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 BCAT2

Basic gene info.	Gene symbol	BCAT2
	Gene name	branched chain amino-acid transaminase 2, mitochondrial
	Synonyms	BCAM\|BCATM\|BCT2\|PP18
	Cytomap	UCSC genome browser: 19q13
	Genomic location	chr19 :49298318-49314320
	Type of gene	protein-coding
	RefGenes	NM_001164773.1, NM_001190.3,NM_001284325.1,NR_028451.1,
	Ensembl id	ENSG00000105552
	Description	branched chain aminotransferase 2, mitochondrialbranched-chain-amino-acid aminotransferase, mitochondrialplacental protein 18
	Modification date	20141207
dbXrefs	MIM : 113530
	HGNC : HGNC
	Ensembl : ENSG00000105552
	HPRD : 00217
	Vega : OTTHUMG00000183327
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_BCAT2
	BioGPS: 587
	Gene Expression Atlas: ENSG00000105552
	The Human Protein Atlas: ENSG00000105552
Pathway	NCI Pathway Interaction Database: BCAT2
	KEGG: BCAT2
	REACTOME: BCAT2
	ConsensusPathDB
	Pathway Commons: BCAT2
Metabolism	MetaCyc: BCAT2
	HUMANCyc: BCAT2
Regulation	Ensembl's Regulation: ENSG00000105552
	miRBase: chr19 :49,298,318-49,314,320
	TargetScan: NM_001164773
	cisRED: ENSG00000105552
Context	iHOP: BCAT2
	cancer metabolism search in PubMed: BCAT2
	UCL Cancer Institute: BCAT2
Assigned class in ccmGDB	C

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Phenotypic Information for BCAT2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: BCAT2
	Familial Cancer Database: BCAT2

* 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: BCAT2
	MedGen: BCAT2 (Human Medical Genetics with Condition)
	ClinVar: BCAT2
Phenotype	MGI: BCAT2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: BCAT2

Mutations for BCAT2

* 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

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows BCAT2 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
BF934808	BCAT2	1	165	19	49310632	49310796	MS4A6A	152	307	11	59942886	59943041
BF062738	BCAT2	2	148	19	49298323	49298468	ZNF76	146	389	6	35253925	35255527

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=29)	Stat. for Synonymous SNVs (# total SNVs=11)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted 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
chr19:49303070-49303070	p.T186R	3
chr19:49303003-49303003	p.P208P	2
chr19:49303312-49303312	p.E153K	2
chr19:49309850-49309850	p.W75L	2
chr19:49309937-49309937	p.H46R	2
chr19:49300525-49300525	p.W254L	2
chr19:49299833-49299833	p.?	2
chr19:49300554-49300554	p.A244A	2
chr19:49303279-49303279	p.G164S	1
chr19:49299906-49299906	p.V332M	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	1	3		2								1	3	1			3	5		8
# mutation	1	3		2								1	3	1			3	5		8
nonsynonymous SNV	1	2		1								1	3	1			1	5		4
synonymous SNV		1		1													2			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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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
chr19:49300560	p.R127Q,BCAT2	1
chr19:49303347	p.A11S	1
chr19:49302952	p.V114M,BCAT2	1
chr19:49303509	p.S113S,BCAT2	1
chr19:49302957	p.V105V,BCAT2	1
chr19:49309780	p.G72S,BCAT2	1
chr19:49302971	p.V62G,BCAT2	1
chr19:49309829	p.P268S,BCAT2	1
chr19:49299747	p.E61K,BCAT2	1
chr19:49303011	p.I267I,BCAT2	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 BCAT2 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 BCAT2

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


BCAT2,SYNE4,CCDC106,CCDC24,FAAH,MZT2B,HPN, IRF2BP1,NAPA,NECAB3,NPDC1,P4HTM,PHLDB3,PIH1D1, PRRG2,PTOV1,RAB17,SCAF1,SIGIRR,SPHK2,TMC4	ALKBH7,BCAT2,CLPP,ECI1,DHPS,ECSIT,GSTZ1, IDH3G,MCAT,MLST8,MRPS18A,MRPS2,MTG1,NUDT22, PMPCA,PPP1R16A,THAP4,TIMM13,TIMM17B,TMEM161A,TUFM

BCAT2,BCKDHA,C19orf48,ECH1,FAM98C,FBL,HSPBP1, ISOC2,MED9,PCCB,PIH1D1,PPP5C,PRMT1,PRPF31, RNMTL1,RPL13A,RPL18,RPL28,RPS19,RUVBL2,SARS2	ADCK2,ARAF,ARHGAP8,BAP1,BCAT2,CCDC61,DNAL4, CRACR2B,EPN3,GAS6,KATNB1,MAZ,MTL5,PQLC1, PTGDR,RAB40B,REPIN1,TMCO4,TMEM129,TMEM44,TP53I11

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 BCAT2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00114	branched chain amino-acid transaminase 2, mitochondrial	nutraceutical	Pyridoxal Phosphate
DB00142	branched chain amino-acid transaminase 2, mitochondrial	approved; nutraceutical	L-Glutamic Acid
DB00149	branched chain amino-acid transaminase 2, mitochondrial	approved; nutraceutical	L-Leucine
DB00167	branched chain amino-acid transaminase 2, mitochondrial	approved; nutraceutical	L-Isoleucine
DB02142	branched chain amino-acid transaminase 2, mitochondrial	experimental	Pyridoxamine-5'-Phosphate
DB02635	branched chain amino-acid transaminase 2, mitochondrial	experimental	N-[O-Phosphono-Pyridoxyl]-Isoleucine
DB04074	branched chain amino-acid transaminase 2, mitochondrial	experimental	Alpha-ketoisovalerate
DB00121	branched chain amino-acid transaminase 2, mitochondrial	approved; nutraceutical	Biotin
DB00161	branched chain amino-acid transaminase 2, mitochondrial	approved; nutraceutical	L-Valine
DB00130	branched chain amino-acid transaminase 2, mitochondrial	approved; nutraceutical; investigational	L-Glutamine

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Cross referenced IDs for BCAT2

* 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