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 BGN

Basic gene info.	Gene symbol	BGN
	Gene name	biglycan
	Synonyms	DSPG1\|PG-S1\|PGI\|SLRR1A
	Cytomap	UCSC genome browser: Xq28
	Genomic location	chrX :152760346-152775004
	Type of gene	protein-coding
	RefGenes	NM_001711.4,
	Ensembl id	ENSG00000269168
	Description	biglycan proteoglycanbone/cartilage proteoglycan Ibone/cartilage proteoglycan-Idermatan sulphate proteoglycan Ismall leucine-rich protein 1A
	Modification date	20141222
dbXrefs	MIM : 301870
	HGNC : HGNC
	Ensembl : ENSG00000182492
	HPRD : 02359
	Vega : OTTHUMG00000024205
Protein	UniProt: P21810 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_BGN
	BioGPS: 633
	Gene Expression Atlas: ENSG00000269168
	The Human Protein Atlas: ENSG00000269168
Pathway	NCI Pathway Interaction Database: BGN
	KEGG: BGN
	REACTOME: BGN
	ConsensusPathDB
	Pathway Commons: BGN
Metabolism	MetaCyc: BGN
	HUMANCyc: BGN
Regulation	Ensembl's Regulation: ENSG00000269168
	miRBase: chrX :152,760,346-152,775,004
	TargetScan: NM_001711
	cisRED: ENSG00000269168
Context	iHOP: BGN
	cancer metabolism search in PubMed: BGN
	UCL Cancer Institute: BGN
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: BGN
	Familial Cancer Database: BGN

* 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	301870; gene.
Orphanet
Disease	KEGG Disease: BGN
	MedGen: BGN (Human Medical Genetics with Condition)
	ClinVar: BGN
Phenotype	MGI: BGN (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: BGN

Mutations for BGN

* 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 BGN 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
BF871520	ADCY9	1	68	16	4099044	4099111	BGN	59	160	X	152774633	152774735
AW613805	NFKBIB	1	303	19	39398899	39399204	BGN	297	429	X	152774168	152774300
BU617112	BGN	19	553	X	152774480	152775004	NCL	552	696	2	232321418	232321799
AX746813	TSHZ1	1	2984	18	72922752	72999940	BGN	2978	3370	X	152774612	152775004
ES309565	LRRFIP2	24	103	3	37190498	37216077	BGN	100	368	X	152774210	152774478
BF437005	BGN	5	201	X	152774808	152775004	ADAMTS1	197	540	21	28209980	28210323
BF930412	SLC25A26	9	287	3	66436618	66436898	BGN	285	350	X	152771406	152771471
DB313457	BGN	1	393	X	152774612	152775004	TSHZ1	387	535	18	72999792	72999940
BF985568	SUPT6H	30	195	17	27027444	27028038	BGN	188	351	X	152773754	152773917
BQ183196	BGN	19	539	X	152774467	152775004	PPP1R12B	529	556	1	202469358	202469394
AW340724	BGN	1	251	X	152774754	152775004	FLNC	248	520	7	128478739	128480617

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=33)	Stat. for Synonymous SNVs (# total SNVs=17)

Stat. for Deletions (# total SNVs=3)	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
chr23:152772344-152772344	p.E245K	3
chr23:152771381-152771381	p.R138W	2
chr23:152773795-152773795	p.N333N	2
chr23:152773816-152773816	p.N340N	2
chr23:152772362-152772362	p.R251C	2
chr23:152771478-152771478	p.R170H	2
chr23:152771484-152771484	p.R172H	2
chr23:152773750-152773750	p.N318N	1
chr23:152770766-152770766	p.S103S	1
chr23:152771995-152771995	p.G192R	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	2		6					1			7	1				3	3	1	8
# mutation	2	2		6					1			9	1				3	3	1	9
nonsynonymous SNV	1	1		6								6	1				3	2	1	6
synonymous SNV	1	1							1			3						1		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
chrX:152772037	p.R170H	2
chrX:152772344	p.D206N	2
chrX:152771478	p.E245K	2
chrX:152771484	p.P277P	1
chrX:152773715	p.R72R	1
chrX:152770152	p.G295A	1
chrX:152771995	p.N100D	1
chrX:152773722	p.L307V	1
chrX:152770154	p.S103S	1
chrX:152772036	p.S309Y	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 BGN 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 BGN

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


BGN,BMP1,COL1A1,COL5A1,COL6A1,COL6A2,COPZ2, EFEMP2,ENPEP,LEPRE1,LOXL2,MRC2,MXRA8,OLFML2B, P4HA3,PCDHGC3,SERPINH1,SNAI2,SPARC,TGFB1I1,THY1	AEBP1,BGN,C1QTNF2,CALHM2,ELN,F10,FBLN1, FEZ1,GDF10,IGFBP7,INMT,MAN1C1,MSX1,NRGN, OLFML2B,P4HA3,PODN,PTGIR,SSC5D,TBXA2R,TNFAIP8L3

AEBP1,BGN,CERCAM,CLEC11A,COL6A2,CTHRC1,EFEMP2, GGT5,MRC2,MXRA8,NOX4,OLFML2B,PDGFRB,PRRX1, RAB31,SCARF2,SERPINF1,SPARC,THBS2,VCAN,VIM	ADAMTS5,AEBP1,BGN,C3,CCDC3,CHRD,CPT1C, DCLK1,EBF1,EDNRA,FAM198A,LRRC32,MFAP2,MFGE8, NOTCH3,NRIP2,PDGFRB,SPON2,THSD7A,VCAN,WTIP

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 BGN

There's no related Drug.

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Cross referenced IDs for BGN

* 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