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 UGT2A1

Basic gene info.	Gene symbol	UGT2A1
	Gene name	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus
	Synonyms	UDPGT2A1
	Cytomap	UCSC genome browser: 4q13
	Genomic location	chr4 :70454134-70518967
	Type of gene	protein-coding
	RefGenes	NM_001252274.2, NM_001252275.2,NM_001301239.1,NM_006798.4,
	Ensembl id	ENSG00000173610
	Description	UDP glycosyltransferase 2 family, polypeptide A1UDP-glucuronosyltransferase 2A1uridine diphosphate glycosyltransferase 2 family, member A1
	Modification date	20141207
dbXrefs	MIM : 604716
	HGNC : HGNC
	Ensembl : ENSG00000173610
	HPRD : 05279
	Vega : OTTHUMG00000184942
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_UGT2A1
	BioGPS: 10941
	Gene Expression Atlas: ENSG00000173610
	The Human Protein Atlas: ENSG00000173610
Pathway	NCI Pathway Interaction Database: UGT2A1
	KEGG: UGT2A1
	REACTOME: UGT2A1
	ConsensusPathDB
	Pathway Commons: UGT2A1
Metabolism	MetaCyc: UGT2A1
	HUMANCyc: UGT2A1
Regulation	Ensembl's Regulation: ENSG00000173610
	miRBase: chr4 :70,454,134-70,518,967
	TargetScan: NM_001252274
	cisRED: ENSG00000173610
Context	iHOP: UGT2A1
	cancer metabolism search in PubMed: UGT2A1
	UCL Cancer Institute: UGT2A1
Assigned class in ccmGDB	C

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Phenotypic Information for UGT2A1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: UGT2A1
	Familial Cancer Database: UGT2A1

* 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: UGT2A1
	MedGen: UGT2A1 (Human Medical Genetics with Condition)
	ClinVar: UGT2A1
Phenotype	MGI: UGT2A1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: UGT2A1

Mutations for UGT2A1

* 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	UGT2A1	chr4	70467363	70467563	UGT2A1	chr4	70472750	70472950
ovary	UGT2A1	chr4	70467448	70467468	UGT2A1	chr4	70472793	70472813
ovary	UGT2A1	chr4	70493450	70493470	UGT2A1	chr4	70493695	70493715
ovary	UGT2A1	chr4	70509236	70509256	UGT2A1	chr4	70505863	70505883
pancreas	UGT2A1	chr4	70491911	70491931	UGT2A1	chr4	70495126	70495146

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 UGT2A1 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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=59)	Stat. for Synonymous SNVs (# total SNVs=15)

Stat. for Deletions (# total SNVs=4)	Stat. for Insertions (# total SNVs=1)

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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
chr4:70455340-70455340	p.R445I	3
chr4:70455304-70455304	p.R457Q	3
chr4:70455305-70455305	p.R457*	3
chr4:70465074-70465074	p.E252K	3
chr4:70513122-70513122	p.E81*	3
chr4:70460341-70460341	p.V386V	2
chr4:70455274-70455274	p.R467H	2
chr4:70465030-70465030	p.R266R	2
chr4:70465032-70465032	p.R266C	2
chr4:70512854-70512854	p.S170Y	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=2

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			2	1		5			1		2	3	3			8	2		4
# mutation	1			2	1		5			1		2	3	3			8	2		5
nonsynonymous SNV	1			1	1		3			1		2	2	3			5	2		4
synonymous SNV				1			2						1				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
chr4:70513300	p.G21G,UGT2A1	2
chr4:70512731	p.R209I,UGT2A1	1
chr4:70513331	p.T103A,UGT2A1	1
chr4:70512912	p.S205Y,UGT2A1	1
chr4:70513145	p.S102L,UGT2A1	1
chr4:70512732	p.Q203L,UGT2A1	1
chr4:70512938	p.V86L,UGT2A1	1
chr4:70513183	p.V193A,UGT2A1	1
chr4:70512737	p.P77P,UGT2A1	1
chr4:70512978	p.S191F,UGT2A1	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 UGT2A1 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 UGT2A1

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


BRF2,C9orf72,CAAP1,EIF4EBP1,FGF13,FGFR1,HOXB4, IFT74,IL19,KLRC2,LOC158696,LOC728024,PLAA,PLAC1, PPAPDC1B,PROSC,RRAGA,SCGB1D4,SPAG16,TUSC3,UGT2A1	C9orf84,CCL27,CRYAA,DEFB109P1B,IL36A,IRGC,KRT3, KRT84,LOC285740,LINC00159,OR1F1,OR1L1,OTOP3,PPY, RPTN,SCARNA27,SNORA22,SNORA71D,TSHB,UGT2A1,ZNRF4

CT45A5,CT45A6,CTAG2,CYP2A7,DPY19L2P1,LOC285501,LOC389705, MAGEA9B,OR1D4,OR2M2,OR5J2,SAGE1,SLC6A13,SPAG11A, SPAG11B,ST8SIA5,TAAR5,TCERG1L,TCF23,TNFRSF18,UGT2A1	ADH7,AMTN,C6orf15,CT83,PRR32,DUSP13,FOXE1, GAGE12J,KRT13,KRT34,KRT4,KRT6A,KRTAP4-7,LCE1F, LCE4A,SERPINB13,SERPINB4,SSX1,SSX2,TMPRSS11A,UGT2A1

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 UGT2A1

There's no related Drug.

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Cross referenced IDs for UGT2A1

* 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