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 SDC3

Basic gene info.	Gene symbol	SDC3
	Gene name	syndecan 3
	Synonyms	SDCN\|SYND3
	Cytomap	UCSC genome browser: 1p35.2
	Genomic location	chr1 :31342312-31381480
	Type of gene	protein-coding
	RefGenes	NM_014654.3,
	Ensembl id	ENSG00000162512
	Description	N-syndecansyndecan neural typesyndecan proteoglycan 3syndecan-3
	Modification date	20141207
dbXrefs	MIM : 186357
	HGNC : HGNC
	HPRD : 01719
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SDC3
	BioGPS: 9672
	Gene Expression Atlas: ENSG00000162512
	The Human Protein Atlas: ENSG00000162512
Pathway	NCI Pathway Interaction Database: SDC3
	KEGG: SDC3
	REACTOME: SDC3
	ConsensusPathDB
	Pathway Commons: SDC3
Metabolism	MetaCyc: SDC3
	HUMANCyc: SDC3
Regulation	Ensembl's Regulation: ENSG00000162512
	miRBase: chr1 :31,342,312-31,381,480
	TargetScan: NM_014654
	cisRED: ENSG00000162512
Context	iHOP: SDC3
	cancer metabolism search in PubMed: SDC3
	UCL Cancer Institute: SDC3
Assigned class in ccmGDB	C

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Phenotypic Information for SDC3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SDC3
	Familial Cancer Database: SDC3

* 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
Orphanet
Disease	KEGG Disease: SDC3
	MedGen: SDC3 (Human Medical Genetics with Condition)
	ClinVar: SDC3
Phenotype	MGI: SDC3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SDC3

Mutations for SDC3

* 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

There's no inter-chromosomal structural variation.

- 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	SDC3	chr1	31363439	31363459	SDC3	chr1	31365464	31365484
ovary	SDC3	chr1	31364415	31364435	SDC3	chr1	31365778	31365798
ovary	SDC3	chr1	31366737	31366757		chr1	81591224	81591244
ovary	SDC3	chr1	31376217	31376237	SDC3	chr1	31377405	31377425

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 SDC3 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
DA180215	MAP7D2	1	125	X	20134892	20135016	SDC3	126	569	1	31345191	31345634
BF935530	LAS1L	5	127	X	64739134	64739256	SDC3	113	294	1	31345192	31345374
AI148370	SIRT6	2	67	19	4174106	4174171	SDC3	64	484	1	31346053	31346473
AW166100	YWHAH	18	412	22	32353196	32353590	SDC3	407	502	1	31378064	31378159
DB262991	MYH11	1	351	16	15931864	15950885	SDC3	345	598	1	31343631	31349869
BM991776	SDC3	18	367	1	31342313	31342662	SDC3	360	651	1	31345788	31346079
BE925576	CD97	1	192	19	14518023	14518974	SDC3	186	304	1	31344486	31344859
DA194626	LOC100507412	1	151	?	112030	112180	SDC3	152	543	1	31344753	31345143

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=25)	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
chr1:31349607-31349607	p.T221M	2
chr1:31346080-31346080	p.K436R	2
chr1:31346158-31346158	p.R410H	2
chr1:31350004-31350004	p.Q89*	2
chr1:31347355-31347355	p.F317F	2
chr1:31349583-31349583	p.A229V	1
chr1:31349839-31349839	p.V144M	1
chr1:31346183-31346183	p.F402V	1
chr1:31347401-31347401	p.R302L	1
chr1:31351496-31351496	p.D77G	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			1	2	1			7	4	1	3
# mutation	2	1		8					1			1	2	1			7	4	1	3
nonsynonymous SNV	1			5					1			1	2				4	4	1	1
synonymous SNV	1	1		3										1			3			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
chr1:31349607	p.T221M	3
chr1:31346158	p.R410H	2
chr1:31351554	p.F317F	1
chr1:31347255	p.V107L	1
chr1:31349713	p.R302L	1
chr1:31351564	p.A106A	1
chr1:31347287	p.F297F	1
chr1:31349783	p.S84L	1
chr1:31351566	p.T296T	1
chr1:31347355	p.P58A	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 SDC3 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 SDC3

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


AHDC1,CDH23,CLIP2,DAB2IP,GLG1,H6PD,KCND1, MAP3K6,NGFR,PDGFA,PHC2,PLEKHA4,PLEKHM2,PPM1F, S1PR2,SDC3,SLC12A4,SLC22A11,ST3GAL2,SUN2,ZNF319	AGRN,ATP13A1,EMC10,CHPF2,FBXL19,FRMD8,GPSM1, ICAM5,KCNIP3,LRRN2,NACC1,NCDN,NGFR,NKD2, NRG2,PLEKHA4,QSOX1,SDC3,SRC,TRAF7,U2AF2

ADAMTSL4,AHDC1,AOC3,BOC,CLU,DPYSL3,FLNA, KANK2,LRRN4CL,PALM,PDLIM7,PGR,PNMAL2,PRKD1, PRX,SCN2B,SDC3,TNFSF12,TNS1,TUBB6,ZBTB47	C20orf166-AS1,CACNA1C,CCBE1,DYSF,EMILIN1,FBXL22,GNAO1, GRIK5,KANK2,KCNMA1,LOC728264,MEIS2,MRVI1,NRG2, NRP2,TENM3___TENM1,RGAG4,SDC3,SPEG,TRPS1,TSHZ3

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 SDC3

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB00987	syndecan 3	approved; investigational	Cytarabine

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Cross referenced IDs for SDC3

* 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