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 DGKI
Basic gene info.Gene symbolDGKI
Gene namediacylglycerol kinase, iota
SynonymsDGK-IOTA
CytomapUCSC genome browser: 7q32.3-q33
Genomic locationchr7 :137074384-137531609
Type of geneprotein-coding
RefGenesNM_004717.2,
Ensembl idENSG00000157680
DescriptionDAG kinase iotadiacylglycerol kinase iotadiglyceride kinase iota
Modification date20141207
dbXrefs MIM : 604072
HGNC : HGNC
Ensembl : ENSG00000157680
HPRD : 07238
Vega : OTTHUMG00000155697
ProteinUniProt: O75912
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DGKI
BioGPS: 9162
Gene Expression Atlas: ENSG00000157680
The Human Protein Atlas: ENSG00000157680
PathwayNCI Pathway Interaction Database: DGKI
KEGG: DGKI
REACTOME: DGKI
ConsensusPathDB
Pathway Commons: DGKI
MetabolismMetaCyc: DGKI
HUMANCyc: DGKI
RegulationEnsembl's Regulation: ENSG00000157680
miRBase: chr7 :137,074,384-137,531,609
TargetScan: NM_004717
cisRED: ENSG00000157680
ContextiHOP: DGKI
cancer metabolism search in PubMed: DGKI
UCL Cancer Institute: DGKI
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for DGKI(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DGKI
Familial Cancer Database: DGKI
* 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 604072; gene.
Orphanet
DiseaseKEGG Disease: DGKI
MedGen: DGKI (Human Medical Genetics with Condition)
ClinVar: DGKI
PhenotypeMGI: DGKI (International Mouse Phenotyping Consortium)
PhenomicDB: DGKI

Mutations for DGKI
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryDGKIchr7137249433137249453chr7102359990102360010
ovaryDGKIchr7137344896137344916DGKIchr7137344368137344388
ovaryDGKIchr7137493229137493249chr156508761665087636
ovaryDGKIchr7137513427137513447DGKIchr7137509899137509919
pancreasDGKIchr7137275912137275932DGKIchr7137276197137276217
pancreasDGKIchr7137280670137280690ATRNL1chr10117056109117056129
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 DGKI related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF962288DGKI14587137466791137466835RAPGEF4562192173901377173916432
AA665202CCDC152113354280029342800425DGKI1231427137390839137390858
BF357704SP1408292231118475231118497DGKI134417137498017137498447
BF948083DGKI142197137078838137079042RBFOX12005311668095096809840

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 6    1 1 1 17   
GAIN (# sample) 6    1 1 1 17   
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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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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=138)
Stat. for Synonymous SNVs
(# total SNVs=40)
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
chr7:137206693-137206693p.R723C8
chr7:137263038-137263038p.R559Q4
chr7:137263039-137263039p.R559*4
chr7:137282621-137282621p.R428Q3
chr7:137148282-137148282p.Y904*3
chr7:137076012-137076012p.Q1051R2
chr7:137262005-137262005p.R575I2
chr7:137080353-137080353p.T1024T2
chr7:137172408-137172408p.R777H2
chr7:137076016-137076016p.R1050C2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample57 221 9 3  32124  2714 16
# mutation57 231 10 3  37144  2914 28
nonsynonymous SNV56 211 8 1  27123  1910 17
synonymous SNV 1 2  2 2  1021  104 11
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
chr7:137282621p.R428Q2
chr7:137170135p.R575I2
chr7:137262005p.P816L2
chr7:137082151p.R1006W2
chr7:137237203p.Q804H2
chr7:137339506p.R139Q2
chr7:137172389p.R559Q2
chr7:137263038p.E985K2
chr7:137374734p.R237L2
chr7:137271945p.D1060Y2

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 DGKI 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 DGKI

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

APP,BCAN,C6orf15,CNTNAP3,DGKI,EFS,FBXO10,
IFIT2,LOC728276,LRRC39,MEST,MPO,NGDN,NRXN1,
PDC,PSMB5,PTGS2,PTN,SCGB1D1,SPATA16,TNFRSF21
AHNAK,ARHGAP21,ATL3,ATP9A,CHRDL1,COBLL1,DDR2,
DGKI,ECM2,GLP2R,ITGA1,ITGB1,ITSN1,LPGAT1,
PARD3B,PDZD2,PEAK1,SORBS1,SPTBN1,UTRN,CHMP3

ANTXR1,ARHGEF17,CDH2,CLIC4,DGKI,DKK3,EHD2,
FBXL7,GLI3,LAYN,MMP16,NRP2,PKD2,PTRF,
RAB31,S1PR3,SGCD,SPARC,SPOCK1,SYDE1,VIM
ADAM33,C20orf194,CACNA2D1,CHST3,COL6A2,COL8A1,CSDC2,
DGKI,EVC,FGFR1,GLI3,MTCL1,NFATC4,NPR2,
PRELP,RBMS3,RUSC2,SACS,SDK1,SSC5D,ZNF532
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 DGKI


There's no related Drug.
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Cross referenced IDs for DGKI
* 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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