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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for BCAT2 |
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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 | Significant driver gene in |
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) |
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 |
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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 |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=29) | (# total SNVs=11) |
(# total SNVs=1) | (# total SNVs=0) |
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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 |
chr19:49303271-49303271 | p.S166S | 1 |
chr19:49299896-49299896 | p.V335A | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |
chr19:49303279 | p.T193T,BCAT2 | 1 |
chr19:49310321 | p.S98S,BCAT2 | 1 |
chr19:49300263 | p.D186H,BCAT2 | 1 |
chr19:49303308 | p.P82H,BCAT2 | 1 |
chr19:49310325 | p.E172V,BCAT2 | 1 |
chr19:49300454 | p.D72E,BCAT2 | 1 |
chr19:49303312 | p.Q150H,BCAT2 | 1 |
chr19:49300495 | p.L21L | 1 |
chr19:49303323 | p.V133V,BCAT2 | 1 |
chr19:49300560 | p.S16F | 1 |
Other DBs for Point Mutations |
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. |
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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 |
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 |
* 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 |
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Interacting Genes (from Pathway Commons) |
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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 |
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