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 HSPG2

Basic gene info.	Gene symbol	HSPG2
	Gene name	heparan sulfate proteoglycan 2
	Synonyms	HSPG\|PLC\|PRCAN\|SJA\|SJS\|SJS1
	Cytomap	UCSC genome browser: 1p36.1-p34
	Genomic location	chr1 :22148736-22263750
	Type of gene	protein-coding
	RefGenes	NM_001291860.1, NM_005529.6,
	Ensembl id	ENSG00000142798
	Description	basement membrane-specific heparan sulfate proteoglycan core proteinendorepellin (domain V region)perlecan proteoglycan
	Modification date	20141207
dbXrefs	MIM : 142461
	HGNC : HGNC
	Ensembl : ENSG00000142798
	HPRD : 00804
	Vega : OTTHUMG00000002674
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HSPG2
	BioGPS: 3339
	Gene Expression Atlas: ENSG00000142798
	The Human Protein Atlas: ENSG00000142798
Pathway	NCI Pathway Interaction Database: HSPG2
	KEGG: HSPG2
	REACTOME: HSPG2
	ConsensusPathDB
	Pathway Commons: HSPG2
Metabolism	MetaCyc: HSPG2
	HUMANCyc: HSPG2
Regulation	Ensembl's Regulation: ENSG00000142798
	miRBase: chr1 :22,148,736-22,263,750
	TargetScan: NM_001291860
	cisRED: ENSG00000142798
Context	iHOP: HSPG2
	cancer metabolism search in PubMed: HSPG2
	UCL Cancer Institute: HSPG2
Assigned class in ccmGDB	C

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Phenotypic Information for HSPG2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: HSPG2
	Familial Cancer Database: HSPG2

* 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_LIPIDS_AND_LIPOPROTEINS REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_LIPOPROTEIN_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: HSPG2
	MedGen: HSPG2 (Human Medical Genetics with Condition)
	ClinVar: HSPG2
Phenotype	MGI: HSPG2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: HSPG2

Mutations for HSPG2

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_b

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HSPG2 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
CD676182	HSPG2	1	208	1	22212789	22212997	MOV10	204	625	1	113242372	113243187
AW604468	HSPG2	25	340	1	22241959	22242274	HSPG2	337	650	1	22206711	22207023
AW855179	EIF3B	32	348	7	2405457	2405778	HSPG2	336	416	1	22178575	22178654
BE927253	HSPG2	20	339	1	22206705	22207023	HSPG2	336	646	1	22241964	22242274

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=11

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=244)	Stat. for Synonymous SNVs (# total SNVs=105)

Stat. for Deletions (# total SNVs=5)	Stat. for Insertions (# total SNVs=1)

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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
chr1:22149935-22149935	p.S4350S	11
chr1:22191454-22191454	p.A1503V	7
chr1:22176683-22176683	p.L2433V	4
chr1:22222458-22222458	p.D67D	3
chr1:22154901-22154901	p.R4086W	3
chr1:22214000-22214000	p.A291T	3
chr1:22165987-22165987	p.H3256Y	3
chr1:22174253-22174253	p.V2652M	3
chr1:22182404-22182404	p.A1859A	3
chr1:22214554-22214554	p.Q194*	3

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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	9	8	3	23	7		13	2	10	2	2	28	16	12		5	35	29		25
# mutation	13	8	3	24	7		14	2	10	2	2	32	16	12		5	44	36		38
nonsynonymous SNV	7	6	1	15	7		9	2	9	1	1	25	11	9		4	25	23		25
synonymous SNV	6	2	2	9			5		1	1	1	7	5	3		1	19	13		13

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
chr1:22168062	p.F912F,HSPG2	2
chr1:22174305	p.A3101T,HSPG2	2
chr1:22157780	p.P1534P,HSPG2	2
chr1:22186712	p.S709S,HSPG2	2
chr1:22206927	p.N1812N,HSPG2	2
chr1:22183650	p.R2698L,HSPG2	2
chr1:22173921	p.I3831I,HSPG2	2
chr1:22214000	p.R4087W,HSPG2	2
chr1:22203098	p.V2653M,HSPG2	2
chr1:22191363	p.I2635I,HSPG2	2

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 HSPG2 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 HSPG2

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


BCL6B,VSTM4,CD93,CDH5,COL15A1,GPR124,HEG1, HSPG2,KIAA1462,LAMA4,LRP1,LRRC32,NOTCH4,PDGFRB, PHLDB1,PODN,RHOJ,STARD8,SYNPO,TIE1,TNS1	SYNE3,FAM212B,CDC42BPB,COL4A1,COL4A2,DAAM2,DOCK6, EHD2,HSPG2,ITGA7,KANK2,CTIF,LRP1,MCAM, MPRIP,MYO1C,PLIN4,PTPRS,PXDN,TFE3,TLN1

ARHGEF17,CD93,COL4A2,COL8A1,DDR2,EHD2,EMILIN1, ENG,FBN1,FLT4,GPR124,HEG1,HSPG2,IL1R1, LAMA4,LAMC1,MMRN2,PXDN,STARD8,TIE1,VWF	AHDC1,AHNAK2,AR,CNTNAP1,COL15A1,COL4A1,COL4A2, DCHS1,FLNA,GLI2,HSPG2,IGSF9B,LDLRAD2,MAP1A, MICALL1,NACC2,NID1,PXDN,SETBP1,TLN1,VCL

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 HSPG2

There's no related Drug.

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Cross referenced IDs for HSPG2

* 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