
BF930562	SOX6	10	159	11	16594593	16594743	DGKH	152	321	13	42681634	42681803
W80598	ENTPD1	114	133	10	97602912	97602931	DGKH	134	418	13	42811785	42812066
BG571504	UBQLN1	1	423	9	86306517	86306939	DGKH	418	621	13	42708464	42708668
AW818534	GDA	2	103	9	74822564	74822665	DGKH	93	167	13	42774590	42774664

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=9

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=90)	Stat. for Synonymous SNVs (# total SNVs=28)

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
chr13:42772717-42772717	p.P757P	4
chr13:42793918-42793918	p.S1144G	4
chr13:42734172-42734172	p.E252G	4
chr13:42733403-42733403	p.V208V	3
chr13:42789733-42789733	p.T1048S	3
chr13:42733400-42733400	p.?	3
chr13:42793919-42793919	p.S1144N	3
chr13:42793377-42793377	p.S1075S	2
chr13:42793920-42793920	p.S1144R	2
chr13:42773954-42773954	p.R801Q	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=4

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	1		25	1		4		7			9	1	4		1	9	13	1	13
# mutation	3	1		21	1		4		7			10	1	4		1	12	14	1	13
nonsynonymous SNV	2	1		19	1		4		4			8		4		1	8	10	1	11
synonymous SNV	1			4					3			2	1				4	4		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
chr13:42793918	p.S899G,DGKH	4
chr13:42793919	p.S899N,DGKH	3
chr13:42783190	p.S899S,DGKH	2
chr13:42761271	p.Q654Q,DGKH	2
chr13:42773954	p.Y1032H,DGKH	2
chr13:42793920	p.A297V,DGKH	2
chr13:42795459	p.R1038H,DGKH	2
chr13:42729884	p.E908K,DGKH	2
chr13:42793377	p.S830S,DGKH	2
chr13:42795478	p.V55M,DGKH	2

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 DGKH 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 DGKH

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


AKAP11,ASXL2,BIRC6,GPATCH2L,CDKL5,DGKH,FER, GTF2A1,VWA8,MAP3K2,KMT2A,NBEAL1,RAD54L2,REST, SNX29,SMG1,STRN,TTBK2,ZBTB37,ZDHHC20,ZNF81	ASH1L,BIRC6,CDKL5,DGKH,EP300,FAM63B,HMBOX1, EPG5,LPP,KMT2C,KMT2A,MYO9A,MYSM1,KAT6A, NBEAL1,SMG1,UBXN7,VPS13B,WDFY3,ZKSCAN8,ZNF81

AKAP11,ASH1L,ASXL2,DGKH,DKFZp686O24166,VWA8,MPHOSPH8, MYCBP2,MYSM1,PARP4,RASA2,RBM26,SLC7A1,SMG1, SPATA13,USP12,UTP14C,XPO4,ZC3H13,ZDHHC20,ZMYM2	BDP1,FAM208B,C17orf85,CELF1,CLOCK,DDI2,DGKH, DICER1,AGO2,ELK4,KIAA0754,MDN1,MUC4,MUC5B, POLR3A,PTPRG,RBM25,RC3H2,RIF1,SHROOM4,SUMO4

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 DGKH

There's no related Drug.

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Cross referenced IDs for DGKH

* 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