Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolBCAT2
Gene namebranched chain amino-acid transaminase 2, mitochondrial
SynonymsBCAM|BCATM|BCT2|PP18
CytomapUCSC genome browser: 19q13
Genomic locationchr19 :49298318-49314320
Type of geneprotein-coding
RefGenesNM_001164773.1,
NM_001190.3,NM_001284325.1,NR_028451.1,
Ensembl idENSG00000105552
Descriptionbranched chain aminotransferase 2, mitochondrialbranched-chain-amino-acid aminotransferase, mitochondrialplacental protein 18
Modification date20141207
dbXrefs MIM : 113530
HGNC : HGNC
Ensembl : ENSG00000105552
HPRD : 00217
Vega : OTTHUMG00000183327
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_BCAT2
BioGPS: 587
Gene Expression Atlas: ENSG00000105552
The Human Protein Atlas: ENSG00000105552
PathwayNCI Pathway Interaction Database: BCAT2
KEGG: BCAT2
REACTOME: BCAT2
ConsensusPathDB
Pathway Commons: BCAT2
MetabolismMetaCyc: BCAT2
HUMANCyc: BCAT2
RegulationEnsembl's Regulation: ENSG00000105552
miRBase: chr19 :49,298,318-49,314,320
TargetScan: NM_001164773
cisRED: ENSG00000105552
ContextiHOP: BCAT2
cancer metabolism search in PubMed: BCAT2
UCL Cancer Institute: BCAT2
Assigned class in ccmGDBC

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Phenotypic Information for BCAT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: BCAT2
MedGen: BCAT2 (Human Medical Genetics with Condition)
ClinVar: BCAT2
PhenotypeMGI: BCAT2 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows BCAT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF934808BCAT21165194931063249310796MS4A6A152307115994288659943041
BF062738BCAT22148194929832349298468ZNF7614638963525392535255527

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

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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=3

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check002.gifSomatic 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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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
chr19:49303070-49303070p.T186R3
chr19:49303003-49303003p.P208P2
chr19:49303312-49303312p.E153K2
chr19:49309850-49309850p.W75L2
chr19:49309937-49309937p.H46R2
chr19:49300525-49300525p.W254L2
chr19:49299833-49299833p.?2
chr19:49300554-49300554p.A244A2
chr19:49303308-49303308p.V154G1
chr19:49309838-49309849p.W75_R79>*1

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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
# sample13 2       131  35 8
# mutation13 2       131  35 8
nonsynonymous SNV12 1       131  15 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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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
chr19:49302957p.G72S,BCAT21
chr19:49309780p.V62G,BCAT21
chr19:49302971p.P268S,BCAT21
chr19:49309829p.E61K,BCAT21
chr19:49299747p.R57H,BCAT21
chr19:49303011p.I267I,BCAT21
chr19:49309858p.K49T,BCAT21
chr19:49299748p.V240L,BCAT21
chr19:49303012p.R24S,BCAT21
chr19:49310293p.R220R,BCAT21

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 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

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

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
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 BCAT2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00114branched chain amino-acid transaminase 2, mitochondrialnutraceuticalPyridoxal Phosphate
DB00142branched chain amino-acid transaminase 2, mitochondrialapproved; nutraceuticalL-Glutamic Acid
DB00149branched chain amino-acid transaminase 2, mitochondrialapproved; nutraceuticalL-Leucine
DB00167branched chain amino-acid transaminase 2, mitochondrialapproved; nutraceuticalL-Isoleucine
DB02142branched chain amino-acid transaminase 2, mitochondrialexperimentalPyridoxamine-5'-Phosphate
DB02635branched chain amino-acid transaminase 2, mitochondrialexperimentalN-[O-Phosphono-Pyridoxyl]-Isoleucine
DB04074branched chain amino-acid transaminase 2, mitochondrialexperimentalAlpha-ketoisovalerate
DB00121branched chain amino-acid transaminase 2, mitochondrialapproved; nutraceuticalBiotin
DB00161branched chain amino-acid transaminase 2, mitochondrialapproved; nutraceuticalL-Valine
DB00130branched chain amino-acid transaminase 2, mitochondrialapproved; nutraceutical; investigationalL-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



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