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 BCKDHB
Basic gene info.Gene symbolBCKDHB
Gene namebranched chain keto acid dehydrogenase E1, beta polypeptide
SynonymsE1B|dJ279A18.1
CytomapUCSC genome browser: 6q14.1
Genomic locationchr6 :80816343-81055987
Type of geneprotein-coding
RefGenesNM_000056.3,
NM_183050.2,
Ensembl idENSG00000083123
Description2-oxoisovalerate dehydrogenase beta subunit2-oxoisovalerate dehydrogenase subunit beta, mitochondrialBCKDE1BBCKDH E1-betaE1b-beta subunit of the branched-chain complexbranched chain alpha-ketoacid dehydrogenase E1-beta subunitbranched-chain alpha-ke
Modification date20141219
dbXrefs MIM : 248611
HGNC : HGNC
Ensembl : ENSG00000083123
HPRD : 02011
Vega : OTTHUMG00000016430
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_BCKDHB
BioGPS: 594
Gene Expression Atlas: ENSG00000083123
The Human Protein Atlas: ENSG00000083123
PathwayNCI Pathway Interaction Database: BCKDHB
KEGG: BCKDHB
REACTOME: BCKDHB
ConsensusPathDB
Pathway Commons: BCKDHB
MetabolismMetaCyc: BCKDHB
HUMANCyc: BCKDHB
RegulationEnsembl's Regulation: ENSG00000083123
miRBase: chr6 :80,816,343-81,055,987
TargetScan: NM_000056
cisRED: ENSG00000083123
ContextiHOP: BCKDHB
cancer metabolism search in PubMed: BCKDHB
UCL Cancer Institute: BCKDHB
Assigned class in ccmGDBC

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Phenotypic Information for BCKDHB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: BCKDHB
Familial Cancer Database: BCKDHB
* 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
Orphanet
DiseaseKEGG Disease: BCKDHB
MedGen: BCKDHB (Human Medical Genetics with Condition)
ClinVar: BCKDHB
PhenotypeMGI: BCKDHB (International Mouse Phenotyping Consortium)
PhenomicDB: BCKDHB

Mutations for BCKDHB
* 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
ovaryBCKDHBchr68104937181049391BCKDHBchr68104368981043709
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 BCKDHB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP391782DBI11082120124584120125818BCKDHB10950268105343281055987
AF161393SEC31A1156248373981483765613BCKDHB1559157868086555780865576
CR933696SEC31A1368748373981483812306BCKDHB3684370368086555780865576
AF161452SEC31A1138248373981483763567BCKDHB1379139868086555780865576

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  2   1   1 1
GAIN (# sample)1  1  1   1      
LOSS (# sample)      1       1 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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=27)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr6:80878698-80878698p.Y195C2
chr6:80912938-80912938p.?2
chr6:80982870-80982870p.R324R2
chr6:80878687-80878688p.G192fs*101
chr6:80816557-80816557p.R49R1
chr6:80910698-80910698p.E264K1
chr6:80838934-80838934p.R111*1
chr6:81053415-81053415p.S358L1
chr6:80878689-80878689p.G192V1
chr6:80816606-80816606p.G66R1

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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
# sample   42 2    91   32 7
# mutation   42 2    91   32 8
nonsynonymous SNV   31 1    81   2  5
synonymous SNV   11 1    1    12 3
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
chr6:80982871p.G109G,BCKDHB1
chr6:80838886p.W310S,BCKDHB1
chr6:80878708p.G115V,BCKDHB1
chr6:80982905p.V319V,BCKDHB1
chr6:80838915p.P123S,BCKDHB1
chr6:80881045p.R324R,BCKDHB1
chr6:80982916p.A145A,BCKDHB1
chr6:80838930p.R324Q,BCKDHB1
chr6:80881055p.I153I,BCKDHB1
chr6:81053415p.G335G,BCKDHB1

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 BCKDHB 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 BCKDHB

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

CARF,BCKDHB,DCAF17,DOPEY1,DTWD2,FBXL3,HBP1,
HEATR5B,IBTK,IRAK1BP1,UFL1,CEP162,LCA5,LMBRD1,
MANEA,MYO6,PHIP,SENP6,SLC35A1,SNX14,STAM2
AASS,ACSS3,ACVR1C,ALDH6A1,BCKDHB,CALCRL,RHOV___CHP1,
CSPG5,DNAH9,EYS,GYS2,LPIN1,MAP3K5,MCCC1,
MOGAT1,PDK1,PLCXD1,RNF125,ST3GAL6,STOX1,USP30

ABCD3,ACADM,AK9,BCKDHB,TRIQK,CDHR1,COX18,
SMIM11,GPD1L,HADH,HSDL2,NDUFA5,NIPSNAP3A,PDSS2,
PEX7,SH3BGRL2,SLC35B3,SNX4,SUCLG2,TMEM56,TTPA
ATP5F1,BCKDHB,BZW2,TMEM251,KATNBL1,CAAP1,CD9,
DRD5,DTWD2,MICU2,MGC87042,MRPL35,MRPS33,NIPSNAP3A,
OXSM,PDHX,SLC37A2,STEAP1,TMED5,TMEM38B,TMEM68
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 BCKDHB


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