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 BCAT1

Basic gene info.	Gene symbol	BCAT1
	Gene name	branched chain amino-acid transaminase 1, cytosolic
	Synonyms	BCATC\|BCT1\|ECA39\|MECA39\|PNAS121\|PP18
	Cytomap	UCSC genome browser: 12p12.1
	Genomic location	chr12 :24962957-25056009
	Type of gene	protein-coding
	RefGenes	NM_001178091.1, NM_001178092.1,NM_001178093.1,NM_001178094.1,NM_005504.6,
	Ensembl id	ENSG00000060982
	Description	branched chain aminotransferase 1, cytosolicbranched-chain-amino-acid aminotransferase, cytosolicplacental protein 18
	Modification date	20141207
dbXrefs	MIM : 113520
	HGNC : HGNC
	Ensembl : ENSG00000060982
	HPRD : 00216
	Vega : OTTHUMG00000169053
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_BCAT1
	BioGPS: 586
	Gene Expression Atlas: ENSG00000060982
	The Human Protein Atlas: ENSG00000060982
Pathway	NCI Pathway Interaction Database: BCAT1
	KEGG: BCAT1
	REACTOME: BCAT1
	ConsensusPathDB
	Pathway Commons: BCAT1
Metabolism	MetaCyc: BCAT1
	HUMANCyc: BCAT1
Regulation	Ensembl's Regulation: ENSG00000060982
	miRBase: chr12 :24,962,957-25,056,009
	TargetScan: NM_001178091
	cisRED: ENSG00000060982
Context	iHOP: BCAT1
	cancer metabolism search in PubMed: BCAT1
	UCL Cancer Institute: BCAT1
Assigned class in ccmGDB	C

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Phenotypic Information for BCAT1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: BCAT1
	Familial Cancer Database: BCAT1

* 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: BCAT1
	MedGen: BCAT1 (Human Medical Genetics with Condition)
	ClinVar: BCAT1
Phenotype	MGI: BCAT1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: BCAT1

Mutations for BCAT1

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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	BCAT1	chr12	24991057	24991077	BCAT1	chr12	24992462	24992482
pancreas	BCAT1	chr12	25014200	25014220	ITPR2	chr12	26542091	26542111

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 BCAT1 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
AA743391	BCAT1	1	89	12	24967746	24967834	BCAT1	87	363	12	24968777	24969053
AL120469	BCAT1	65	126	12	24966325	24966386	MDGA2	111	130	14	47647579	47647598
AI275099	BCAT1	1	63	12	24964071	24964353	DNAJC18	57	380	5	138746937	138747260
BF996876	BCAT1	21	260	12	24968749	24968990	SLC9A1	255	482	1	27429218	27432495
AI399863	BCAT1	1	63	12	24964071	24964353	DNAJC18	57	354	5	138746937	138747234

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=46)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=2)	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
chr12:24982809-24982809	p.E356G	3
chr12:25031487-25031487	p.R163C	3
chr12:25054762-25054762	p.V22M	3
chr12:24982785-24982785	p.R364H	2
chr12:25002740-25002740	p.T218T	2
chr12:24989523-24989525	p.E275delE	2
chr12:25047292-25047292	p.F66V	2
chr12:24985736-24985736	p.G322E	2
chr12:25047312-25047312	p.T59M	2
chr12:25047326-25047326	p.T54T	2

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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		4		6	1		1		1			2	2				11	6		3
# mutation		4		6	1		1		1			2	2				11	6		4
nonsynonymous SNV		4		5					1			1	2				9	3		4
synonymous SNV				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
chr12:25031487	p.G261E,BCAT1	2
chr12:24985736	p.R102C,BCAT1	2
chr12:24995049	p.S134L,BCAT1	1
chr12:25031472	p.M1T,BCAT1	1
chr12:25054777	p.C274R,BCAT1	1
chr12:24982786	p.L125L,BCAT1	1
chr12:24995112	p.K119N,BCAT1	1
chr12:25101865	p.A258A,BCAT1	1
chr12:24985698	p.K115R,BCAT1	1
chr12:24995140	p.T257K,BCAT1	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 BCAT1 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 BCAT1

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


BCAT1,C12orf77,LINC01548,CNPY1,FAM150A,GABRA4,GBX2, GFI1B,GLT1D1,KCNA6,LRMP,MC3R,MEGF11,PIRT, POU2F3,RELN,SCN3A,SLC7A14,SPIC,ST18,T	ARSB,BCAT1,CD200R1,CD33,CMKLR1,DAB2,FBN1, FOLR2,FSTL1,LGI2,LGMN,LILRB5,MPEG1,MRC1, MS4A4A,RASGRP4,SIGLEC1,SIRPB2,SLC24A4,TLR8,VSIG4

ADAM12,ALPK2,BCAT1,CHSY3,COL1A1,COL1A2,COL3A1, COL5A1,COL5A2,GFPT2,GPR176,LOX,LZTS1,MRC2, NRP1,NTNG2,POSTN,PXDN,SPARC,ST6GALNAC5,WISP1	ABCA6,ADAMTS6,AIF1L,APCDD1,BCAT1,C1R,C1S, CARD6,CTSK,CXCL12,DCLK1,MAP3K12,MMP2,PODN, RSPO3,SCN1B,SERPINF1,SERPING1,SRGAP2,SRPX,TGFBR2

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 BCAT1

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 1, cytosolic	nutraceutical	Pyridoxal Phosphate
DB00142	branched chain amino-acid transaminase 1, cytosolic	approved; nutraceutical	L-Glutamic Acid
DB00149	branched chain amino-acid transaminase 1, cytosolic	approved; nutraceutical	L-Leucine
DB00161	branched chain amino-acid transaminase 1, cytosolic	approved; nutraceutical	L-Valine
DB00167	branched chain amino-acid transaminase 1, cytosolic	approved; nutraceutical	L-Isoleucine
DB07544	branched chain amino-acid transaminase 1, cytosolic	experimental	N'-(5-CHLOROBENZOFURAN-2-CARBONYL)-2-(TRIFLUOROMETHYL)BENZENESULFONOHYDRAZIDE
DB00121	branched chain amino-acid transaminase 1, cytosolic	approved; nutraceutical	Biotin
DB00130	branched chain amino-acid transaminase 1, cytosolic	approved; nutraceutical; investigational	L-Glutamine

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Cross referenced IDs for BCAT1

* 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