Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolSDC2
Gene namesyndecan 2
SynonymsCD362|HSPG|HSPG1|SYND2
CytomapUCSC genome browser: 8q22-q23
Genomic locationchr8 :97505881-97624037
Type of geneprotein-coding
RefGenesNM_002998.3,
Ensembl idENSG00000169439
Descriptioncell surface-associated heparan sulfate proteoglycan 1fibroglycanheparan sulfate proteoglycan 1, cell surface-associatedheparan sulfate proteoglycan core proteinsyndecan proteoglycan 2syndecan-2
Modification date20141222
dbXrefs MIM : 142460
HGNC : HGNC
Ensembl : ENSG00000169439
HPRD : 00803
Vega : OTTHUMG00000164689
ProteinUniProt: P34741
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SDC2
BioGPS: 6383
Gene Expression Atlas: ENSG00000169439
The Human Protein Atlas: ENSG00000169439
PathwayNCI Pathway Interaction Database: SDC2
KEGG: SDC2
REACTOME: SDC2
ConsensusPathDB
Pathway Commons: SDC2
MetabolismMetaCyc: SDC2
HUMANCyc: SDC2
RegulationEnsembl's Regulation: ENSG00000169439
miRBase: chr8 :97,505,881-97,624,037
TargetScan: NM_002998
cisRED: ENSG00000169439
ContextiHOP: SDC2
cancer metabolism search in PubMed: SDC2
UCL Cancer Institute: SDC2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for SDC2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 142460; gene.
Orphanet
DiseaseKEGG Disease: SDC2
MedGen: SDC2 (Human Medical Genetics with Condition)
ClinVar: SDC2
PhenotypeMGI: SDC2 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovarySDC2chr89755143497551454chr159029809290298112
ovarySDC2chr89762286397622883chr89762524497625264
pancreasSDC2chr89750814797508167SDC2chr89750851097508530
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SDC2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE762893SDC28515989761468297614756SDC215442389761468297621671
AA632874SDC2116889762269997622867SDC216530289762263997622776
AI366039FRZB1852183699292183699376SDC26845589762233897622731

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample5       1        
GAIN (# sample)5       1        
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr8:97620628-97620628p.A124A3
chr8:97614661-97614661p.S71T3
chr8:97620629-97620629p.E125K3
chr8:97605800-97605800p.Y51Y3
chr8:97621679-97621679p.R170H2
chr8:97605717-97605717p.L24M2
chr8:97605773-97605773p.G42G2
chr8:97614730-97614730p.Q94E2
chr8:97506525-97506525p.T9S1
chr8:97621657-97621657p.L163I1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample 2191 2    242 114 4
# mutation 2191 2    242 113 4
nonsynonymous SNV 2161 2    142  12 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr8:97620628p.A124A3
chr8:97620629p.E125K2
chr8:97506525p.T9S1
chr8:97614730p.A18V1
chr8:97621634p.S41S1
chr8:97506552p.E125E1
chr8:97614732p.V43G1
chr8:97621642p.T132T1
chr8:97605770p.D47Y1
chr8:97620595p.R142L1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA35589; -.
Organism-specific databasesCTD 6383; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00860syndecan 2approvedPrednisolone


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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



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