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 B3GAT3

Basic gene info.	Gene symbol	B3GAT3
	Gene name	beta-1,3-glucuronyltransferase 3
	Synonyms	GLCATI\|glcUAT-I
	Cytomap	UCSC genome browser: 11q12.3
	Genomic location	chr11 :62382767-62389647
	Type of gene	protein-coding
	RefGenes	NM_001288721.1, NM_001288722.1,NM_001288723.1,NM_012200.3,NR_109991.1,
	Ensembl id	ENSG00000149541
	Description	Sqv-8-like proteinUDP-GlcUA:Gal beta-1,3-Gal-R glucuronyltransferasebeta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3
	Modification date	20141207
dbXrefs	MIM : 606374
	HGNC : HGNC
	Ensembl : ENSG00000149541
	HPRD : 07564
	Vega : OTTHUMG00000167685
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_B3GAT3
	BioGPS: 26229
	Gene Expression Atlas: ENSG00000149541
	The Human Protein Atlas: ENSG00000149541
Pathway	NCI Pathway Interaction Database: B3GAT3
	KEGG: B3GAT3
	REACTOME: B3GAT3
	ConsensusPathDB
	Pathway Commons: B3GAT3
Metabolism	MetaCyc: B3GAT3
	HUMANCyc: B3GAT3
Regulation	Ensembl's Regulation: ENSG00000149541
	miRBase: chr11 :62,382,767-62,389,647
	TargetScan: NM_001288721
	cisRED: ENSG00000149541
Context	iHOP: B3GAT3
	cancer metabolism search in PubMed: B3GAT3
	UCL Cancer Institute: B3GAT3
Assigned class in ccmGDB	C

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Phenotypic Information for B3GAT3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: B3GAT3
	Familial Cancer Database: B3GAT3

* 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
REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM
Orphanet
Disease	KEGG Disease: B3GAT3
	MedGen: B3GAT3 (Human Medical Genetics with Condition)
	ClinVar: B3GAT3
Phenotype	MGI: B3GAT3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: B3GAT3

Mutations for B3GAT3

* 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	B3GAT3	chr11	62387068	62387088		chr11	62694837	62694857
ovary	B3GAT3	chr11	62387069	62387089		chr11	62694837	62694857

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 B3GAT3 related fusion information.

ID	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
BP227858	SHC4	1	437	15	49170287	49170723	B3GAT3	430	564	11	62387968	62388102
BX107986	B3GAT3	1	139	11	62388055	62389397	SLC8A3	136	488	14	70513747	70514099
BU738636	B3GAT3	18	57	11	62382768	62382807	ATP1B2	54	593	17	7558922	7559565

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=17)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr11:62384058-62384058	p.R277W	2
chr11:62384117-62384117	p.A257V	2
chr11:62384468-62384468	p.L203L	1
chr11:62384793-62384793	p.R95Q	1
chr11:62389381-62389381	p.F13F	1
chr11:62384053-62384053	p.G278G	1
chr11:62384485-62384485	p.T198A	1
chr11:62384806-62384806	p.A91T	1
chr11:62389397-62389397	p.V8A	1
chr11:62384056-62384056	p.R277R	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=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	1		3			3		1			2		2		2	5	3		2
# mutation	1	1		3			3		1			2		2		2	5	3		2
nonsynonymous SNV	1	1		1			3		1			1		1		2	4	3		2
synonymous SNV				2								1		1			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
chr11:62384617	p.H154Y,B3GAT3	2
chr11:62384591	p.G28S,B3GAT3	1
chr11:62384058	p.A257V,B3GAT3	1
chr11:62384595	p.Q26H,B3GAT3	1
chr11:62384117	p.P250L,B3GAT3	1
chr11:62384138	p.F13F,B3GAT3	1
chr11:62384683	p.D233D,B3GAT3	1
chr11:62384188	p.N7K,B3GAT3	1
chr11:62384793	p.Q230E,B3GAT3	1
chr11:62384199	p.T198A,B3GAT3	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 B3GAT3 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 B3GAT3

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


ARL6IP4,AURKAIP1,B3GAT3,BAD,UQCC3,TSR3,C19orf60, C1orf86,LAMTOR4,FKBP2,MBD3,NDUFA11,NDUFB7,NUDT22, PIN1,PRDX5,RNASEH2C,THAP3,TMUB1,UBXN1,ZFPL1	ARFGAP1,ARMC5,B3GAT3,BRMS1,ENKD1,OXLD1,C19orf25, C9orf142,CCDC12,CCDC61,GSDMD,HSPBP1,MFSD10,RABEP2, RRP1,SIRT6,SNAPC2,TCEA2,THOC6,TRMT61A,TSSC4

AURKAIP1,B3GAT3,BRMS1,TSR3,C1orf86,C9orf142,DRAP1, FKBP2,HRAS,MRPL28,NARFL,NDUFS8,NME3,NUDC, RFNG,SAC3D1,SCRN2,SCYL1,STUB1,THAP3,ZFPL1	ARRDC1,B3GAT3,B4GALT3,DUS1L,DUSP23,CRACR2B,FASTK, FBXW9,GAS6,MAN1B1,MRPL41,NARFL,NOL12,PGLS, QPCTL,QTRT1,RABEP2,SIGIRR,TMEM129,TMEM44,ZDHHC24

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 B3GAT3

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
DB03041	beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)	experimental	Udp-Glucuronic Acid
DB03435	beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)	experimental	Uridine-5'-Diphosphate

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Cross referenced IDs for B3GAT3

* 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