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 LDHA
Basic gene info.Gene symbolLDHA
Gene namelactate dehydrogenase A
SynonymsGSD11|HEL-S-133P|LDH1|LDHM
CytomapUCSC genome browser: 11p15.4
Genomic locationchr11 :18415935-18429765
Type of geneprotein-coding
RefGenesNM_001135239.1,
NM_001165414.1,NM_001165415.1,NM_001165416.1,NM_005566.3,
NR_028500.1,
Ensembl idENSG00000134333
DescriptionL-lactate dehydrogenase A chainLDH muscle subunitLDH-ALDH-Mcell proliferation-inducing gene 19 proteinepididymis secretory sperm binding protein Li 133Plactate dehydrogenase Mproliferation-inducing gene 19renal carcinoma antigen NY-REN-59
Modification date20141222
dbXrefs MIM : 150000
HGNC : HGNC
Ensembl : ENSG00000134333
HPRD : 01025
Vega : OTTHUMG00000167721
ProteinUniProt: P00338
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LDHA
BioGPS: 3939
Gene Expression Atlas: ENSG00000134333
The Human Protein Atlas: ENSG00000134333
PathwayNCI Pathway Interaction Database: LDHA
KEGG: LDHA
REACTOME: LDHA
ConsensusPathDB
Pathway Commons: LDHA
MetabolismMetaCyc: LDHA
HUMANCyc: LDHA
RegulationEnsembl's Regulation: ENSG00000134333
miRBase: chr11 :18,415,935-18,429,765
TargetScan: NM_001135239
cisRED: ENSG00000134333
ContextiHOP: LDHA
cancer metabolism search in PubMed: LDHA
UCL Cancer Institute: LDHA
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of LDHA in cancer cell metabolism1. Dai Q, Yin Q, Wei L, Zhou Y, Qiao C, et al. (2015) Oroxylin A regulates glucose metabolism in response to hypoxic stress with the involvement of Hypoxia-inducible factor-1 in human hepatoma HepG2 cells. Mol Carcinog. doi: 10.1002/mc.22369. go to article
2. Intlekofer AM, Dematteo RG, Venneti S, Finley LW, Lu C, et al. (2015) Hypoxia Induces Production of L-2-Hydroxyglutarate. Cell Metab 22: 304-311. doi: 10.1016/j.cmet.2015.06.023. pmid: 4527873. go to article
3. Ooi AT, Gomperts BN (2015) Molecular Pathways: Targeting Cellular Energy Metabolism in Cancer via Inhibition of SLC2A1 and LDHA. Clin Cancer Res 21: 2440-2444. doi: 10.1158/1078-0432.CCR-14-1209. pmid: 4452440. go to article
4. Maiso P, Huynh D, Moschetta M, Sacco A, Aljawai Y, et al. (2015) Metabolic signature identifies novel targets for drug resistance in multiple myeloma. Cancer Res 75: 2071-2082. doi: 10.1158/0008-5472.CAN-14-3400. pmid: 4433568. go to article

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

check002.gifOthers
OMIM 150000; gene.
150000; gene.
612933; phenotype.
612933; phenotype.
Orphanet 284426; Glycogen storage disease due to lactate dehydrogenase M-subunit deficiency.
284426; Glycogen storage disease due to lactate dehydrogenase M-subunit deficiency.
DiseaseKEGG Disease: LDHA
MedGen: LDHA (Human Medical Genetics with Condition)
ClinVar: LDHA
PhenotypeMGI: LDHA (International Mouse Phenotyping Consortium)
PhenomicDB: LDHA

