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 LDHAL6A
Basic gene info.Gene symbolLDHAL6A
Gene namelactate dehydrogenase A-like 6A
SynonymsLDH6A
CytomapUCSC genome browser: 11p15.1
Genomic locationchr11 :18477373-18501147
Type of geneprotein-coding
RefGenesNM_001144071.1,
NM_144972.4,
Ensembl idENSG00000166800
DescriptionL-lactate dehydrogenase A-like 6A
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000166800
HPRD : 13980
Vega : OTTHUMG00000167724
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LDHAL6A
BioGPS: 160287
Gene Expression Atlas: ENSG00000166800
The Human Protein Atlas: ENSG00000166800
PathwayNCI Pathway Interaction Database: LDHAL6A
KEGG: LDHAL6A
REACTOME: LDHAL6A
ConsensusPathDB
Pathway Commons: LDHAL6A
MetabolismMetaCyc: LDHAL6A
HUMANCyc: LDHAL6A
RegulationEnsembl's Regulation: ENSG00000166800
miRBase: chr11 :18,477,373-18,501,147
TargetScan: NM_001144071
cisRED: ENSG00000166800
ContextiHOP: LDHAL6A
cancer metabolism search in PubMed: LDHAL6A
UCL Cancer Institute: LDHAL6A
Assigned class in ccmGDBC

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Phenotypic Information for LDHAL6A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LDHAL6A
Familial Cancer Database: LDHAL6A
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: LDHAL6A
MedGen: LDHAL6A (Human Medical Genetics with Condition)
ClinVar: LDHAL6A
PhenotypeMGI: LDHAL6A (International Mouse Phenotyping Consortium)
PhenomicDB: LDHAL6A

Mutations for LDHAL6A
* 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
ovaryLDHAL6Achr111850027618500296LDHAL6Achr111849405518494075
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 LDHAL6A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
T05071NAP1L11188127644881876450247LDHAL6A188378111849478618494974

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=25)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=2)

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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
chr11:18487305-18487305p.P122P2
chr11:18497109-18497110p.Y172fs*11
chr11:18498032-18498032p.V234fs*11
chr11:18485507-18485507p.?1
chr11:18497130-18497130p.G179D1
chr11:18499237-18499237p.E261*1
chr11:18485515-18485515p.S45N1
chr11:18487325-18487325p.P129L1
chr11:18497159-18497159p.I189F1
chr11:18478243-18478243p.S6C1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  41      321  3 18
# mutation1  41      421  4 19
nonsynonymous SNV1  31      32   3  7
synonymous SNV   1       1 1  1 12
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
chr11:18487325p.V209I,LDHAL6A1
chr11:18499251p.D217D,LDHAL6A1
chr11:18487327p.F12F,LDHAL6A1
chr11:18500293p.I218L,LDHAL6A1
chr11:18478263p.W227S,LDHAL6A1
chr11:18497100p.S45N,LDHAL6A1
chr11:18500303p.E228V,LDHAL6A1
chr11:18485515p.E47E,LDHAL6A1
chr11:18497130p.I263S,LDHAL6A1
chr11:18500331p.V49V,LDHAL6A1

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 LDHAL6A 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 LDHAL6A

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

ANKRD33,ANKRD55,ANPEP,FAM217A,CNGA3,TXLNGY,FAM41AY1,
FOXI2,GRK1,KRT82,LDHAL6A,LRRC3B,NCRNA00185,NETO2,
NOBOX,NT5C1B,POU5F1B,RAB40A,RGAG1,TNFSF11,ZNF486
ATG2B,BIRC6,C11orf30,CCNT1,FAM178A,ICE1,EPG5,
LDHAL6A,LOC100190986,KMT2C,KMT2A,MYO9A,NKTR,NR2C2,
SMG1,UBN2,ZKSCAN8,ZNF347,ZNF354C,ZNF573,ZNF585A

ASB18,LINC01565,TOPAZ1,CST9,F7,FATE1,FBLL1,
GK,GK3P,GRIN2C,LDHAL6A,DNMBP-AS1,LINC00114,NKPD1,
OPCML,PER4,POLM,PRG3,SLC45A2,SOX30,ZMAT1
AGAP4,BMS1P5,MSANTD2,MROH7,N4BP2L2-IT2,CREBZF,GABRE,
PAXBP1,GHRLOS,GK5,LDHAL6A,LOC100128842,LOC256880,LOC646471,
MDM4,PROCA1,TAS2R5,CFAP44,WDR59,ZNF587,ZNF841
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 LDHAL6A
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
DB00157lactate dehydrogenase A-like 6Aapproved; nutraceuticalNADH


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Cross referenced IDs for LDHAL6A
* 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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