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 TBXAS1

Basic gene info.	Gene symbol	TBXAS1
	Gene name	thromboxane A synthase 1 (platelet)
	Synonyms	BDPLT14\|CYP5\|CYP5A1\|GHOSAL\|THAS\|TS\|TXAS\|TXS
	Cytomap	UCSC genome browser: 7q34-q35
	Genomic location	chr7 :139528951-139720125
	Type of gene	protein-coding
	RefGenes	NM_001061.4, NM_001130966.2,NM_001166253.1,NM_001166254.1,NM_030984.3, NR_029394.1,
	Ensembl id	ENSG00000059377
	Description	TXA synthasecytochrome P450 5A1cytochrome P450, family 5, subfamily A, polypeptide 1platelet, cytochrome P450, subfamily Vthromboxane-A synthase
	Modification date	20141207
dbXrefs	MIM : 274180
	HGNC : HGNC
	Ensembl : ENSG00000059377
	HPRD : 02035
	Vega : OTTHUMG00000157302
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TBXAS1
	BioGPS: 6916
	Gene Expression Atlas: ENSG00000059377
	The Human Protein Atlas: ENSG00000059377
Pathway	NCI Pathway Interaction Database: TBXAS1
	KEGG: TBXAS1
	REACTOME: TBXAS1
	ConsensusPathDB
	Pathway Commons: TBXAS1
Metabolism	MetaCyc: TBXAS1
	HUMANCyc: TBXAS1
Regulation	Ensembl's Regulation: ENSG00000059377
	miRBase: chr7 :139,528,951-139,720,125
	TargetScan: NM_001061
	cisRED: ENSG00000059377
Context	iHOP: TBXAS1
	cancer metabolism search in PubMed: TBXAS1
	UCL Cancer Institute: TBXAS1
Assigned class in ccmGDB	C

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Phenotypic Information for TBXAS1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_ARACHIDONIC_ACID_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: TBXAS1
	MedGen: TBXAS1 (Human Medical Genetics with Condition)
	ClinVar: TBXAS1
Phenotype	MGI: TBXAS1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	TBXAS1	chr7	139624113	139624133	KIAA1549	chr7	138613017	138613037
ovary	TBXAS1	chr7	139624113	139624133	KIAA1549	chr7	138613020	138613040
pancreas	TBXAS1	chr7	139572213	139572233	HIPK2	chr7	139352937	139352957
pancreas	TBXAS1	chr7	139692607	139692807		chr7	127767128	127767328
pancreas	TBXAS1	chr7	139694212	139694232	TBXAS1	chr7	139681622	139681642

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 TBXAS1 related fusion information.

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

BF893936

RPAP2

92813801

92813854

TBXAS1

425

139548448

139548814

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=5

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Somatic 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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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
chr7:139655362-139655362	p.R216H	4
chr7:139657436-139657436	p.S232L	3
chr7:139529205-139529205	p.F7L	2
chr7:139657492-139657492	p.E251K	2
chr7:139706905-139706905	p.F384L	2
chr7:139653250-139653250	p.I179I	2
chr7:139611040-139611040	p.R86W	2
chr7:139661740-139661740	p.M282T	2
chr7:139661880-139661880	p.V329L	1
chr7:139719888-139719888	p.V532I	1

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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=3

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	3	1		14	1		5		2			8	5	2			15	6		9
# mutation	3	1		14	1		5		2			7	5	2			20	6		10
nonsynonymous SNV	2	1		10	1		5		2			7	2	2			11	5		7
synonymous SNV	1			4									3				9	1		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
chr7:139657436	p.S232L,TBXAS1	3
chr7:139655362	p.R216H,TBXAS1	2
chr7:139653250	p.I179I,TBXAS1	2
chr7:139715537	p.S289F,TBXAS1	1
chr7:139529205	p.A416G,TBXAS1	1
chr7:139655336	p.V17M,TBXAS1	1
chr7:139719875	p.E135D,TBXAS1	1
chr7:139611072	p.R216C,TBXAS1	1
chr7:139657535	p.I300I,TBXAS1	1
chr7:139661861	p.G423R,TBXAS1	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 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

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


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

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 TBXAS1

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
DB01207	thromboxane A synthase 1 (platelet)	approved	Ridogrel
DB03052	thromboxane A synthase 1 (platelet)	experimental	Dazoxiben
DB00564	thromboxane A synthase 1 (platelet)	approved; investigational	Carbamazepine
DB00252	thromboxane A synthase 1 (platelet)	approved	Phenytoin
DB00945	thromboxane A synthase 1 (platelet)	approved	Acetylsalicylic acid
DB00917	thromboxane A synthase 1 (platelet)	approved	Dinoprostone
DB01240	thromboxane A synthase 1 (platelet)	approved	Epoprostenol
DB00184	thromboxane A synthase 1 (platelet)	approved	Nicotine
DB00482	thromboxane A synthase 1 (platelet)	approved; investigational	Celecoxib

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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