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 TH

Basic gene info.	Gene symbol	TH
	Gene name	tyrosine hydroxylase
	Synonyms	DYT14\|DYT5b\|TYH
	Cytomap	UCSC genome browser: 11p15.5
	Genomic location	chr11 :2185158-2193035
	Type of gene	protein-coding
	RefGenes	NM_000360.3, NM_199292.2,NM_199293.2,
	Ensembl id	ENSG00000180176
	Description	dystonia 14tyrosine 3-hydroxylasetyrosine 3-monooxygenase
	Modification date	20141219
dbXrefs	MIM : 191290
	HGNC : HGNC
	Ensembl : ENSG00000180176
	HPRD : 01865
	Vega : OTTHUMG00000009559
Protein	UniProt: P07101 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TH
	BioGPS: 7054
	Gene Expression Atlas: ENSG00000180176
	The Human Protein Atlas: ENSG00000180176
Pathway	NCI Pathway Interaction Database: TH
	KEGG: TH
	REACTOME: TH
	ConsensusPathDB
	Pathway Commons: TH
Metabolism	MetaCyc: TH
	HUMANCyc: TH
Regulation	Ensembl's Regulation: ENSG00000180176
	miRBase: chr11 :2,185,158-2,193,035
	TargetScan: NM_000360
	cisRED: ENSG00000180176
Context	iHOP: TH
	cancer metabolism search in PubMed: TH
	UCL Cancer Institute: TH
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: TH
	Familial Cancer Database: TH

* 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_TYROSINE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM	191290; gene. 191290; gene. 605407; phenotype. 605407; phenotype.
Orphanet	101150; Autosomal recessive dopa-responsive dystonia. 101150; Autosomal recessive dopa-responsive dystonia.
Disease	KEGG Disease: TH
	MedGen: TH (Human Medical Genetics with Condition)
	ClinVar: TH
Phenotype	MGI: TH (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: TH

Mutations for TH

* 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 TH 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

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

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

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=33)	Stat. for Synonymous SNVs (# total SNVs=18)

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
chr11:2186500-2186500	p.F463F	2
chr11:2186573-2186573	p.E439A	2
chr11:2189733-2189733	p.A190S	2
chr11:2186909-2186909	p.G428W	2
chr11:2193002-2193002	p.D5D	2
chr11:2193005-2193005	p.P4P	2
chr11:2189794-2189794	p.R169R	2
chr11:2188238-2188238	p.K271K	2
chr11:2185608-2185608	p.R481H	2
chr11:2191098-2191098	p.P63T	2

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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=1

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		6	1		2					5	4	1			11	4		3
# mutation		1		7	1		2					5	4	1			12	5		4
nonsynonymous SNV		1		2			1					4	2	1			9	2		3
synonymous SNV				5	1		1					1	2				3	3		1

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
chr11:2191098	p.P32T,TH	2
chr11:2185535	p.P461P,TH	1
chr11:2191095	p.C176Y,TH	1
chr11:2186909	p.K24K,TH	1
chr11:2189775	p.V457M,TH	1
chr11:2185559	p.P167S,TH	1
chr11:2186914	p.E20Q,TH	1
chr11:2189797	p.S456F,TH	1
chr11:2185574	p.G160R,TH	1
chr11:2192945	p.D5D,TH	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 TH 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 TH

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


AP1G2,C14orf93,DCAF11,FBP1,GHDC,GMPR2,HAUS4, HOMEZ,HSD17B8,LRP10,MDP1,ZNF205-AS1,NEDD8,RAB17, RBM23,RNF31,SDR39U1,THTPA,TINF2,TM9SF1,WDR25	AARS,ACAD9,ASCC2,BCAP31,CRELD1,GRHPR,HINT2, HOOK2,IFI27L1,ITFG3,KLHL22,LOC729991,MRPL24,NME4, POLR2L,PRR5,PSMD8,SNX17,THTPA,TST,UROD

AP4S1,APEX1,DNAAF2,TMEM251,C14orf119,CCDC71,CHMP4A, GMPR2,LOC100009676,MDP1,MGAT2,NEDD8,NGDN,PSMB5, RBM23,SCAF11___GEMIN2___ZEB2,THTPA,TINF2,TMEM55B,TOX4,TTC5	AIP,AMZ2,ARL2,BBS4,BCL7C,BOLA1,FAM216A, C1orf54,C6orf1,CAMLG,CUEDC2,MPV17,MRPL40,MYL6B, SNAPIN,SNRPN,THTPA,TMSB15B,TRMT112,UROD,ZNF32

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 TH

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P07101; -.
Chemistry	ChEMBL	CHEMBL1969; -.
Chemistry	GuidetoPHARMACOLOGY	1243; -.
Chemistry	BindingDB	P07101; -.
Chemistry	ChEMBL	CHEMBL1969; -.
Chemistry	GuidetoPHARMACOLOGY	1243; -.
Organism-specific databases	PharmGKB	PA351; -.
Organism-specific databases	PharmGKB	PA351; -.
Organism-specific databases	CTD	7054; -.
Organism-specific databases	CTD	7054; -.

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
DB00120	tyrosine hydroxylase	approved; nutraceutical	L-Phenylalanine
DB00135	tyrosine hydroxylase	approved; nutraceutical	L-Tyrosine
DB00360	tyrosine hydroxylase	approved; investigational	Tetrahydrobiopterin
DB00765	tyrosine hydroxylase	approved	Metyrosine
DB03552	tyrosine hydroxylase	experimental	Meta-Tyrosine
DB04400	tyrosine hydroxylase	experimental	7,8-Dihydrobiopterin
DB01394	tyrosine hydroxylase	approved	Colchicine
DB00988	tyrosine hydroxylase	approved	Dopamine
DB00864	tyrosine hydroxylase	approved; investigational	Tacrolimus
DB01235	tyrosine hydroxylase	approved	Levodopa
DB00368	tyrosine hydroxylase	approved	Norepinephrine

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Cross referenced IDs for TH

* 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