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 TBXAS1
Basic gene info.Gene symbolTBXAS1
Gene namethromboxane A synthase 1 (platelet)
SynonymsBDPLT14|CYP5|CYP5A1|GHOSAL|THAS|TS|TXAS|TXS
CytomapUCSC genome browser: 7q34-q35
Genomic locationchr7 :139528951-139720125
Type of geneprotein-coding
RefGenesNM_001061.4,
NM_001130966.2,NM_001166253.1,NM_001166254.1,NM_030984.3,
NR_029394.1,
Ensembl idENSG00000059377
DescriptionTXA synthasecytochrome P450 5A1cytochrome P450, family 5, subfamily A, polypeptide 1platelet, cytochrome P450, subfamily Vthromboxane-A synthase
Modification date20141207
dbXrefs MIM : 274180
HGNC : HGNC
Ensembl : ENSG00000059377
HPRD : 02035
Vega : OTTHUMG00000157302
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TBXAS1
BioGPS: 6916
Gene Expression Atlas: ENSG00000059377
The Human Protein Atlas: ENSG00000059377
PathwayNCI Pathway Interaction Database: TBXAS1
KEGG: TBXAS1
REACTOME: TBXAS1
ConsensusPathDB
Pathway Commons: TBXAS1
MetabolismMetaCyc: TBXAS1
HUMANCyc: TBXAS1
RegulationEnsembl's Regulation: ENSG00000059377
miRBase: chr7 :139,528,951-139,720,125
TargetScan: NM_001061
cisRED: ENSG00000059377
ContextiHOP: TBXAS1
cancer metabolism search in PubMed: TBXAS1
UCL Cancer Institute: TBXAS1
Assigned class in ccmGDBC

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Phenotypic Information for TBXAS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TBXAS1
Familial Cancer Database: TBXAS1
* 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
KEGG_ARACHIDONIC_ACID_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: TBXAS1
MedGen: TBXAS1 (Human Medical Genetics with Condition)
ClinVar: TBXAS1
PhenotypeMGI: TBXAS1 (International Mouse Phenotyping Consortium)
PhenomicDB: TBXAS1

Mutations for TBXAS1
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryTBXAS1chr7139624113139624133KIAA1549chr7138613017138613037
ovaryTBXAS1chr7139624113139624133KIAA1549chr7138613020138613040
pancreasTBXAS1chr7139572213139572233HIPK2chr7139352937139352957
pancreasTBXAS1chr7139692607139692807chr7127767128127767328
pancreasTBXAS1chr7139694212139694232TBXAS1chr7139681622139681642
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TBXAS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF893936RPAP2156819281380192813854TBXAS1574257139548448139548814

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample11    1      11  
GAIN (# sample)11           11  
LOSS (# sample)      1          
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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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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=50)
Stat. for Synonymous SNVs
(# total SNVs=12)
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
chr7:139655362-139655362p.R216H4
chr7:139657436-139657436p.S232L3
chr7:139611040-139611040p.R86W2
chr7:139661740-139661740p.M282T2
chr7:139529205-139529205p.F7L2
chr7:139657492-139657492p.E251K2
chr7:139706905-139706905p.F384L2
chr7:139653250-139653250p.I179I2
chr7:139655381-139655381p.I222I1
chr7:139706955-139706955p.T401M1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample31 141 5 2  852  156 9
# mutation31 141 5 2  752  206 10
nonsynonymous SNV21 101 5 2  722  115 7
synonymous SNV1  4        3   91 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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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
chr7:139657436p.S232L,TBXAS13
chr7:139655362p.R216H,TBXAS12
chr7:139653250p.I179I,TBXAS12
chr7:139611041p.F7L,TBXAS11
chr7:139657497p.E134K,TBXAS11
chr7:139719853p.E207D,TBXAS11
chr7:139636105p.L284L,TBXAS11
chr7:139661818p.A415E,TBXAS11
chr7:139529205p.V17M,TBXAS11
chr7:139655336p.E135D,TBXAS11

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 TBXAS1 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 TBXAS1

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

ABI3,ADAP2,AIF1,C3AR1,CD33,CD68,CSF1R,
CYTH4,FERMT3,LAIR1,LAPTM5,LRRC25,MS4A6A,MYO1F,
PLEKHO2,RNASE6,SIGLEC9,SLCO2B1,SPI1,TBXAS1,TYROBP
ARRB2,C1QB,C1QC,C3AR1,CD300C,CD4,CD86,
CTSS,FCER1G,HAVCR2,HCK,LILRB4,LRRC25,NFAM1,
PI4K2A,PIK3R5,SLC37A2,SLC7A7,SPI1,TBXAS1,TNFAIP8L2

ARID5A,ASRGL1,CCDC149,FAIM2,FAM3D,FOXA2,GALNT4,
HOXA7,IL17RD,KCNN4,KLK1,LMOD3,LPL,ODF3L2,
OSCP1,OXGR1,PLD1,ARHGEF28,TBXAS1,TTC39A,ZG16B
C3AR1,CD4,CD86,CMKLR1,EBI3,FPR3,GBGT1,
IL10RA,LAIR1,LILRB4,LRRC25,MAFB,NFAM1,NPL,
OSCAR,PILRA,PTAFR,SIGLEC7,TBXAS1,TLR2,TMEM86A
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 TBXAS1
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
DB01207thromboxane A synthase 1 (platelet)approvedRidogrel
DB03052thromboxane A synthase 1 (platelet)experimentalDazoxiben
DB00564thromboxane A synthase 1 (platelet)approved; investigationalCarbamazepine
DB00252thromboxane A synthase 1 (platelet)approvedPhenytoin
DB00945thromboxane A synthase 1 (platelet)approvedAcetylsalicylic acid
DB00917thromboxane A synthase 1 (platelet)approvedDinoprostone
DB01240thromboxane A synthase 1 (platelet)approvedEpoprostenol
DB00184thromboxane A synthase 1 (platelet)approvedNicotine
DB00482thromboxane A synthase 1 (platelet)approved; investigationalCelecoxib


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Cross referenced IDs for TBXAS1
* 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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