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 symbolDGKD
Gene namediacylglycerol kinase, delta 130kDa
SynonymsDGKdelta|dgkd-2
CytomapUCSC genome browser: 2q37.1
Genomic locationchr2 :234263152-234380743
Type of geneprotein-coding
RefGenesNM_003648.2,
NM_152879.2,
Ensembl idENSG00000077044
DescriptionDAG kinase deltaDGK-deltadiacylglycerol kinase deltadiglyceride kinase delta
Modification date20141207
dbXrefs MIM : 601826
HGNC : HGNC
Ensembl : ENSG00000077044
HPRD : 03492
Vega : OTTHUMG00000133290
ProteinUniProt: Q16760
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DGKD
BioGPS: 8527
Gene Expression Atlas: ENSG00000077044
The Human Protein Atlas: ENSG00000077044
PathwayNCI Pathway Interaction Database: DGKD
KEGG: DGKD
REACTOME: DGKD
ConsensusPathDB
Pathway Commons: DGKD
MetabolismMetaCyc: DGKD
HUMANCyc: DGKD
RegulationEnsembl's Regulation: ENSG00000077044
miRBase: chr2 :234,263,152-234,380,743
TargetScan: NM_003648
cisRED: ENSG00000077044
ContextiHOP: DGKD
cancer metabolism search in PubMed: DGKD
UCL Cancer Institute: DGKD
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DGKD in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_GLYCEROLIPID_METABOLISM
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM

check002.gifOthers
OMIM 601826; gene.
Orphanet
DiseaseKEGG Disease: DGKD
MedGen: DGKD (Human Medical Genetics with Condition)
ClinVar: DGKD
PhenotypeMGI: DGKD (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastDGKDchr2234361403234361403LOC285692chr598345389834538
ovaryDGKDchr2234374735234374755DGKDchr2234377078234377098
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DGKD related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE245442BRD91985863856863953DGKD942952234373442234373643
BM151326BRD9171145863856863953DGKD1103092234373444234373643
BM150804BRD9171145863856863953DGKD1103612234373392234373643

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        2        
GAIN (# sample)                 
LOSS (# sample)        2        
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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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=4

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check002.gifSomatic 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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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
chr2:234368926-234368926p.M972I3
chr2:234359623-234359623p.S698S3
chr2:234345025-234345025p.D253N2
chr2:234371341-234371341p.R1049H2
chr2:234377116-234377116p.S1158C2
chr2:234355371-234355371p.A450T2
chr2:234346077-234346077p.K292E2
chr2:234343527-234343527p.S189L2
chr2:234343074-234343074p.E133*2
chr2:234296985-234296985p.R80Q2

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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
# sample351256 1 11 874  137 14
# mutation351256 1 11 884  158 21
nonsynonymous SNV321206 1  1 653  94 17
synonymous SNV 3 5    1  231  64 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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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
chr2:234359623p.S654S,DGKD3
chr2:234371341p.D209N,DGKD2
chr2:234296986p.R36R,DGKD2
chr2:234345025p.R1005H,DGKD2
chr2:234368407p.R856H,DGKD2
chr2:234368410p.T857R,DGKD2
chr2:234296985p.R36Q,DGKD2
chr2:234346078p.Y436C,DGKD1
chr2:234356752p.E623K,DGKD1
chr2:234365629p.K776N,DGKD1

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 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

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

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
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 DGKD
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL1075120; -.
Organism-specific databasesPharmGKB PA27312; -.
Organism-specific databasesCTD 8527; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00144diacylglycerol kinase, delta 130kDaapproved; nutraceuticalPhosphatidylserine


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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



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