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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for BCAT1
check button Gene summary
Basic gene informationGene symbolBCAT1
Gene namebranched chain amino-acid transaminase 1, cytosolic
SynonymsBCATC|BCT1|ECA39|MECA39|PNAS121|PP18
CytomapUCSC genome browser: 12p12.1
Type of geneprotein-coding
RefGenesNM_001178091.1,
NM_001178092.1,NM_001178093.1,NM_001178094.1,NM_005504.6,
Descriptionbranched chain aminotransferase 1, cytosolicbranched-chain-amino-acid aminotransferase, cytosolicplacental protein 18
Modification date20141207
dbXrefs MIM : 113520
HGNC : HGNC
Ensembl : ENSG00000060982
HPRD : 00216
Vega : OTTHUMG00000169053
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_BCAT1
BioGPS: 586
PathwayNCI Pathway Interaction Database: BCAT1
KEGG: BCAT1
REACTOME: BCAT1
Pathway Commons: BCAT1
ContextiHOP: BCAT1
ligand binding site mutation search in PubMed: BCAT1
UCL Cancer Institute: BCAT1
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)PancreasTestis
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)PAADTGCT
Reference showing the relevant tissue of BCAT1
Description by TissGene annotationsTissgsLTS
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID


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TissGeneExp for BCAT1

check button Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
gene exp


check button Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)
gene isoform exp


check button Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.
normal gene exp


check button Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
HNSC0.839735366-1.0029064951.842641867.46E-087.56E-07
LIHC-1.827102262-2.9787622621.151667.97E-074.34E-06
THCA-0.43252033-1.6235982961.1910779667.51E-062.49E-05
KIRC0.260348738-0.9888957071.2492444444.69E-142.21E-13
KICH0.720919738-1.6425922622.3635123.92E-071.59E-06


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TissGene-miRNA for BCAT1

check button Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))
Cancer typemiRNA idmiRNA accessionP-val.Coeff.# samples
UCShsa-let-7f-5pMIMAT00000670.046-0.2756


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TissGeneMut for BCAT1
TissGeneSNV for BCAT1

check button nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)

* Click on the image to enlarge it in a new window.
SNV lollipop
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check button Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.G322ESKCM3
p.R364HBRCA2
p.N200TPAAD1
p.R163CUCEC1
p.L234PACC1
p.P164SSKCM1
p.A298TSTAD1
p.T198PACC1
p.E377QSKCM1
p.G197ESKCM1
p.T59MPRAD1
p.C335RLUSC1
p.G259EHNSC1
p.V34ASTAD1
p.V384ABRCA1
p.R163CBLCA1
p.V70IREAD1
p.P87TTHYM1
p.G259RHNSC1
p.M1TUCEC1
p.Q244*CESC1
p.S18LBRCA1
p.G50*LUAD1
p.G168RSKCM1
p.A233VLGG1
p.T54MSTAD1
p.E19ACOAD1
p.L231FHNSC1
p.W62*STAD1
p.P178HLIHC1
p.P83LHNSC1
p.L295PLIHC1
p.G283DSKCM1
p.G168EPAAD1
p.I108TSKCM1
p.G17ESKCM1
p.T59MMESO1
p.S195LSKCM1
p.L97XCOAD1
p.D380NUCEC1
p.T66MSTAD1
p.G17RUCEC1
p.S195*BLCA1
p.D239HBLCA1
p.L307PACC1
p.G16ESKCM1
p.W74XSTAD1
p.L6PCOAD1
p.S86*BLCA1
p.G261ESKCM1
p.T71MPRAD1
p.I107TSKCM1
p.T35MCOAD1
p.M313ISKCM1
p.P190HLIHC1
p.E316XREAD1
p.G107RSKCM1
p.G180EPAAD1
p.R163CSKCM1
p.A310TSTAD1
p.L295PACC1
p.P153SSKCM1
p.E275*UCEC1
p.G136ESKCM1
p.P164LSKCM1
p.K176TSTAD1
p.R102*SKCM1
p.W205CLUAD1
p.L307PLIHC1
p.V22ASTAD1
p.P280LBRCA1
p.K188TSTAD1
p.R303CCOAD1
p.E316QSKCM1


