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 SDC1
Basic gene info.Gene symbolSDC1
Gene namesyndecan 1
SynonymsCD138|SDC|SYND1|syndecan
CytomapUCSC genome browser: 2p24.1
Genomic locationchr2 :20400557-20425194
Type of geneprotein-coding
RefGenesNM_001006946.1,
NM_002997.4,
Ensembl idENSG00000115884
DescriptionCD138 antigenheparan sulfate proteoglycan fibroblast growth factor receptorsyndecan proteoglycan 1syndecan-1
Modification date20141222
dbXrefs MIM : 186355
HGNC : HGNC
Ensembl : ENSG00000115884
HPRD : 01718
Vega : OTTHUMG00000090751
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SDC1
BioGPS: 6382
Gene Expression Atlas: ENSG00000115884
The Human Protein Atlas: ENSG00000115884
PathwayNCI Pathway Interaction Database: SDC1
KEGG: SDC1
REACTOME: SDC1
ConsensusPathDB
Pathway Commons: SDC1
MetabolismMetaCyc: SDC1
HUMANCyc: SDC1
RegulationEnsembl's Regulation: ENSG00000115884
miRBase: chr2 :20,400,557-20,425,194
TargetScan: NM_001006946
cisRED: ENSG00000115884
ContextiHOP: SDC1
cancer metabolism search in PubMed: SDC1
UCL Cancer Institute: SDC1
Assigned class in ccmGDBC

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Phenotypic Information for SDC1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_LIPOPROTEIN_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SDC1
MedGen: SDC1 (Human Medical Genetics with Condition)
ClinVar: SDC1
PhenotypeMGI: SDC1 (International Mouse Phenotyping Consortium)
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.

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

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasSDC1chr22040580420405824SDC1chr22040591620405936
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 SDC1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI055855TRIM291022911119986046119991324SDC121731922040381120403913
BG002190ERVV-226597195355233653552907SDC159073222041715320417299
BE185151SDC11218022040190120402069PROS117643339362882293629079
AA368147SDC116122040174820401808PRRC2B602569134374752134374948

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 # sample          1     1
GAIN (# sample)          1     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=3

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check002.gifSomatic 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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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
chr2:20403822-20403822p.E127K3
chr2:20403740-20403740p.H154R2
chr2:20402566-20402566p.A298A2
chr2:20403949-20403949p.E84E2
chr2:20403831-20403831p.R124*2
chr2:20403674-20403674p.H176R2
chr2:20402911-20402911p.P234S1
chr2:20405124-20405124p.N43S1
chr2:20402564-20402564p.Y299F1
chr2:20403920-20403920p.P94L1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  71 1 3  525  44 1
# mutation2  61 1 3  635  44 1
nonsynonymous SNV1  51 1    5 5  11 1
synonymous SNV1  1    3  13   33  
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
chr2:20402566p.A298A,SDC12
chr2:20403740p.H154R,SDC12
chr2:20402923p.Y299F,SDC11
chr2:20403763p.Q172K,SDC11
chr2:20402564p.G36A,SDC11
chr2:20405145p.Q158Q,SDC11
chr2:20402951p.D35N,SDC11
chr2:20403769p.G297W,SDC11
chr2:20405149p.R155M,SDC11
chr2:20403631p.V25A,SDC11

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 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

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

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
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 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



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