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 BCKDHA
Basic gene info.Gene symbolBCKDHA
Gene namebranched chain keto acid dehydrogenase E1, alpha polypeptide
SynonymsBCKDE1A|MSU|MSUD1|OVD1A
CytomapUCSC genome browser: 19q13.1-q13.2
Genomic locationchr19 :41903693-41930910
Type of geneprotein-coding
RefGenesNM_000709.3,
NM_001164783.1,
Ensembl idENSG00000248098
Description2-oxoisovalerate dehydrogenase (lipoamide)2-oxoisovalerate dehydrogenase subunit alpha, mitochondrialBCKDH E1-alphabranched-chain alpha-keto acid dehydrogenase E1 component alpha chain
Modification date20141219
dbXrefs MIM : 608348
HGNC : HGNC
Ensembl : ENSG00000248098
HPRD : 02009
Vega : OTTHUMG00000168128
ProteinUniProt: P12694
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_BCKDHA
BioGPS: 593
Gene Expression Atlas: ENSG00000248098
The Human Protein Atlas: ENSG00000248098
PathwayNCI Pathway Interaction Database: BCKDHA
KEGG: BCKDHA
REACTOME: BCKDHA
ConsensusPathDB
Pathway Commons: BCKDHA
MetabolismMetaCyc: BCKDHA
HUMANCyc: BCKDHA
RegulationEnsembl's Regulation: ENSG00000248098
miRBase: chr19 :41,903,693-41,930,910
TargetScan: NM_000709
cisRED: ENSG00000248098
ContextiHOP: BCKDHA
cancer metabolism search in PubMed: BCKDHA
UCL Cancer Institute: BCKDHA
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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

check002.gifOthers
OMIM 248600; phenotype.
608348; gene.
Orphanet 268145; Classic maple syrup urine disease.
268162; Intermediate maple syrup urine disease.
268173; Intermittent maple syrup urine disease.
268184; Thiamine-responsive maple syrup urine disease.
DiseaseKEGG Disease: BCKDHA
MedGen: BCKDHA (Human Medical Genetics with Condition)
ClinVar: BCKDHA
PhenotypeMGI: BCKDHA (International Mouse Phenotyping Consortium)
PhenomicDB: BCKDHA

Mutations for BCKDHA
* 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 BCKDHA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample1            1   
GAIN (# sample)1            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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=26)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=2)
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
chr19:41928158-41928158p.A246T3
chr19:41920016-41920016p.A146A2
chr19:41916646-41916646p.N71N2
chr19:41903744-41903744p.A4A2
chr19:41928649-41928649p.P323P2
chr19:41928178-41928178p.F252F2
chr19:41928667-41928667p.M329I2
chr19:41916548-41916548p.P39T2
chr19:41919968-41919968p.F130L1
chr19:41928941-41928941p.Y345C1

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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
# sample12 6  1 11 13  164 6
# mutation12 6  1 11 13  164 8
nonsynonymous SNV11 4  1 11  1  121 4
synonymous SNV 1 2       12   43 4
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
chr19:41928178p.F252F,BCKDHA2
chr19:41903744p.N71N,BCKDHA2
chr19:41916646p.A4A,BCKDHA2
chr19:41930437p.A34D,BCKDHA1
chr19:41916712p.V231I,BCKDHA1
chr19:41928179p.P39S,BCKDHA1
chr19:41930481p.A246T,BCKDHA1
chr19:41920002p.Q44Q,BCKDHA1
chr19:41928188p.F250L,BCKDHA1
chr19:41903833p.K51M,BCKDHA1

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 BCKDHA 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 BCKDHA

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

ADCK4,ATP5SL,B9D2,BCKDHA,CCDC61,CCDC9,DMWD,
ERCC1,ERCC2,EXOSC5,IRF2BP1,NR1H2,PHLDB3,PNKP,
SPHK2,SYMPK,TBC1D17,TRAPPC6A,UBXN6,XRCC1,ZNF576
ATP5D,BAG6,BCKDHA,C7orf55,COX8A,CYC1,ECI1,
ECSIT,FAM195A,IDH3B,MRPL12,MRPL2,MRPL38,MRPS7,
NDUFS7,NDUFV1,PRDX2,SPAG7,STK25,TIMM44,TIMM50

ADCK4,ATP5SL,ATPAF2,B9D2,BCAT2,BCKDHA,C19orf48,
NOA1,CAPNS1,ECH1,FAM98C,LRRC75A-AS1,PIH1D1,PPP5C,
PRMT1,PRPF31,PSMD8,RPL13A,RPL18,RPS5,SARS2
BCKDHA,BTBD2,VPS51___IFT46,ADCK3,CCDC61,EIF3F,F8A1,
IRF2BP1,KATNB1,MOSPD3,PCIF1,PSKH1,SLC25A6,SNX15,
TAF6L,TCF25,TMEM143,TUSC1,UBL7,WDR13,ZNF414
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 BCKDHA


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