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 symbolDGKA
Gene namediacylglycerol kinase, alpha 80kDa
SynonymsDAGK|DAGK1|DGK-alpha
CytomapUCSC genome browser: 12q13.3
Genomic locationchr12 :56324945-56347807
Type of geneprotein-coding
RefGenesNM_001345.4,
NM_201444.2,NM_201445.1,NM_201554.1,
Ensembl idENSG00000065357
Description80 kDa diacylglycerol kinaseDAG kinase alphadiacylglycerol kinase alphadiglyceride kinase alpha
Modification date20141207
dbXrefs MIM : 125855
HGNC : HGNC
Ensembl : ENSG00000065357
HPRD : 00517
Vega : OTTHUMG00000170109
ProteinUniProt: P23743
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DGKA
BioGPS: 1606
Gene Expression Atlas: ENSG00000065357
The Human Protein Atlas: ENSG00000065357
PathwayNCI Pathway Interaction Database: DGKA
KEGG: DGKA
REACTOME: DGKA
ConsensusPathDB
Pathway Commons: DGKA
MetabolismMetaCyc: DGKA
HUMANCyc: DGKA
RegulationEnsembl's Regulation: ENSG00000065357
miRBase: chr12 :56,324,945-56,347,807
TargetScan: NM_001345
cisRED: ENSG00000065357
ContextiHOP: DGKA
cancer metabolism search in PubMed: DGKA
UCL Cancer Institute: DGKA
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DGKA in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_GLYCEROLIPID_METABOLISM
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM

check002.gifOthers
OMIM 125855; gene.
Orphanet
DiseaseKEGG Disease: DGKA
MedGen: DGKA (Human Medical Genetics with Condition)
ClinVar: DGKA
PhenotypeMGI: DGKA (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DGKA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW340041DGKA22123125634768156347782RGS221245098101051221101059795
AI653235EML31166116236969162369856DGKA163391125632499156325219
BU948429NDUFB584303179341970179342392DGKA426511125634772056347805
AI203264EML31166116236969162369856DGKA163391125632499156325219
BE717774NAV221263111984194419842188DGKA259493125634692056347616

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr12:56346633-56346633p.G620E2
chr12:56347487-56347487p.N715Y2
chr12:56346661-56346661p.L629L2
chr12:56336007-56336007p.G462G2
chr12:56347514-56347514p.R726fs*92
chr12:56347534-56347534p.F730L2
chr12:56345564-56345564p.G528G2
chr12:56347164-56347164p.D698D2
chr12:56334722-56334722p.K353K2
chr12:56330872-56330872p.D46N2

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample42 101 11 1 944  69 10
# mutation42 101 11 1 944  710 16
nonsynonymous SNV12 7  11 1 833  33 9
synonymous SNV3  31      111  47 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr12:56347534p.F730L,DGKA2
chr12:56345564p.L629L,DGKA2
chr12:56346661p.G528G,DGKA2
chr12:56333079p.L16L,DGKA1
chr12:56346566p.V271M,DGKA1
chr12:56334431p.P414L,DGKA1
chr12:56346688p.R616G,DGKA1
chr12:56330335p.I709M,DGKA1
chr12:56335359p.Q17Q,DGKA1
chr12:56347471p.G276V,DGKA1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA27310; -.
Organism-specific databasesCTD 1606; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00163diacylglycerol kinase, alpha 80kDaapproved; nutraceuticalVitamin 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



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