Mutations for LDHA
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LDHA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM044090LDHA164111842704318427106WIPI265875752622355270683
BG179712LDHA1150111842903118429180MEST1438027130145346130146013
BQ928549LDHA162111842704518427106WIPI263848752622355270662
CA424367BOLA219570162982193429822485LDHA571654111842438518424469
BM049309LDHA164111842704318427106WIPI265782752622355270603
CA414218LDHA18339111842907218429394EIF4EBP2338632107216381372181544
BG775162LDHA164111842704318427106WIPI265794752622355270616
BC025288SKI1443122386702239112LDHA4362093111841611518429394
BG122659PRPF811831715792261579560LDHA178765111842865818429243
BC051361SKI1443122386702239112LDHA4362093111841611518429394
BF893167GORASP211472171806733171807914LDHA139460111841611018421075
CB143668LDHA1158111842525018427044ATP5G31504342176043940176046436
BC072009SKI1443122386702239112LDHA4362093111841611518429394

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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=38)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=2)
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
chr11:18425274-18425274p.V209A6
chr11:18424398-18424398p.T144A3
chr11:18418496-18418496p.A36V2
chr11:18421003-18421003p.V51G2
chr11:18421014-18421014p.E55K2
chr11:18424527-18424527p.G187W2
chr11:18425290-18425290p.L214L1
chr11:18421070-18421070p.R73R1
chr11:18428747-18428747p.V306V1
chr11:18424404-18424404p.V146L1

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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=7

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   134 1 1  6 1  4226
# mutation   75 1 1  6 1  4228
nonsynonymous SNV   53 1    5 1  4227
synonymous SNV   22   1  1       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
chr11:18425274p.V151A,LDHA7
chr11:18424398p.G60G,LDHA2
chr11:18421014p.T86A,LDHA2
chr11:18421031p.E55K,LDHA2
chr11:18418501p.G60E,LDHA1
chr11:18427047p.P158S,LDHA1
chr11:18421013p.E178Q,LDHA1
chr11:18424399p.L70V,LDHA1
chr11:18427054p.I194T,LDHA1
chr11:18424404p.L72F,LDHA1

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 LDHA 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 LDHA

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

AFAP1L1,ARHGAP31,EOGT,AGPAT4-IT1,CAV2,CCDC82,CLIC4,
CPNE8,EHBP1,FAM126A,FERMT2,FNDC3B,LATS2,LDHAL6B,
LOC400927,MAML2,MYO1E,PLEKHG1,QKI,RBMS1,TMEM43
ABHD13,ABL2,AHR,TMEM263,CTTNBP2NL,FAM91A1,GNAI3,
GNB4,HIAT1,KRAS,LDHAL6B,MAPK1IP1L,NCOA7,PAQR3,
PIGA,RIPK2,SERPINB8,SGMS2,SLC25A32,ZNF207,ZBTB21

AKAP13,ARL14,ELMSAN1,MIR22HG,DENND3,DOCK5,EHBP1L1,
FRMD4B,JOSD1,KDM6B,LDHAL6B,MNT,MXD1,MYO1E,
NBEAL1,NEAT1,PTPRH,RREB1,TET2,TLN2,ZZEF1
AKAP8,BCL3,CFAP45,DGCR11,EPHA2,GADD45A,HRH1,
LDHAL6B,LDLR,MAP2K3,MCL1,NRG1,NABP1,SENP2,
SKIL,SLC25A44,SLC25A45,TRIM51,TCTE1,TNFRSF12A,ZNF800
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 LDHA
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P00338; -.
ChemistryChEMBL CHEMBL4835; -.
ChemistryBindingDB P00338; -.
ChemistryChEMBL CHEMBL4835; -.
Organism-specific databasesPharmGKB PA30319; -.
Organism-specific databasesPharmGKB PA30319; -.
Organism-specific databasesCTD 3939; -.
Organism-specific databasesCTD 3939; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00157lactate dehydrogenase Aapproved; nutraceuticalNADH
DB01907lactate dehydrogenase AexperimentalNicotinamide-Adenine-Dinucleotide
DB02483lactate dehydrogenase AexperimentalEtheno-Nad
DB02701lactate dehydrogenase AexperimentalNicotinamide
DB03940lactate dehydrogenase AexperimentalOxamic Acid
DB00171lactate dehydrogenase Aapproved; nutraceuticalAdenosine triphosphate
DB00119lactate dehydrogenase Aapproved; nutraceuticalPyruvic acid


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Cross referenced IDs for LDHA
* 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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