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 DBT

Basic gene info.	Gene symbol	DBT
	Gene name	dihydrolipoamide branched chain transacylase E2
	Synonyms	BCATE2\|BCKAD-E2\|BCKADE2\|E2\|E2B
	Cytomap	UCSC genome browser: 1p31
	Genomic location	chr1 :100652477-100715409
	Type of gene	protein-coding
	RefGenes	NM_001918.3,
	Ensembl id	ENSG00000137992
	Description	BCKAD E2 subunitE2 component of branched chain alpha-keto acid dehydrogenase complexbranched chain acyltransferase, E2 componentbranched-chain alpha-keto acid dehydrogenase complex component E2dihydrolipoamide acetyltransferase component of branched-c
	Modification date	20141219
dbXrefs	MIM : 248610
	HGNC : HGNC
	Ensembl : ENSG00000137992
	HPRD : 02010
	Vega : OTTHUMG00000010921
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DBT
	BioGPS: 1629
	Gene Expression Atlas: ENSG00000137992
	The Human Protein Atlas: ENSG00000137992
Pathway	NCI Pathway Interaction Database: DBT
	KEGG: DBT
	REACTOME: DBT
	ConsensusPathDB
	Pathway Commons: DBT
Metabolism	MetaCyc: DBT
	HUMANCyc: DBT
Regulation	Ensembl's Regulation: ENSG00000137992
	miRBase: chr1 :100,652,477-100,715,409
	TargetScan: NM_001918
	cisRED: ENSG00000137992
Context	iHOP: DBT
	cancer metabolism search in PubMed: DBT
	UCL Cancer Institute: DBT
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: DBT
	Familial Cancer Database: DBT

* 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: DBT
	MedGen: DBT (Human Medical Genetics with Condition)
	ClinVar: DBT
Phenotype	MGI: DBT (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: DBT

Mutations for DBT

* 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	DBT	chr1	100685748	100685768	DBT	chr1	100675421	100675441

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 DBT 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
BE832547	HLA-DMA	261	295	6	32918651	32918685	DBT	287	398	1	100661530	100661644
AI432188	STIM1	198	277	11	3925156	3925235	DBT	274	413	1	100660264	100660403

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

There's no copy number variation information in COSMIC data for this gene.

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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=33)	Stat. for Synonymous SNVs (# total SNVs=6)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=4)

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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
chr1:100696322-100696323	p.P134fs*19	3
chr1:100676288-100676288	p.A327S	2
chr1:100706430-100706430	p.R21H	2
chr1:100684199-100684199	p.L180L	2
chr1:100672123-100672123	p.Q363*	2
chr1:100661845-100661847	p.E472delE	1
chr1:100681611-100681611	p.D234Y	1
chr1:100671867-100671867	p.?	1
chr1:100696362-100696362	p.K120fs*6	1
chr1:100661876-100661876	p.R462C	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=2

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	1			7	1		4		1	1		9	2				2	2	1	7
# mutation	1			8	1		4		1	1		14	2				2	2	1	7
nonsynonymous SNV	1			7	1		4		1	1		11	1				1	2	1	6
synonymous SNV				1								3	1				1			1

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
chr1:100684199	p.L180M	2
chr1:100661908	p.R462C	1
chr1:100696372	p.I336R	1
chr1:100672140	p.T140M	1
chr1:100681598	p.D451A	1
chr1:100661970	p.A327S	1
chr1:100696436	p.V117A	1
chr1:100672154	p.P430P	1
chr1:100681606	p.L305L	1
chr1:100671808	p.D96H	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 DBT 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 DBT

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


ANKRD13C,APOOL,CLCN3,DBT,EVI5,FAM73A,GMCL1, HEATR5B,HIAT1,HS2ST1,IPP,PKN2,RPAP2,SASS6, SLC30A7,SLC35A3,STXBP3,TMED5,UBR3,WDR47,ZNF644	ALDH6A1,CLASP1,DBT,DCTN4,DHTKD1,HECTD1,KIAA1715, KLHL24,L2HGDH,MPHOSPH9,MUT,OXR1,PPARA,PPM1A, PTCD2,RMND5A,SNX13,TMLHE,TOMM70A,TRIM23,UBR2

ABCD3,ACADM,AGL,AHCYL1,ANKRD13C,CEPT1,CSDE1, DBT,HIAT1,PIGK,RSBN1,SERBP1,SIKE1,SLC25A24, SLC35A3,STXBP3,TMED5,TRIM33,USP33,ZNF644,ZZZ3	AASDHPPT,AGK,AKIP1,XXYLT1,C5orf24,DBT,DHX40, ESD,EXD2,FAM149B1,FIG4,KITLG,MBLAC2,POLK, RSBN1L,THAP2,TMEM123,USP28,ZBTB41,ZMYM1,ZNF214

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 DBT

There's no related Drug.

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Cross referenced IDs for DBT

* 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