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 GPC3

Basic gene info.	Gene symbol	GPC3
	Gene name	glypican 3
	Synonyms	DGSX\|GTR2-2\|MXR7\|OCI-5\|SDYS\|SGB\|SGBS\|SGBS1
	Cytomap	UCSC genome browser: Xq26.1
	Genomic location	chrX :132669775-133119673
	Type of gene	protein-coding
	RefGenes	NM_001164617.1, NM_001164618.1,NM_001164619.1,NM_004484.3,
	Ensembl id	ENSG00000147257
	Description	glypican proteoglycan 3glypican-3heparan sulphate proteoglycanintestinal protein OCI-5secreted glypican-3
	Modification date	20141222
dbXrefs	MIM : 300037
	HGNC : HGNC
	Ensembl : ENSG00000147257
	HPRD : 02074
	Vega : OTTHUMG00000022448
Protein	UniProt: P51654 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GPC3
	BioGPS: 2719
	Gene Expression Atlas: ENSG00000147257
	The Human Protein Atlas: ENSG00000147257
Pathway	NCI Pathway Interaction Database: GPC3
	KEGG: GPC3
	REACTOME: GPC3
	ConsensusPathDB
	Pathway Commons: GPC3
Metabolism	MetaCyc: GPC3
	HUMANCyc: GPC3
Regulation	Ensembl's Regulation: ENSG00000147257
	miRBase: chrX :132,669,775-133,119,673
	TargetScan: NM_001164617
	cisRED: ENSG00000147257
Context	iHOP: GPC3
	cancer metabolism search in PubMed: GPC3
	UCL Cancer Institute: GPC3
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for GPC3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GPC3
	Familial Cancer Database: GPC3

* 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	300037; gene. 312870; phenotype.
Orphanet	373; Simpson-Golabi-Behmel syndrome.
Disease	KEGG Disease: GPC3
	MedGen: GPC3 (Human Medical Genetics with Condition)
	ClinVar: GPC3
Phenotype	MGI: GPC3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GPC3

Mutations for GPC3

* 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 GPC3 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
BI905820	LRPPRC	1	205	2	44209547	44223116	GPC3	204	390	X	132669773	132669958
R64084	TNKS	1	317	8	9636790	9637105	GPC3	308	369	X	132669781	132669842
AI468457	GPC3	4	202	X	132669773	132669971	PDGFRA	196	348	4	55163307	55163459
BG153241	CD74	56	121	5	149781425	149781490	GPC3	116	135	X	132846201	132846220
BC036707	TTL	1	328	2	113260721	113289983	GPC3	317	344	X	132690723	132690986

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=61)	Stat. for Synonymous SNVs (# total SNVs=21)

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
chr23:132670253-132670253	p.E548K	2
chr23:132887945-132887945	p.R199Q	2
chr23:132730611-132730611	p.S477F	2
chr23:132887946-132887946	p.R199*	2
chr23:132887676-132887676	p.V289L	2
chr23:132887698-132887698	p.V281V	2
chr23:133119341-133119341	p.Q46*	2
chr23:132888051-132888051	p.D164H	2
chr23:132887753-132887753	p.S263F	1
chr23:133087081-133087081	p.F111L	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		10	1		2		2			8	4	1			9	1		10
# mutation	1	1		10	1		2		2			8	4	1			9	1		14
nonsynonymous SNV	1	1		9	1				2			4	3	1			7	1		9
synonymous SNV				1			2					4	1				2			5

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:132888183	p.R66C,GPC3	2
chrX:132887945	p.R145Q,GPC3	2
chrX:133119363	p.C211W,GPC3	1
chrX:132833946	p.K69N,GPC3	1
chrX:132887866	p.G454G,GPC3	1
chrX:132888160	p.S209F,GPC3	1
chrX:132730510	p.I452F,GPC3	1
chrX:133119399	p.T188T,GPC3	1
chrX:132833959	p.Q112P,GPC3	1
chrX:132887885	p.D431N,GPC3	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 GPC3 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 GPC3

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


AFP,C9orf135,CEACAM16,CHRNA6,CNTN4,CRH,CXorf30, CHDC2,DLX1,DLX2,ENOX1,GHRH,GPC3,HS6ST2, C7orf62,OPTC,PART1,PLA2G2C,PRSS21,RASSF6,TAF1L	AIDA,ANGPTL2,CELF2,CNRIP1,CRTAP,EBF3,FBLN5, GPC3,HOXC8,HSD17B11,LAMC1,MXRA7,NEGR1,NPR2, PCOLCE2,PID1,PMP22,RNASE4,TIMP3,SLC35G2,VIM

ANKRD53,BSX,CADM3,CFC1B,EBF3,GABRG2,GFRA2, GPC3,GRIA1,KCNS2,KIAA1045,MC4R,NR2E1,OR7E5P, PM20D1,PYDC2,RSPO1,SLC17A7,TAC3,TNXB,TSHR	ANKRD1,ACTRT3,LINC00323,C2orf69,PXDC1,C8orf22,COLEC11, DRD5,FAM35A,FAM35DP,FAM35BP,FGF5,FMO3,GPC3, HAR1B,ITGB8,LOC645166,LOC654342,POPDC3,SLC14A2,TNFRSF12A

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 GPC3

There's no related Drug.

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Cross referenced IDs for GPC3

* 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