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 symbolSDC3
Gene namesyndecan 3
SynonymsSDCN|SYND3
CytomapUCSC genome browser: 1p35.2
Genomic locationchr1 :31342312-31381480
Type of geneprotein-coding
RefGenesNM_014654.3,
Ensembl idENSG00000162512
DescriptionN-syndecansyndecan neural typesyndecan proteoglycan 3syndecan-3
Modification date20141207
dbXrefs MIM : 186357
HGNC : HGNC
HPRD : 01719
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SDC3
BioGPS: 9672
Gene Expression Atlas: ENSG00000162512
The Human Protein Atlas: ENSG00000162512
PathwayNCI Pathway Interaction Database: SDC3
KEGG: SDC3
REACTOME: SDC3
ConsensusPathDB
Pathway Commons: SDC3
MetabolismMetaCyc: SDC3
HUMANCyc: SDC3
RegulationEnsembl's Regulation: ENSG00000162512
miRBase: chr1 :31,342,312-31,381,480
TargetScan: NM_014654
cisRED: ENSG00000162512
ContextiHOP: SDC3
cancer metabolism search in PubMed: SDC3
UCL Cancer Institute: SDC3
Assigned class in ccmGDBC

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Phenotypic Information for SDC3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SDC3
MedGen: SDC3 (Human Medical Genetics with Condition)
ClinVar: SDC3
PhenotypeMGI: SDC3 (International Mouse Phenotyping Consortium)
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.

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
ovarySDC3chr13136343931363459SDC3chr13136546431365484
ovarySDC3chr13136441531364435SDC3chr13136577831365798
ovarySDC3chr13136673731366757chr18159122481591244
ovarySDC3chr13137621731376237SDC3chr13137740531377425
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 SDC3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA180215MAP7D21125X2013489220135016SDC312656913134519131345634
BF935530LAS1L5127X6473913464739256SDC311329413134519231345374
AI148370SIRT62671941741064174171SDC36448413134605331346473
AW166100YWHAH18412223235319632353590SDC340750213137806431378159
DB262991MYH111351161593186415950885SDC334559813134363131349869
BM991776SDC31836713134231331342662SDC336065113134578831346079
BE925576CD971192191451802314518974SDC318630413134448631344859
DA194626LOC1005074121151?112030112180SDC315254313134475331345143

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 # sample1  1      2      
GAIN (# sample)1  1      2      
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=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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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
chr1:31346080-31346080p.K436R2
chr1:31346158-31346158p.R410H2
chr1:31350004-31350004p.Q89*2
chr1:31347355-31347355p.F317F2
chr1:31349607-31349607p.T221M2
chr1:31349748-31349748p.P174L1
chr1:31349951-31349951p.A106A1
chr1:31347253-31347253p.P351P1
chr1:31349513-31349513p.T253fs*461
chr1:31346149-31346149p.K413T1

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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
# sample21 9    1  121  7413
# mutation21 8    1  121  7413
nonsynonymous SNV1  5    1  12   4411
synonymous SNV11 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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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
chr1:31349607p.T221M3
chr1:31346158p.R410H2
chr1:31349510p.A229V1
chr1:31349871p.A186T1
chr1:31346183p.F402V1
chr1:31349520p.T162T1
chr1:31349950p.L398L1
chr1:31346193p.S153S1
chr1:31349582p.K377K1
chr1:31349951p.E151E1

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 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

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

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
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 SDC3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00987syndecan 3approved; investigationalCytarabine


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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



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