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 BSG

Basic gene info.	Gene symbol	BSG
	Gene name	basigin (Ok blood group)
	Synonyms	5F7\|CD147\|EMMPRIN\|M6\|OK\|TCSF
	Cytomap	UCSC genome browser: 19p13.3
	Genomic location	chr19 :572453-583493
	Type of gene	protein-coding
	RefGenes	NM_001728.3, NM_198589.2,NM_198590.2,NM_198591.2,
	Ensembl id	ENSG00000172270
	Description	CD147 antigenOK blood group antigenbasigincollagenase stimulatory factorextracellular matrix metalloproteinase inducerleukocyte activation antigen M6tumor cell-derived collagenase stimulatory factor
	Modification date	20141222
dbXrefs	MIM : 109480
	HGNC : HGNC
	Ensembl : ENSG00000172270
	HPRD : 00176
	Vega : OTTHUMG00000177718
Protein	UniProt: P35613 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_BSG
	BioGPS: 682
	Gene Expression Atlas: ENSG00000172270
	The Human Protein Atlas: ENSG00000172270
Pathway	NCI Pathway Interaction Database: BSG
	KEGG: BSG
	REACTOME: BSG
	ConsensusPathDB
	Pathway Commons: BSG
Metabolism	MetaCyc: BSG
	HUMANCyc: BSG
Regulation	Ensembl's Regulation: ENSG00000172270
	miRBase: chr19 :572,453-583,493
	TargetScan: NM_001728
	cisRED: ENSG00000172270
Context	iHOP: BSG
	cancer metabolism search in PubMed: BSG
	UCL Cancer Institute: BSG
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of BSG in cancer cell metabolism	1. Marchiq I, Le Floch R, Roux D, Simon MP, Pouyssegur J (2015) Genetic disruption of lactate/H+ symporters (MCTs) and their subunit CD147/BASIGIN sensitizes glycolytic tumor cells to phenformin. Cancer Res 75: 171-180. doi: 10.1158/0008-5472.CAN-14-2260. go to article 2. Granja S, Marchiq I, Le Floch R, Moura CS, Baltazar F, et al. (2015) Disruption of BASIGIN decreases lactic acid export and sensitizes non-small cell lung cancer to biguanides independently of the LKB1 status. Oncotarget 6: 6708-6721. pmid: 4466644. go to article

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

Cancer Description
Cancer	CGAP: BSG
	Familial Cancer Database: BSG

* 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_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE REACTOME_PYRUVATE_METABOLISM

Others
OMIM	109480; gene. 111380; phenotype.
Orphanet
Disease	KEGG Disease: BSG
	MedGen: BSG (Human Medical Genetics with Condition)
	ClinVar: BSG
Phenotype	MGI: BSG (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: BSG

Mutations for BSG

* 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 BSG 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
BP379102	ACTB	1	419	7	5568820	5570232	BSG	419	568	19	580716	581397
DA210402	BSG	1	328	19	572596	580441	SLC1A3	329	555	5	36686310	36686536
XX000018	BSG	1	83	19	580706	580787	NFIX	76	151	19	13135833	13135908
BG491011	BSG	15	107	19	580384	580660	BSG	104	925	19	580655	583075
BF762451	BSG	8	78	19	583357	583428	FBXL19	76	242	16	30935819	30935985
AA535665	BSG	10	210	19	583091	583290	BSG	206	351	19	583296	583441
BM706468	BSG	14	84	19	581372	581442	BSG	80	484	19	581435	582903
AA570609	BSG	8	208	19	583091	583290	BSG	204	348	19	583296	583441
BG333059	BSG	15	107	19	580384	580660	BSG	104	821	19	580655	582966
AW973156	BSG	114	313	19	583091	583290	BSG	309	454	19	583296	583441
CA422684	BSG	18	565	19	582940	583487	BSG	550	647	19	582859	583230
BF819563	BSG	9	293	19	579499	580692	ZKSCAN1	288	572	7	99613281	99621265

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=22)	Stat. for Synonymous SNVs (# total SNVs=11)

Stat. for Deletions (# total SNVs=2)	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
chr19:579603-579603	p.G175fs*4	2
chr19:579609-579609	p.G175G	2
chr19:579627-579627	p.D181D	2
chr19:580426-580426	p.P207L	2
chr19:580665-580665	p.A225A	2
chr19:579577-579577	p.E165K	2
chr19:581455-581455	p.Q311H	2
chr19:580714-580714	p.C242G	1
chr19:581471-581471	p.R317C	1
chr19:577922-577922	p.D72D	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			2	1				1		1			3	1		4
# mutation	1	1		3			2	1				1		1			4	1		4
nonsynonymous SNV	1	1						1				1		1			2	1		2
synonymous SNV				3			2										2			2

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
chr19:580426	p.P27L,BSG	2
chr19:580779	p.A47T,BSG	1
chr19:578038	p.H53R,BSG	1
chr19:581345	p.G59G,BSG	1
chr19:579570	p.P41L,BSG	1
chr19:581411	p.M59V,BSG	1
chr19:579571	p.S66S,BSG	1
chr19:581444	p.K77N,BSG	1
chr19:579590	p.D83D,BSG	1
chr19:581473	p.F95V,BSG	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 BSG 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 BSG

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


AES,ATP5D,BSG,R3HDM4,C19orf24,C9orf16,CDC34, COPE,COX4I1,FKBP2,GPX4,LSM7,POLR2E,RNF126, RPS15,SERF2,SF3A2,SGTA,SIRT6,UQCR11,ZNHIT1	BSG,C20orf27,CNPPD1,DCXR,EIF4EBP1,ETFB,FPGS, GCDH,GCHFR,HSD17B10,MPST,MRPL53,PCYT2,PLEKHJ1, PMM1,POLR2E,PQLC1,PSMA7,SLC2A4RG,TP53I13,TSPO

ALDOA,ATG4D,ATP5D,BSG,C19orf10,C19orf24,CDC34, COPE,COX8A,ECHS1,ELOF1,FKBP8,GAPDH,INO80C, NCLN,NDUFS7,POLR2E,PSMD9,RNF126,SGTA,WIBG	ANXA11,ARF3,BSG,CNPPD1,C4orf48,CA4,CAPN2, CEACAM7,RHOV___CHP1,CLIP2,FUT3,GBA,LITAF,MFSD11, MGLL,PEX26,PKIB,PPARG,RUNDC1,TMEM171,TPRN

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 BSG

There's no related Drug.

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Cross referenced IDs for BSG

* 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