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TissGeneCNV for BCAT1

check button Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)
CNV


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TissGeneFusions for BCAT1

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
Chimerdb3.0ChiTaRsNAAA743391BCAT1-BCAT1chr12:24967834chr12:24968777
Chimerdb3.0ChiTaRsNAAL120469BCAT1-MDGA2chr12:24966386chr14:47647579
Chimerdb3.0ChiTaRsNAAI275099BCAT1-DNAJC18chr12:24964353chr5:138746937
Chimerdb3.0ChiTaRsNABF996876BCAT1-SLC9A1chr12:24968990chr1:27429218
Chimerdb3.0FusionScanBRCATCGA-D8-A1XW-01ABCAT1-MRPS35In-Framechr12:25031463chr12:27908113
Chimerdb3.0TopHat-FusionBRCATCGA-BH-A0DG-01ABCAT1-GYG2Out-of-Framechr12:24983722chrX:2799092
TCGAfusionPortalPRADABRCATCGA-A2-A04U-01ABCAT1-ITPR2In-frameChr12:25101861Chr12:26493261
TCGAfusionPortalPRADABRCATCGA-E2-A1LL-01ABCAT1-RECQLCDS-5UTRChr12:25101861Chr12:21652549
TCGAfusionPortalPRADAOVTCGA-25-1870-01ABCAT1-PRB3In-frameChr12:24995016Chr12:11421602


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TissGeneNet for BCAT1

check button Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)
BRCA (tumor)BRCA (normal)
BCAT1, UBC, SMAD5 (tumor)BCAT1, UBC, SMAD5 (normal)
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COAD (tumor)COAD (normal)
BCAT1, UBC, SMAD5 (tumor)BCAT1, UBC, SMAD5 (normal)
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HNSC (tumor)HNSC (normal)
BCAT1, UBC, SMAD5 (tumor)BCAT1, UBC, SMAD5 (normal)
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KICH (tumor)KICH (normal)
BCAT1, UBC, SMAD5 (tumor)BCAT1, UBC, SMAD5 (normal)
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KIRC (tumor)KIRC (normal)
BCAT1, UBC, SMAD5 (tumor)BCAT1, UBC, SMAD5 (normal)
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KIRP (tumor)KIRP (normal)
BCAT1, UBC, SMAD5 (tumor)BCAT1, UBC, SMAD5 (normal)
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LIHC (tumor)LIHC (normal)
BCAT1, UBC, SMAD5 (tumor)BCAT1, UBC, SMAD5 (normal)
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LUAD (tumor)LUAD (normal)
BCAT1, UBC, SMAD5 (tumor)BCAT1, UBC, SMAD5 (normal)
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LUSC (tumor)LUSC (normal)
BCAT1, UBC, SMAD5 (tumor)BCAT1, UBC, SMAD5 (normal)
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PRAD (tumor)PRAD (normal)
BCAT1, UBC, SMAD5 (tumor)BCAT1, UBC, SMAD5 (normal)
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STAD (tumor)STAD (normal)
BCAT1, UBC, SMAD5 (tumor)BCAT1, UBC, SMAD5 (normal)
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THCA (tumor)THCA (normal)
BCAT1, UBC, SMAD5 (tumor)BCAT1, UBC, SMAD5 (normal)
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TissGeneProg for BCAT1

check button Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image to enlarge it in a new window.
survival 1

check button Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 2

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 3

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 4

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TissGeneClin for BCAT1
TissGeneDrug for BCAT1

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status
DB00149L-LeucineSmall moleculeApproved|Nutraceutical
DB00161L-ValineSmall moleculeApproved|Nutraceutical
DB00167L-IsoleucineSmall moleculeApproved|Nutraceutical


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TissGeneDisease for BCAT1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0009402Colorectal Carcinoma2BeFree
umls:C0027627Neoplasm Metastasis2BeFree
umls:C1527249Colorectal Cancer2BeFree
umls:C2931822Nasopharyngeal carcinoma2BeFree
umls:C0009404Colorectal Neoplasms1LHGDN
umls:C0011854Diabetes Mellitus, Insulin-Dependent1BeFree
umls:C0017636Glioblastoma1BeFree
umls:C0017638Glioma1BeFree
umls:C0017661IGA Glomerulonephritis1CTD_human
umls:C0025149Medulloblastoma1BeFree
umls:C0040336Tobacco Use Disorder1GAD
umls:C0043094Weight Gain1CTD_human
umls:C1520166Xenograft Model1BeFree
umls:C1709246Non-Neoplastic Disorder1BeFree
umls:C2718067Alcoholic Steatohepatitis1BeFree