Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolDGKG
Gene namediacylglycerol kinase, gamma 90kDa
SynonymsDAGK3|DGK-GAMMA
CytomapUCSC genome browser: 3q27.2-q27.3
Genomic locationchr3 :185864989-186080023
Type of geneprotein-coding
RefGenesNM_001080744.1,
NM_001080745.1,NM_001346.2,
Ensembl idENSG00000058866
DescriptionDAG kinase gammadiacylglycerol kinase gammadiacylglyerol kinase gammadiglyceride kinase gamma
Modification date20141207
dbXrefs MIM : 601854
HGNC : HGNC
Ensembl : ENSG00000058866
HPRD : 03510
Vega : OTTHUMG00000156617
ProteinUniProt: P49619
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DGKG
BioGPS: 1608
Gene Expression Atlas: ENSG00000058866
The Human Protein Atlas: ENSG00000058866
PathwayNCI Pathway Interaction Database: DGKG
KEGG: DGKG
REACTOME: DGKG
ConsensusPathDB
Pathway Commons: DGKG
MetabolismMetaCyc: DGKG
HUMANCyc: DGKG
RegulationEnsembl's Regulation: ENSG00000058866
miRBase: chr3 :185,864,989-186,080,023
TargetScan: NM_001080744
cisRED: ENSG00000058866
ContextiHOP: DGKG
cancer metabolism search in PubMed: DGKG
UCL Cancer Institute: DGKG
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DGKG in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_GLYCEROLIPID_METABOLISM
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM

check002.gifOthers
OMIM 601854; gene.
Orphanet
DiseaseKEGG Disease: DGKG
MedGen: DGKG (Human Medical Genetics with Condition)
ClinVar: DGKG
PhenotypeMGI: DGKG (International Mouse Phenotyping Consortium)
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.

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
ovaryDGKGchr3185870654185870674chr3186094451186094471
ovaryDGKGchr3185903150185903170DGKGchr3185899362185899382
ovaryDGKGchr3185947388185947408ZC3H18chr168864436088644380
ovaryDGKGchr3186040698186040718DGKGchr3186039491186039511
ovaryDGKGchr3186068824186068844NSMCE2chr8126267459126267479
pancreasDGKGchr3185960886185960906AGPAT3chr214535656945356589
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 DGKG related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF921517DGKG283123185996755185997040PCDH9308480136766142067661592
AA322377FAM107B177211101471685414717034DGKG2042773185969588185969661
BI020438DGKG22783185905959185906234RUNX1272423213628962436289775
BF732626GRINA12208145064317145065536DGKG2165173185910768185911069
BF902754DGKG1833185882770185906035TECPR27824814102846004102846174

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 # sample51      7        
GAIN (# sample)41      7        
LOSS (# sample)1                
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=3

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check002.gifSomatic 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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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
chr3:185906047-185906047p.I680S2
chr3:186006591-186006591p.S151F2
chr3:185986591-185986591p.T372M2
chr3:185867951-185867951p.A768A2
chr3:185970917-185970917p.G522E2
chr3:186006602-186006602p.V148fs*142
chr3:186015888-186015888p.T92M2
chr3:186024722-186024722p.G38S2
chr3:185986618-185986618p.A363V2
chr3:185882787-185882787p.E706K2

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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
# sample67 92 3 21 145   203 12
# mutation66 102 3 21 165   223 14
nonsynonymous SNV44 42   21 154   162 10
synonymous SNV22 6  3    11   61 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
chr3:186006591p.A743A,DGKG2
chr3:186006599p.S151F,DGKG2
chr3:185986591p.V148V,DGKG2
chr3:186015231p.T372M,DGKG2
chr3:185867951p.E118K,DGKG2
chr3:185906067p.P578S,DGKG1
chr3:185986619p.V375M,DGKG1
chr3:186015890p.I318S,DGKG1
chr3:185970902p.S154L,DGKG1
chr3:185993435p.R60S,DGKG1

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 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

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

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
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 DGKG
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL1075157; -.
Organism-specific databasesPharmGKB PA27314; -.
Organism-specific databasesCTD 1608; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00144diacylglycerol kinase, gamma 90kDaapproved; nutraceuticalPhosphatidylserine


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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



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