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 DLAT
Basic gene info.Gene symbolDLAT
Gene namedihydrolipoamide S-acetyltransferase
SynonymsDLTA|PDC-E2|PDCE2
CytomapUCSC genome browser: 11q23.1
Genomic locationchr11 :111895537-111935002
Type of geneprotein-coding
RefGenesNM_001931.4,
Ensembl idENSG00000263032
Description70 kDa mitochondrial autoantigen of primary biliary cirrhosisE2 component of pyruvate dehydrogenase complexM2 antigen complex 70 kDa subunitPBCdihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complexdihydrolipoyllysine-residue a
Modification date20141207
dbXrefs MIM : 608770
HGNC : HGNC
Ensembl : ENSG00000150768
HPRD : 10578
Vega : OTTHUMG00000133751
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DLAT
BioGPS: 1737
Gene Expression Atlas: ENSG00000263032
The Human Protein Atlas: ENSG00000263032
PathwayNCI Pathway Interaction Database: DLAT
KEGG: DLAT
REACTOME: DLAT
ConsensusPathDB
Pathway Commons: DLAT
MetabolismMetaCyc: DLAT
HUMANCyc: DLAT
RegulationEnsembl's Regulation: ENSG00000263032
miRBase: chr11 :111,895,537-111,935,002
TargetScan: NM_001931
cisRED: ENSG00000263032
ContextiHOP: DLAT
cancer metabolism search in PubMed: DLAT
UCL Cancer Institute: DLAT
Assigned class in ccmGDBC

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Phenotypic Information for DLAT(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DLAT
Familial Cancer Database: DLAT
* 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_GLYCOLYSIS_GLUCONEOGENESIS
KEGG_PYRUVATE_METABOLISM
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE
REACTOME_PYRUVATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: DLAT
MedGen: DLAT (Human Medical Genetics with Condition)
ClinVar: DLAT
PhenotypeMGI: DLAT (International Mouse Phenotyping Consortium)
PhenomicDB: DLAT

Mutations for DLAT
* 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
There's no inter-chromosomal structural variation.
- 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
breastDLATchr11111932285111932285IL18chr11112030719112030719
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 DLAT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI022776SPTB34154146531895265319074DLAT14931311111896173111896337
AL079484DLAT249711111933848111933924DLAT8746211111933916111934296
H49884DLAT1118911111896173111896352SPTB184293146531896665319074

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=30)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

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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
chr11:111896927-111896927p.P95P3
chr11:111896324-111896324p.A43V3
chr11:111904183-111904183p.E239G3
chr11:111915910-111915910p.P416S2
chr11:111899614-111899614p.S202L2
chr11:111904177-111904177p.R237T2
chr11:111896360-111896360p.V55G2
chr11:111899524-111899524p.D172A2
chr11:111922036-111922036p.E493K2
chr11:111915876-111915876p.V404V1

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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
# sample1  41 2 2  631  4514
# mutation1  41 2 2  831  4514
nonsynonymous SNV1  4  1 1  611  1513
synonymous SNV    1 1 1  22   3  1
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
chr11:111922036p.S202L2
chr11:111899614p.E493K2
chr11:111899569p.G470V1
chr11:111910097p.C488F1
chr11:111930640p.S202S1
chr11:111899602p.P492P1
chr11:111915865p.P216P1
chr11:111930706p.H218D1
chr11:111915876p.D510Y1
chr11:111930750p.E239G1

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 DLAT 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 DLAT

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

AASDHPPT,ALG9,ARCN1,C11orf57,CHEK1,CUL5,DDX10,
DLAT,EI24,EXPH5,NPAT,PAFAH1B2,RBM7,RDX,
RNF214,SDHD,STT3A,TMEM123,UBE4A,USP28,ZW10
ALPK3,ATP5B,CHCHD3,DLAT,DLD,ETFDH,IMMT,
MRS2,PDHA1,PDHB,PDHX,PGM1,PPM1B,SDHD,
SGCG,SLC2A4,SLC2A5,SLC6A8,SOX6,TBX15,UQCRC2

ACAT1,CHCHD4,CHEK1,DLAT,DPAGT1,FASTKD1,GFM1,
HSPA9,IMMT,LRPPRC,MTCH2,NCAPD3,NDUFS1,PDE12,
PDHX,SDHB,SDHD,NDC1,TMX2,UCHL5,ZW10
CENPN,DBF4,DLAT,DPH2,EIF4A3,FAM136A,FARSB,
FASTKD1,FH,GOT1,HSPA9,MIPEP,MRPL35,PDHX,
PIGW,PPIF,QRSL1,SEH1L,TBRG4,TDG,WDR12
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 DLAT
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00157dihydrolipoamide S-acetyltransferaseapproved; nutraceuticalNADH
DB03758dihydrolipoamide S-acetyltransferaseexperimentalRadicicol
DB03760dihydrolipoamide S-acetyltransferaseexperimentalDihydrolipoic Acid


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Cross referenced IDs for DLAT
* 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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