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 STS
Basic gene info.Gene symbolSTS
Gene namesteroid sulfatase (microsomal), isozyme S
SynonymsARSC|ARSC1|ASC|ES|SSDD|XLI
CytomapUCSC genome browser: Xp22.32
Genomic locationchrX :7137471-7272682
Type of geneprotein-coding
RefGenesNM_000351.4,
Ensembl idENSG00000101846
Descriptionarylsulfatase Cestrone sulfatasesteryl-sulfatasesteryl-sulfate sulfohydrolase
Modification date20141222
dbXrefs MIM : 300747
HGNC : HGNC
Ensembl : ENSG00000101846
HPRD : 02389
Vega : OTTHUMG00000021102
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_STS
BioGPS: 412
Gene Expression Atlas: ENSG00000101846
The Human Protein Atlas: ENSG00000101846
PathwayNCI Pathway Interaction Database: STS
KEGG: STS
REACTOME: STS
ConsensusPathDB
Pathway Commons: STS
MetabolismMetaCyc: STS
HUMANCyc: STS
RegulationEnsembl's Regulation: ENSG00000101846
miRBase: chrX :7,137,471-7,272,682
TargetScan: NM_000351
cisRED: ENSG00000101846
ContextiHOP: STS
cancer metabolism search in PubMed: STS
UCL Cancer Institute: STS
Assigned class in ccmGDBC

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Phenotypic Information for STS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: STS
Familial Cancer Database: STS
* 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_GLYCOSPHINGOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_PROTEINS
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

Mutations for STS
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows STS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF956604STS218241X71761907176214SEPW1238377194828413648284572

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
There's no copy number variation information in COSMIC data for this gene.

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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=45)
Stat. for Synonymous SNVs
(# total SNVs=15)
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
chr23:7175602-7175602p.D124N3
chr23:7252080-7252080p.S437F3
chr23:7177623-7177623p.V211M2
chr23:7268042-7268042p.D498N2
chr23:7268151-7268151p.A534V2
chr23:7223223-7223223p.K365N1
chr23:7268184-7268184p.P545R1
chr23:7177621-7177621p.H210R1
chr23:7252077-7252077p.R436H1
chr23:7194044-7194044p.A292T1

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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
# sample31 122 1 1  1151 110219
# mutation31 112 1 1  1051 1112110
nonsynonymous SNV2  72 1 1  841 16217
synonymous SNV11 4       21   5  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
chrX:7175299p.R57W2
chrX:7177531p.V211L2
chrX:7175602p.V215I2
chrX:7177623p.D124N2
chrX:7177635p.T180M2
chrX:7267975p.G207W1
chrX:7177480p.P405S1
chrX:7177682p.E525K1
chrX:7243496p.H210R1
chrX:7177509p.T406A1

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 STS 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 STS

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

ABCA12,ADRB3,SPACA7,CYP51A1,DUPD1,FAM43B,GPR160,
HDHD1,KDM6A,KMO,LRRK2,MYLK3,POF1B,PRKCI,
SLC22A24,SLC22A25,SPTLC2,STS,TMEM131,TSPYL6,ZNF423
ANGPT1,ARHGAP21,ASPH,BHMT2,CHRDL1,COBLL1,ECM2,
EPB41L2,GCOM1,GNG2,GNS,ITGB1,ITSN1,KLHL5,
PALM2-AKAP2,PCDH9,RHOQ,SAR1A,SEPT11,SORBS1,STS

APOL2,ASS1,CASP10,CCDC68,DOCK5,EIF4E3,GPR126,
HPSE,KCNK1,PI3,RAB27B,RNF152,SEMG1,SEMG2,
SGMS1,SLC37A1,SNPH,STS,STYK1,SYT12,TC2N
ADM,ALPP,ASS1,BACE2,BATF2,C4BPA,CALR,
CASP10,CASP5,CEACAM6,CLCA3P,CLEC6A,GPX2,GRAMD2,
GRIN3A,NOS2,PARP9,STS,USP18,XDH,YPEL2
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 STS
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
DB01808steroid sulfatase (microsomal), isozyme SexperimentalThiarsahydroxy-Cysteine
DB03352steroid sulfatase (microsomal), isozyme SexperimentalS-Arsonocysteine
DB04456steroid sulfatase (microsomal), isozyme SexperimentalTrihydroxyarsenite(Iii)
DB02763steroid sulfatase (microsomal), isozyme Sexperimental5-Mercapto-2-Nitro-Benzoic Acid
DB03138steroid sulfatase (microsomal), isozyme SexperimentalPerchlorate Ion


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Cross referenced IDs for STS
* 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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