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 DLD
Basic gene info.Gene symbolDLD
Gene namedihydrolipoamide dehydrogenase
SynonymsDLDD|DLDH|E3|GCSL|LAD|PHE3
CytomapUCSC genome browser: 7q31-q32
Genomic locationchr7 :107531585-107561643
Type of geneprotein-coding
RefGenesNM_000108.4,
NM_001289750.1,NM_001289751.1,NM_001289752.1,
Ensembl idENSG00000091140
DescriptionE3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complexdiaphorasedihydrolipoyl dehydrogenase, mitochondrialglycine cleavage system L proteinglycine cleavage system protein Llipoamide deh
Modification date20141207
dbXrefs MIM : 238331
HGNC : HGNC
Ensembl : ENSG00000091140
HPRD : 02006
Vega : OTTHUMG00000154813
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DLD
BioGPS: 1738
Gene Expression Atlas: ENSG00000091140
The Human Protein Atlas: ENSG00000091140
PathwayNCI Pathway Interaction Database: DLD
KEGG: DLD
REACTOME: DLD
ConsensusPathDB
Pathway Commons: DLD
MetabolismMetaCyc: DLD
HUMANCyc: DLD
RegulationEnsembl's Regulation: ENSG00000091140
miRBase: chr7 :107,531,585-107,561,643
TargetScan: NM_000108
cisRED: ENSG00000091140
ContextiHOP: DLD
cancer metabolism search in PubMed: DLD
UCL Cancer Institute: DLD
Assigned class in ccmGDBC

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

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

Mutations for DLD
* 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
breastDLDchr7107535122107535122NRCAMchr7107818574107818574
ovaryDLDchr7107551266107551286chr7107374232107374252
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 DLD related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CV348467IKBKB131484218115542181470DLD3044977107557272107557773
BG952037DLD91147107560077107560184SURF41022989136228391136228587

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        1        
GAIN (# sample)        1        
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=33)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr7:107557813-107557813p.A381D3
chr7:107558487-107558487p.G452A2
chr7:107545876-107545876p.G170D2
chr7:107558488-107558488p.G452G2
chr7:107557721-107557721p.I350M2
chr7:107557761-107557761p.H364Y2
chr7:107557346-107557346p.G328E2
chr7:107545828-107545828p.G154E1
chr7:107546788-107546788p.G220V1
chr7:107542828-107542828p.I86T1

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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
# sample11152   31192   24 4
# mutation11142   511102   24 4
nonsynonymous SNV11122   41181   23 4
synonymous SNV   2    1  21    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
chr7:107545876p.G353G,DLD2
chr7:107558488p.G71D,DLD2
chr7:107546743p.V30L,DLD1
chr7:107557761p.G106C,DLD1
chr7:107543968p.S347L,DLD1
chr7:107555972p.V46G,DLD1
chr7:107557789p.G106A,DLD1
chr7:107545454p.G353A,DLD1
chr7:107556003p.Q62K,DLD1
chr7:107558381p.G137C,DLD1

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 DLD 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 DLD

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

CBLL1,COG5,DLD,DUS4L,GCC1,GTPBP10,LRPPRC,
LUZP6,METTL2B,MRPL19,NUP205,ORC5,PMPCB,PNPLA8,
PSMC2,PUS7,RINT1,SLC25A13,THAP5,TNPO3,UBE3C
ACAT1,AK3,ATPAF1,DLD,ETFDH,GHITM,GNPAT,
HADHB,HOXA10,HSDL2,HSPB6,PDHX,PGM1,PHYH,
RDX,RRAGD,SLC2A4,SOX6,STRADB,SUCLA2,TBX15

ARMC10,CHCHD3,COG5,CYCS,DLD,FAM185A,GHITM,
GPD1L,GTPBP10,LRPPRC,MDH2,MRPS33,NDUFA5,ORC5,
PEX1,PMPCB,RINT1,SLC25A13,SUCLG2,SYPL1,ZNF800
AIFM2,ANKRD13C,CA2,CYCS,DLAT,DLD,ETNK1,
FH,GCLM,GHITM,LRP12,ME2,MIER1,NAA50,
NDUFS1,RTN4IP1,SLC25A33,STK39,UBE2K,UGDH,VPS26A
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 DLD
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 dehydrogenaseapproved; nutraceuticalNADH
DB01907dihydrolipoamide dehydrogenaseexperimentalNicotinamide-Adenine-Dinucleotide
DB03147dihydrolipoamide dehydrogenaseexperimentalFlavin-Adenine Dinucleotide


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Cross referenced IDs for DLD
* 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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