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 UGT1A3

Basic gene info.	Gene symbol	UGT1A3
	Gene name	UDP glucuronosyltransferase 1 family, polypeptide A3
	Synonyms	UDPGT\|UDPGT 1-3\|UGT-1C\|UGT1-03\|UGT1.3\|UGT1C
	Cytomap	UCSC genome browser: 2q37
	Genomic location	chr2 :234637772-234681945
	Type of gene	protein-coding
	RefGenes	NM_019093.2,
	Ensembl id	ENSG00000243135
	Description	UDP glycosyltransferase 1 family, polypeptide A3UDP-glucuronosyltransferase 1-3UDP-glucuronosyltransferase 1-CUDP-glucuronosyltransferase 1A3UGT1*3
	Modification date	20141211
dbXrefs	MIM : 606428
	HGNC : HGNC
	Ensembl : ENSG00000243135
	HPRD : 07566
	Vega : OTTHUMG00000059118
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_UGT1A3
	BioGPS: 54659
	Gene Expression Atlas: ENSG00000243135
	The Human Protein Atlas: ENSG00000243135
Pathway	NCI Pathway Interaction Database: UGT1A3
	KEGG: UGT1A3
	REACTOME: UGT1A3
	ConsensusPathDB
	Pathway Commons: UGT1A3
Metabolism	MetaCyc: UGT1A3
	HUMANCyc: UGT1A3
Regulation	Ensembl's Regulation: ENSG00000243135
	miRBase: chr2 :234,637,772-234,681,945
	TargetScan: NM_019093
	cisRED: ENSG00000243135
Context	iHOP: UGT1A3
	cancer metabolism search in PubMed: UGT1A3
	UCL Cancer Institute: UGT1A3
Assigned class in ccmGDB	C

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Phenotypic Information for UGT1A3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: UGT1A3
	Familial Cancer Database: UGT1A3

* 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_ASCORBATE_AND_ALDARATE_METABOLISM KEGG_STARCH_AND_SUCROSE_METABOLISM KEGG_RETINOL_METABOLISM KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 KEGG_DRUG_METABOLISM_CYTOCHROME_P450 KEGG_DRUG_METABOLISM_OTHER_ENZYMES

Others
OMIM
Orphanet
Disease	KEGG Disease: UGT1A3
	MedGen: UGT1A3 (Human Medical Genetics with Condition)
	ClinVar: UGT1A3
Phenotype	MGI: UGT1A3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: UGT1A3

Mutations for UGT1A3

* 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 UGT1A3 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

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=8

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=61)	Stat. for Synonymous SNVs (# total SNVs=32)

Stat. for Deletions (# total SNVs=5)	Stat. for Insertions (# total SNVs=2)

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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
chr2:234638369-234638369	p.T199T	8
chr2:234638394-234638394	p.M208L	5
chr2:234638445-234638445	p.H225Y	4
chr2:234681161-234681161	p.K521E	3
chr2:234676526-234676526	p.S344L	3
chr2:234637988-234637988	p.E72D	3
chr2:234638283-234638283	p.L173fs*1	3
chr2:234681041-234681041	p.D481N	2
chr2:234676494-234676494	p.?	2
chr2:234680936-234680936	p.S446G	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=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	2	1	3			1		1	2		5	1	1			15	1		5
# mutation	3	2	1	3			2		1	2		5	1	1			15	1		5
nonsynonymous SNV	3	1	1	1					1	1		5	1	1			10	1		2
synonymous SNV		1		2			2			1							5			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
chr2:234638622	p.R284G	3
chr2:234638190	p.R91C	1
chr2:234638435	p.P195S	1
chr2:234637988	p.R91H	1
chr2:234638206	p.M214L	1
chr2:234637776	p.T103A	1
chr2:234638459	p.S221S	1
chr2:234637997	p.A2T	1
chr2:234638207	p.H133Y	1
chr2:234637790	p.A229A	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 UGT1A3 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 UGT1A3

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


APCS,APOA2,APOA4,C8A,C9,CFHR2,CREB3L3, CRP,CYP8B1,FABP1,FGF23,HP,MT1B,OR4D11, SERPINA7,TBC1D26,UGT1A1,UGT1A3,UGT1A4,UGT1A6,UGT1A9	C12orf40,C8orf33,CES1P1,CRH,ELOVL6,GOLGA2P3Y,HMX2, HSD17B1,KRTAP10-10,NKX2-4,PISD,PQLC3,SEL1L2,SLC7A4, SPANXA2,SPANXC,SPANXD,SPATA22,SPZ1,SSTR2,UGT1A3

ABCG2,ALPI,C11orf86,LINC00520,C1orf94,CAPN11,CDHR2, CIDEC,CLDN23,DHRS9,FAM25BP,GDPD2,LOC646627,MYPN, NAT8,TRANK1,UGT1A1,UGT1A3,UGT1A4,UGT1A5,VSIG1	ACE,CHRNA2,CREB3L3,CYP2C9,CYP4F2,DPP4,FGF19, HAPLN4,MEP1B,MGAM,MS4A10,MUC17,NTS,RBP2, SLC10A2,SLC23A1,SLC6A4,TM6SF2,UGT1A3,UGT1A4,UGT1A5

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 UGT1A3

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
DB01544	UDP glucuronosyltransferase 1 family, polypeptide A3	illicit; approved	Flunitrazepam
DB00973	UDP glucuronosyltransferase 1 family, polypeptide A3	approved	Ezetimibe
DB00184	UDP glucuronosyltransferase 1 family, polypeptide A3	approved	Nicotine
DB01076	UDP glucuronosyltransferase 1 family, polypeptide A3	approved	Atorvastatin
DB00762	UDP glucuronosyltransferase 1 family, polypeptide A3	approved; investigational	Irinotecan
DB00783	UDP glucuronosyltransferase 1 family, polypeptide A3	approved; investigational	Estradiol
DB00921	UDP glucuronosyltransferase 1 family, polypeptide A3	illicit; approved; investigational	Buprenorphine
DB00363	UDP glucuronosyltransferase 1 family, polypeptide A3	approved	Clozapine
DB00434	UDP glucuronosyltransferase 1 family, polypeptide A3	approved	Cyproheptadine
DB01075	UDP glucuronosyltransferase 1 family, polypeptide A3	approved	Diphenhydramine
DB00678	UDP glucuronosyltransferase 1 family, polypeptide A3	approved	Losartan
DB00313	UDP glucuronosyltransferase 1 family, polypeptide A3	approved; investigational	Valproic Acid
DB00655	UDP glucuronosyltransferase 1 family, polypeptide A3	approved	Estrone
DB00712	UDP glucuronosyltransferase 1 family, polypeptide A3	approved	Flurbiprofen
DB01050	UDP glucuronosyltransferase 1 family, polypeptide A3	approved	Ibuprofen
DB01009	UDP glucuronosyltransferase 1 family, polypeptide A3	approved	Ketoprofen

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Cross referenced IDs for UGT1A3

* 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