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 SDC2

Basic gene info.	Gene symbol	SDC2
	Gene name	syndecan 2
	Synonyms	CD362\|HSPG\|HSPG1\|SYND2
	Cytomap	UCSC genome browser: 8q22-q23
	Genomic location	chr8 :97505881-97624037
	Type of gene	protein-coding
	RefGenes	NM_002998.3,
	Ensembl id	ENSG00000169439
	Description	cell surface-associated heparan sulfate proteoglycan 1fibroglycanheparan sulfate proteoglycan 1, cell surface-associatedheparan sulfate proteoglycan core proteinsyndecan proteoglycan 2syndecan-2
	Modification date	20141222
dbXrefs	MIM : 142460
	HGNC : HGNC
	Ensembl : ENSG00000169439
	HPRD : 00803
	Vega : OTTHUMG00000164689
Protein	UniProt: P34741 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SDC2
	BioGPS: 6383
	Gene Expression Atlas: ENSG00000169439
	The Human Protein Atlas: ENSG00000169439
Pathway	NCI Pathway Interaction Database: SDC2
	KEGG: SDC2
	REACTOME: SDC2
	ConsensusPathDB
	Pathway Commons: SDC2
Metabolism	MetaCyc: SDC2
	HUMANCyc: SDC2
Regulation	Ensembl's Regulation: ENSG00000169439
	miRBase: chr8 :97,505,881-97,624,037
	TargetScan: NM_002998
	cisRED: ENSG00000169439
Context	iHOP: SDC2
	cancer metabolism search in PubMed: SDC2
	UCL Cancer Institute: SDC2
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for SDC2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SDC2
	Familial Cancer Database: SDC2

* 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	142460; gene.
Orphanet
Disease	KEGG Disease: SDC2
	MedGen: SDC2 (Human Medical Genetics with Condition)
	ClinVar: SDC2
Phenotype	MGI: SDC2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SDC2

Mutations for SDC2

* 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

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	SDC2	chr8	97551434	97551454		chr15	90298092	90298112
ovary	SDC2	chr8	97622863	97622883		chr8	97625244	97625264
pancreas	SDC2	chr8	97508147	97508167	SDC2	chr8	97508510	97508530

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 SDC2 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
BE762893	SDC2	85	159	8	97614682	97614756	SDC2	154	423	8	97614682	97621671
AA632874	SDC2	1	168	8	97622699	97622867	SDC2	165	302	8	97622639	97622776
AI366039	FRZB	1	85	2	183699292	183699376	SDC2	68	455	8	97622338	97622731

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=30)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr8:97620628-97620628	p.A124A	3
chr8:97614661-97614661	p.S71T	3
chr8:97620629-97620629	p.E125K	3
chr8:97605800-97605800	p.Y51Y	3
chr8:97605717-97605717	p.L24M	2
chr8:97605773-97605773	p.G42G	2
chr8:97614730-97614730	p.Q94E	2
chr8:97621679-97621679	p.R170H	2
chr8:97614633-97614633	p.E61D	1
chr8:97621685-97621685	p.R172T	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=3

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		2	1	9	1		2					2	4	2		1	1	4		4
# mutation		2	1	9	1		2					2	4	2		1	1	3		4
nonsynonymous SNV		2	1	6	1		2					1	4	2			1	2		1
synonymous SNV				3								1				1		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
chr8:97620628	p.A124A	3
chr8:97620629	p.E125K	2
chr8:97614732	p.V43G	1
chr8:97621642	p.T132T	1
chr8:97605770	p.D47Y	1
chr8:97620595	p.R142L	1
chr8:97621679	p.D48E	1
chr8:97605775	p.V145F	1
chr8:97620598	p.I155T	1
chr8:97621688	p.Y51Y	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 SDC2 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 SDC2

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,BOP1,CYP26B1,EVA1A,FAM20C,KRT34,LEPRE1, LOXL2,MRC2,NKX3-2,NOTUM,OLFML2B,CPQ,PLOD1, PTDSS1,PTPRD,RGR,SDC2,SLC24A4,SNAI2,TSPYL5	AIDA,ANTXR2,LINC00341,CNRIP1,EBF3,FYN,GTF2E2, LOC339524,NEGR1,PCOLCE2,PMP22,PRELP,RHOA,RNF130, SDC2,SDCBP,SLC9A9,SNX3,SNX9,STXBP6,VIM

ANTXR1,CTSK,DCN,DKK3,EFEMP2,FAM26E,FSTL1, GLT8D2,IGFBP7,LGALS1,LUM,PDGFRB,RAB31,RAB34, SDC2,SGIP1,SPARC,SYDE1,TCF4,THY1,VIM	CAB39L,CAV2,CLIP4,FEZ1,FGF2,HDGFRP3,LOC644538, LRCH2,PABPC5,PLN,PTBP2,RERG,RNF180,SDC2, SGCE,SPARCL1,SPG20,STX2,TCEAL4,TRPC1,ZNF25

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 SDC2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA35589; -.
Organism-specific databases	CTD	6383; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00860	syndecan 2	approved	Prednisolone

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Cross referenced IDs for SDC2

* 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