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 DCN

Basic gene info.	Gene symbol	DCN
	Gene name	decorin
	Synonyms	CSCD\|DSPG2\|PG40\|PGII\|PGS2\|SLRR1B
	Cytomap	UCSC genome browser: 12q21.33
	Genomic location	chr12 :91539034-91572329
	Type of gene	protein-coding
	RefGenes	NM_001920.3, NM_133503.2,NM_133504.2,NM_133505.2,NM_133506.2, NM_133507.2,
	Ensembl id	ENSG00000011465
	Description	PG-S2bone proteoglycan IIdecorin proteoglycandermatan sulphate proteoglycans IIproteoglycan core proteinsmall leucine-rich protein 1B
	Modification date	20141219
dbXrefs	MIM : 125255
	HGNC : HGNC
	Ensembl : ENSG00000011465
	HPRD : 00501
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DCN
	BioGPS: 1634
	Gene Expression Atlas: ENSG00000011465
	The Human Protein Atlas: ENSG00000011465
Pathway	NCI Pathway Interaction Database: DCN
	KEGG: DCN
	REACTOME: DCN
	ConsensusPathDB
	Pathway Commons: DCN
Metabolism	MetaCyc: DCN
	HUMANCyc: DCN
Regulation	Ensembl's Regulation: ENSG00000011465
	miRBase: chr12 :91,539,034-91,572,329
	TargetScan: NM_001920
	cisRED: ENSG00000011465
Context	iHOP: DCN
	cancer metabolism search in PubMed: DCN
	UCL Cancer Institute: DCN
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: DCN
	Familial Cancer Database: DCN

* 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: DCN
	MedGen: DCN (Human Medical Genetics with Condition)
	ClinVar: DCN
Phenotype	MGI: DCN (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: DCN

Mutations for DCN

* 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 DCN 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
BG927599	NECAB3	77	122	20	32261363	32261408	DCN	116	475	12	91550912	91558472
M14219	DCN	26	1292	12	91539704	91576454	SSR1	1292	1778	6	7288053	7288539
BM720639	DCN	17	531	12	91552132	91572364	ZNF263	526	687	16	3341286	3341448
CV569111	DCN	1	73	12	91572239	91572312	CRIPAK	73	603	4	1387247	1387781
BP289909	IGFBP4	1	395	17	38613421	38613815	DCN	395	568	12	91572307	91573256
DR979449	CD36	1	103	7	80289884	80289988	DCN	98	148	12	91539474	91539530
AI752586	DCN	8	202	12	91572318	91576581	DCN	190	386	12	91572117	91572313
AA736813	DCN	14	34	12	91571449	91571469	MAGI1	31	56	3	65352758	65352801

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=47)	Stat. for Synonymous SNVs (# total SNVs=14)

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
chr12:91558423-91558423	p.E95K	6
chr12:91540003-91540003	p.I304I	3
chr12:91552212-91552212	p.R133R	3
chr12:91546948-91546948	p.T224M	3
chr12:91539883-91539883	p.F344L	3
chr12:91550854-91550854	p.Q217R	2
chr12:91539849-91539849	p.G356R	2
chr12:91552214-91552214	p.R133*	2
chr12:91539867-91539867	p.R350C	2
chr12:91545456-91545456	p.G287E	2

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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			1	11			1		5			6	3	1			13	6		10
# mutation			1	8			1		5			6	3	1			14	6		9
nonsynonymous SNV				7			1		5			4	1				11	5		7
synonymous SNV			1	1								2	2	1			3	1		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
chr12:91558423	p.T77M,DCN	3
chr12:91552212	p.R133R,DCN	3
chr12:91546948	p.E95K,DCN	3
chr12:91550854	p.G140V,DCN	2
chr12:91550874	p.G17R,DCN	2
chr12:91545456	p.G169R,DCN	2
chr12:91539849	p.P74S,DCN	2
chr12:91572281	p.Q108R,DCN	2
chr12:91540003	p.T101T,DCN	2
chr12:91546958	p.I117I,DCN	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 DCN 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 DCN

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


CDH11,COL3A1,COL5A2,COL6A3,DCN,ECM2,FAM26E, FAP,FBN1,FSTL1,GLT8D2,ITGBL1,LUM,MMP2, OLFML1,OMD,PDGFRL,RASGRF2,RECK,TCF4,TIMP2	C1S,ACKR4___CX3CR1,CLIC2,DCN,DPYSL3,FBLN1,FGL2, GALNT12,MFAP4,NT5E,OGN,OLFML1,OMD,PAM, PDGFRL,CPQ,PMP22,PTGFR,RECK,TIMP2,TPST1

C1R,C1S,CNRIP1,CTSK,DCN,DSEL,EFEMP2, FBLN2,FBN1,FSTL1,GPC6,LUM,MMP2,OLFML1, PDGFRB,RAB31,SERPINF1,SPARC,THBS2,VIM,ZNF521	TMEM237,ARHGAP29,B3GALNT1,CAV2,DCN,MICU3,FXYD1, GNG11,LHFP,LUM,MGP,NME5,NRN1,OGN, OMD,SDC2,SGTB,SNCG,SPG20,TAF9B,SLC35G2

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 DCN

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
DB01006	decorin	approved; investigational	Letrozole

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Cross referenced IDs for DCN

* 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