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 L2HGDH
Basic gene info.Gene symbolL2HGDH
Gene nameL-2-hydroxyglutarate dehydrogenase
SynonymsC14orf160
CytomapUCSC genome browser: 14q21.3
Genomic locationchr14 :50709151-50778947
Type of geneprotein-coding
RefGenesNM_024884.2,
Ensembl idENSG00000087299
Description2-hydroxyglutarate dehydrogenaseL-2-hydroxyglutarate dehydrogenase, mitochondrialL-alpha-hydroxyglutarate dehydrogenasealpha-hydroxyglutarate oxidoreductasealpha-ketoglutarate reductaseduranin
Modification date20141207
dbXrefs MIM : 609584
HGNC : HGNC
Ensembl : ENSG00000087299
HPRD : 12640
Vega : OTTHUMG00000140289
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_L2HGDH
BioGPS: 79944
Gene Expression Atlas: ENSG00000087299
The Human Protein Atlas: ENSG00000087299
PathwayNCI Pathway Interaction Database: L2HGDH
KEGG: L2HGDH
REACTOME: L2HGDH
ConsensusPathDB
Pathway Commons: L2HGDH
MetabolismMetaCyc: L2HGDH
HUMANCyc: L2HGDH
RegulationEnsembl's Regulation: ENSG00000087299
miRBase: chr14 :50,709,151-50,778,947
TargetScan: NM_024884
cisRED: ENSG00000087299
ContextiHOP: L2HGDH
cancer metabolism search in PubMed: L2HGDH
UCL Cancer Institute: L2HGDH
Assigned class in ccmGDBC

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Phenotypic Information for L2HGDH(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: L2HGDH
Familial Cancer Database: L2HGDH
* 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_BUTANOATE_METABOLISM
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: L2HGDH
MedGen: L2HGDH (Human Medical Genetics with Condition)
ClinVar: L2HGDH
PhenotypeMGI: L2HGDH (International Mouse Phenotyping Consortium)
PhenomicDB: L2HGDH

Mutations for L2HGDH
* 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
ovaryL2HGDHchr145071844450718464L2HGDHchr145071936150719381
ovaryL2HGDHchr145071844450718464L2HGDHchr145071936350719383
ovaryL2HGDHchr145077075150770771L2HGDHchr145076210650762126
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 L2HGDH related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE908214L2HGDH1315145071252250712835KRT19309362173967986939679922
DA137061L2HGDH168145071219950712266MBP68519187469680074729012
AF335584L2HGDH1100145071017050710269PDGFD99182811103779888104034738
AW300486L2HGDH1343145071225950712601KIAA11913394565175774557175774674

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   1      
GAIN (# sample)          1      
LOSS (# sample)      1          
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=32)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=1)
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
chr14:50778816-50778816p.L18R5
chr14:50750699-50750699p.V198G3
chr14:50732175-50732175p.S366F2
chr14:50760867-50760867p.Q169L2
chr14:50736035-50736035p.R251P2
chr14:50713876-50713876p.R431H2
chr14:50732104-50732104p.P390S1
chr14:50769675-50769675p.L67L1
chr14:50735971-50735971p.C272W1
chr14:50750674-50750674p.F206F1

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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
# sample1  3  3 1  5 2  43 4
# mutation1  3  3 1  5 2  43 4
nonsynonymous SNV1  2  3 1  4 2  31 4
synonymous SNV   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
chr14:50736035p.R251P2
chr14:50713876p.R431H2
chr14:50734515p.A329T1
chr14:50734531p.Y7C1
chr14:50750625p.G326G1
chr14:50734550p.G321C1
chr14:50750674p.G312E1
chr14:50734557p.D275H1
chr14:50760867p.C272W1
chr14:50734574p.S270G1

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 L2HGDH 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 L2HGDH

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

ARF6,ATP5S,DNAAF2,MIS18BP1,DDHD1,EXOC5,FANCM,
GMFB,GNPNAT1,L2HGDH,NAA30,OR4A15,POLE2,PSMC6,
NEMF,SOCS4,SOS2,STYX,TMX1,TXNDC16,WDHD1
ALPK3,ATP5B,TCAIM,CECR2,COX10,HECTD1,VWA8,
L2HGDH,LOC729082,LYRM7,NDUFS1,NPEPPS,OXNAD1,PAIP2B,
PDHX,PPARA,PTCD3,SATB1,TARSL2,UQCRC2,ZYG11B

DNAAF2,CPSF2,DLGAP5,EIF2S1,FANCM,FCF1,G2E3,
GMFB,GNPNAT1,KIAA0391,KIAA0586,L2HGDH,MTHFD1,AP5M1,
POLE2,PRMT5,SUPT16H,TDP1,TMX1,TRMT5,WDHD1
ACTL6A,DCLRE1A,DNAJA3,G2E3,GMNN,HN1L,L2HGDH,
MRPS35,NARS2,PRMT3,PTCD3,PUS7L,RBBP4,RPE,
SHQ1,TBCCD1,TFAM,TFDP1,TMEM5,TRNT1,ZC3H8
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 L2HGDH


There's no related Drug.
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Cross referenced IDs for L2HGDH
* 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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