Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolBGN
Gene namebiglycan
SynonymsDSPG1|PG-S1|PGI|SLRR1A
CytomapUCSC genome browser: Xq28
Genomic locationchrX :152760346-152775004
Type of geneprotein-coding
RefGenesNM_001711.4,
Ensembl idENSG00000269168
Descriptionbiglycan proteoglycanbone/cartilage proteoglycan Ibone/cartilage proteoglycan-Idermatan sulphate proteoglycan Ismall leucine-rich protein 1A
Modification date20141222
dbXrefs MIM : 301870
HGNC : HGNC
Ensembl : ENSG00000182492
HPRD : 02359
Vega : OTTHUMG00000024205
ProteinUniProt: P21810
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_BGN
BioGPS: 633
Gene Expression Atlas: ENSG00000269168
The Human Protein Atlas: ENSG00000269168
PathwayNCI Pathway Interaction Database: BGN
KEGG: BGN
REACTOME: BGN
ConsensusPathDB
Pathway Commons: BGN
MetabolismMetaCyc: BGN
HUMANCyc: BGN
RegulationEnsembl's Regulation: ENSG00000269168
miRBase: chrX :152,760,346-152,775,004
TargetScan: NM_001711
cisRED: ENSG00000269168
ContextiHOP: BGN
cancer metabolism search in PubMed: BGN
UCL Cancer Institute: BGN
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for BGN(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 301870; gene.
Orphanet
DiseaseKEGG Disease: BGN
MedGen: BGN (Human Medical Genetics with Condition)
ClinVar: BGN
PhenotypeMGI: BGN (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows BGN related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF871520ADCY91681640990444099111BGN59160X152774633152774735
AW613805NFKBIB1303193939889939399204BGN297429X152774168152774300
BU617112BGN19553X152774480152775004NCL5526962232321418232321799
AX746813TSHZ112984187292275272999940BGN29783370X152774612152775004
ES309565LRRFIP22410333719049837216077BGN100368X152774210152774478
BF437005BGN5201X152774808152775004ADAMTS1197540212820998028210323
BF930412SLC25A26928736643661866436898BGN285350X152771406152771471
DB313457BGN1393X152774612152775004TSHZ1387535187299979272999940
BF985568SUPT6H30195172702744427028038BGN188351X152773754152773917
BQ183196BGN19539X152774467152775004PPP1R12B5295561202469358202469394
AW340724BGN1251X152774754152775004FLNC2485207128478739128480617

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr23:152772344-152772344p.E245K3
chr23:152772362-152772362p.R251C2
chr23:152771478-152771478p.R170H2
chr23:152771484-152771484p.R172H2
chr23:152771381-152771381p.R138W2
chr23:152773795-152773795p.N333N2
chr23:152773816-152773816p.N340N2
chr23:152771471-152771471p.D168N1
chr23:152773819-152773819p.P341P1
chr23:152770131-152770131p.S14S1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample12 6    1  71   3318
# mutation22 6    1  91   3319
nonsynonymous SNV11 6       61   3216
synonymous SNV11      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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chrX:152771478p.R170H2
chrX:152772037p.D206N2
chrX:152772344p.E245K2
chrX:152772381p.N100D1
chrX:152770099p.G295A1
chrX:152773837p.S103S1
chrX:152771346p.L307V1
chrX:152772530p.I126N1
chrX:152770100p.S309Y1
chrX:152771381p.R138W1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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



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