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 B4GALT5

Basic gene info.	Gene symbol	B4GALT5
	Gene name	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5
	Synonyms	B4Gal-T5\|BETA4-GALT-IV\|beta4Gal-T5\|beta4GalT-V\|gt-V
	Cytomap	UCSC genome browser: 20q13.1-q13.2
	Genomic location	chr20 :48249482-48330421
	Type of gene	protein-coding
	RefGenes	NM_004776.3,
	Ensembl id	ENSG00000158470
	Description	UDP-Gal:beta-GlcNAc beta-1,4-galactosyltransferase 5UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 5UDP-galactose:beta-N-acetylglucosamine beta-1,4-galactosyltransferase 5beta-1,4-GalT IIbeta-1,4-GalT IVbeta-1,4-GalTase 5beta-1,4-gal
	Modification date	20141207
dbXrefs	MIM : 604016
	HGNC : HGNC
	Ensembl : ENSG00000158470
	HPRD : 06807
	Vega : OTTHUMG00000033086
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_B4GALT5
	BioGPS: 9334
	Gene Expression Atlas: ENSG00000158470
	The Human Protein Atlas: ENSG00000158470
Pathway	NCI Pathway Interaction Database: B4GALT5
	KEGG: B4GALT5
	REACTOME: B4GALT5
	ConsensusPathDB
	Pathway Commons: B4GALT5
Metabolism	MetaCyc: B4GALT5
	HUMANCyc: B4GALT5
Regulation	Ensembl's Regulation: ENSG00000158470
	miRBase: chr20 :48,249,482-48,330,421
	TargetScan: NM_004776
	cisRED: ENSG00000158470
Context	iHOP: B4GALT5
	cancer metabolism search in PubMed: B4GALT5
	UCL Cancer Institute: B4GALT5
Assigned class in ccmGDB	C

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Phenotypic Information for B4GALT5(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: B4GALT5
	Familial Cancer Database: B4GALT5

* 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_PROTEINS REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM
Orphanet
Disease	KEGG Disease: B4GALT5
	MedGen: B4GALT5 (Human Medical Genetics with Condition)
	ClinVar: B4GALT5
Phenotype	MGI: B4GALT5 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: B4GALT5

Mutations for B4GALT5

* 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 B4GALT5 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
BG766572	NIPAL3	1	371	1	24797418	24797788	B4GALT5	366	822	20	48250693	48251153
DB237731	SLC12A6	1	227	15	34610762	34610988	B4GALT5	225	565	20	48260099	48273242
BF812681	B4GALT5	8	207	20	48252621	48252821	PTK7	199	303	6	43113045	43113150
BU955750	B4GALT5	3	387	20	48252534	48252918	HSP90AA1	382	666	14	102549382	102549908
CN280929	SNX2	1	207	5	122110818	122131078	B4GALT5	204	468	20	48249492	48249756
CX164716	B4GALT5	1	177	20	48250835	48251011	CKB	178	574	14	103987747	103988721
AW376281	B4GALT5	6	390	20	48252553	48252939	HNRNPA1	382	619	12	54676361	54676937
AA902204	TAF5L	1	328	1	229728915	229729242	B4GALT5	326	584	20	48252844	48253983
AI207637	DHCR24	1	533	1	55316503	55317035	B4GALT5	518	631	20	48252183	48252296
BF851864	B4GALT5	2	219	20	48276918	48277135	FBXW4	212	373	10	103432775	103433376

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=32)	Stat. for Synonymous SNVs (# total SNVs=11)

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
chr20:48257081-48257081	p.R243H	3
chr20:48330222-48330222	p.R2R	2
chr20:48256282-48256282	p.R284W	2
chr20:48259034-48259034	p.L193L	2
chr20:48253947-48253947	p.P317L	2
chr20:48273211-48273211	p.A48A	2
chr20:48259098-48259098	p.R171R	1
chr20:48256231-48256231	p.D301H	1
chr20:48263558-48263558	p.P103L	1
chr20:48257123-48257123	p.C229Y	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		2		6			2		2			4	3	2			3	5		3
# mutation		2		7			2		2			4	3	2			3	5		3
nonsynonymous SNV		2		5			2		1			3	2	2			2	5		2
synonymous SNV				2					1			1	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
chr20:48330165	p.D226Y	1
chr20:48256306	p.S25L	1
chr20:48263528	p.R210Q	1
chr20:48330184	p.F21F	1
chr20:48256324	p.R171R	1
chr20:48263529	p.L15Q	1
chr20:48252856	p.E387V	1
chr20:48330202	p.C158R	1
chr20:48257081	p.R9L	1
chr20:48263537	p.G311G	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 B4GALT5 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 B4GALT5

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


ACTR3,ATP11C,B4GALT5,BEND3,CBFB,CENPI,CORO1C, CSE1L,DDX27,FAM83D,HIVEP2,MYBL2,PATL1,RNF114, RQCD1,SF3B3,SOS1,STAU1,TRRAP,UBE2V1,YEATS2	AP4E1,ATP11A,B4GALT5,BICC1,CCND2,CHSY3,CPSF2, EIF4G2,CCSER2,HIVEP2,KBTBD2,LRP12,MFAP3,PANX1, PRRG1,RPS6KA3,SSH1,TAF13,TFDP1,TSHZ3,ZNF385D

ADNP,ASXL1,B4GALT5,ELMO2,ITCH,TTI1,KIF3B, MAPRE1,NCOA3,NCOA6,PHF20,PLAGL2,PTPN1,RALGAPB, RBL1,RPRD1B,STAU1,STK4,TTPAL,VAPB,ZNFX1	AAK1,SOWAHC,B4GALT1,B4GALT5,CEACAM5,CTNNA1,DSC2, FLNB,GNA13,GNAQ,GPD2,GTPBP1,KIF16B,MICAL2, OSBPL11,OXSR1,PDLIM5,RAPGEF2,SMCHD1,TCF7L2,TMEM65

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 B4GALT5

There's no related Drug.

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Cross referenced IDs for B4GALT5

* 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