Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	BCKDHB
	Gene name	branched chain keto acid dehydrogenase E1, beta polypeptide
	Synonyms	E1B\|dJ279A18.1
	Cytomap	UCSC genome browser: 6q14.1
	Genomic location	chr6 :80816343-81055987
	Type of gene	protein-coding
	RefGenes	NM_000056.3, NM_183050.2,
	Ensembl id	ENSG00000083123
	Description	2-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 date	20141219
dbXrefs	MIM : 248611
	HGNC : HGNC
	Ensembl : ENSG00000083123
	HPRD : 02011
	Vega : OTTHUMG00000016430
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_BCKDHB
	BioGPS: 594
	Gene Expression Atlas: ENSG00000083123
	The Human Protein Atlas: ENSG00000083123
Pathway	NCI Pathway Interaction Database: BCKDHB
	KEGG: BCKDHB
	REACTOME: BCKDHB
	ConsensusPathDB
	Pathway Commons: BCKDHB
Metabolism	MetaCyc: BCKDHB
	HUMANCyc: BCKDHB
Regulation	Ensembl's Regulation: ENSG00000083123
	miRBase: chr6 :80,816,343-81,055,987
	TargetScan: NM_000056
	cisRED: ENSG00000083123
Context	iHOP: BCKDHB
	cancer metabolism search in PubMed: BCKDHB
	UCL Cancer Institute: BCKDHB
Assigned class in ccmGDB	C

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Phenotypic Information for BCKDHB(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM
Orphanet
Disease	KEGG Disease: BCKDHB
	MedGen: BCKDHB (Human Medical Genetics with Condition)
	ClinVar: BCKDHB
Phenotype	MGI: BCKDHB (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	BCKDHB	chr6	81049371	81049391	BCKDHB	chr6	81043689	81043709

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows BCKDHB related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BP391782	DBI	1	108	2	120124584	120125818	BCKDHB	109	502	6	81053432	81055987
AF161393	SEC31A	1	1562	4	83739814	83765613	BCKDHB	1559	1578	6	80865557	80865576
CR933696	SEC31A	1	3687	4	83739814	83812306	BCKDHB	3684	3703	6	80865557	80865576
AF161452	SEC31A	1	1382	4	83739814	83763567	BCKDHB	1379	1398	6	80865557	80865576

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr6:80878698-80878698	p.Y195C	2
chr6:80912938-80912938	p.?	2
chr6:80982870-80982870	p.R324R	2
chr6:80910723-80910723	p.V272A	1
chr6:80816606-80816606	p.G66R	1
chr6:81053464-81053464	p.F374L	1
chr6:80877395-80877395	p.G115V	1
chr6:80912830-80912830	p.I284I	1
chr6:80837262-80837262	p.?	1
chr6:81053483-81053483	p.K381Q	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample				4	2		2					9	1				3	2		7
# mutation				4	2		2					9	1				3	2		8
nonsynonymous SNV				3	1		1					8	1				2			5
synonymous SNV				1	1		1					1					1	2		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr6:80838915	p.V319V,BCKDHB	1
chr6:80881045	p.G115V,BCKDHB	1
chr6:80982916	p.R324R,BCKDHB	1
chr6:80838930	p.P123S,BCKDHB	1
chr6:80881055	p.R324Q,BCKDHB	1
chr6:81053415	p.A145A,BCKDHB	1
chr6:80877395	p.G335G,BCKDHB	1
chr6:80881059	p.I153I,BCKDHB	1
chr6:81053418	p.S339L,BCKDHB	1
chr6:80877418	p.E163K,BCKDHB	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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