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 SDC1

Basic gene info.	Gene symbol	SDC1
	Gene name	syndecan 1
	Synonyms	CD138\|SDC\|SYND1\|syndecan
	Cytomap	UCSC genome browser: 2p24.1
	Genomic location	chr2 :20400557-20425194
	Type of gene	protein-coding
	RefGenes	NM_001006946.1, NM_002997.4,
	Ensembl id	ENSG00000115884
	Description	CD138 antigenheparan sulfate proteoglycan fibroblast growth factor receptorsyndecan proteoglycan 1syndecan-1
	Modification date	20141222
dbXrefs	MIM : 186355
	HGNC : HGNC
	Ensembl : ENSG00000115884
	HPRD : 01718
	Vega : OTTHUMG00000090751
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SDC1
	BioGPS: 6382
	Gene Expression Atlas: ENSG00000115884
	The Human Protein Atlas: ENSG00000115884
Pathway	NCI Pathway Interaction Database: SDC1
	KEGG: SDC1
	REACTOME: SDC1
	ConsensusPathDB
	Pathway Commons: SDC1
Metabolism	MetaCyc: SDC1
	HUMANCyc: SDC1
Regulation	Ensembl's Regulation: ENSG00000115884
	miRBase: chr2 :20,400,557-20,425,194
	TargetScan: NM_001006946
	cisRED: ENSG00000115884
Context	iHOP: SDC1
	cancer metabolism search in PubMed: SDC1
	UCL Cancer Institute: SDC1
Assigned class in ccmGDB	C

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Phenotypic Information for SDC1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SDC1
	Familial Cancer Database: SDC1

* 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: SDC1
	MedGen: SDC1 (Human Medical Genetics with Condition)
	ClinVar: SDC1
Phenotype	MGI: SDC1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SDC1

Mutations for SDC1

* 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
pancreas	SDC1	chr2	20405804	20405824	SDC1	chr2	20405916	20405936

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 SDC1 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
BI055855	TRIM29	10	229	11	119986046	119991324	SDC1	217	319	2	20403811	20403913
BG002190	ERVV-2	26	597	19	53552336	53552907	SDC1	590	732	2	20417153	20417299
BE185151	SDC1	12	180	2	20401901	20402069	PROS1	176	433	3	93628822	93629079
AA368147	SDC1	1	61	2	20401748	20401808	PRRC2B	60	256	9	134374752	134374948

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=23)	Stat. for Synonymous SNVs (# total SNVs=11)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr2:20403822-20403822	p.E127K	3
chr2:20403831-20403831	p.R124*	2
chr2:20403674-20403674	p.H176R	2
chr2:20403740-20403740	p.H154R	2
chr2:20402566-20402566	p.A298A	2
chr2:20403949-20403949	p.E84E	2
chr2:20403986-20403986	p.T72M	1
chr2:20402613-20402613	p.E283K	1
chr2:20403631-20403631	p.R190R	1
chr2:20404000-20404000	p.D67D	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	2			7	1		1		3			5	2	5			4	4		1
# mutation	2			6	1		1		3			6	3	5			4	4		1
nonsynonymous SNV	1			5	1		1					5		5			1	1		1
synonymous SNV	1			1					3			1	3				3	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
chr2:20403740	p.A298A,SDC1	2
chr2:20402566	p.H154R,SDC1	2
chr2:20402613	p.T144T,SDC1	1
chr2:20403674	p.A242A,SDC1	1
chr2:20403883	p.L131L,SDC1	1
chr2:20402653	p.T240A,SDC1	1
chr2:20403687	p.P112A,SDC1	1
chr2:20403920	p.P234S,SDC1	1
chr2:20402885	p.L107L,SDC1	1
chr2:20403727	p.S233C,SDC1	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 SDC1 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 SDC1

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


ACTB,AEBP1,ANXA2,ANXA2P2,AVEN,COL11A1,CYS1, KRT7,LIMK1,MMP11,NRBP1,NXN,PLAU,PPAPDC1A, S100A10,S100A11,SDC1,SPSB1,TAX1BP3,THBS2,WNT2	AP1M2,APEX2,CACFD1,CAPN1,CLDN7,FAM83H,KRT18, KRT7,KRT8,LSR,PKP3,PRPF19,PRRG2,RUVBL1, SDC1,SLC35A2,SPINT1,SPINT2,ST14,STAP2,TMEM102

ABCC3,CRAT,DNAJB2,DTX2,FAM102A,GPR39,KLHDC7A, MFSD9,MYO7B,P2RX4,PROM2,PTPRF,RNF103,RNPEPL1, SDC1,SDCBP2,SPINT1,TMC4,TMCC1,TMEM53,UGT1A10	AP1M2,ARHGEF16,CACFD1,CAPN5,CBLC,DDR1,HNF1B, KIAA1522,LLGL2,MINK1,NR2F6,PCDH1,PFKL,SCAMP2, SDC1,SGPP2,SIPA1L3,ST14,TMEM102,TMEM8A,TNK1

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 SDC1

There's no related Drug.

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Cross referenced IDs for SDC1

* 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