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 HS3ST3A1
Basic gene info.Gene symbolHS3ST3A1
Gene nameheparan sulfate (glucosamine) 3-O-sulfotransferase 3A1
Synonyms30ST3A1|3OST3A1
CytomapUCSC genome browser: 17p12
Genomic locationchr17 :13399005-13505244
Type of geneprotein-coding
RefGenesNM_006042.1,
Ensembl idENSG00000153976
Description3-OST-3Ah3-OST-3Aheparan sulfate 3-O-sulfotransferase 3A1heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1heparan sulfate glucosamine 3-O-sulfotransferase 3A1heparin-glucosamine 3-O-sulfotransferase
Modification date20141207
dbXrefs MIM : 604057
HGNC : HGNC
Ensembl : ENSG00000153976
HPRD : 04958
Vega : OTTHUMG00000058768
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HS3ST3A1
BioGPS: 9955
Gene Expression Atlas: ENSG00000153976
The Human Protein Atlas: ENSG00000153976
PathwayNCI Pathway Interaction Database: HS3ST3A1
KEGG: HS3ST3A1
REACTOME: HS3ST3A1
ConsensusPathDB
Pathway Commons: HS3ST3A1
MetabolismMetaCyc: HS3ST3A1
HUMANCyc: HS3ST3A1
RegulationEnsembl's Regulation: ENSG00000153976
miRBase: chr17 :13,399,005-13,505,244
TargetScan: NM_006042
cisRED: ENSG00000153976
ContextiHOP: HS3ST3A1
cancer metabolism search in PubMed: HS3ST3A1
UCL Cancer Institute: HS3ST3A1
Assigned class in ccmGDBC

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Phenotypic Information for HS3ST3A1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HS3ST3A1
Familial Cancer Database: HS3ST3A1
* 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: HS3ST3A1
MedGen: HS3ST3A1 (Human Medical Genetics with Condition)
ClinVar: HS3ST3A1
PhenotypeMGI: HS3ST3A1 (International Mouse Phenotyping Consortium)
PhenomicDB: HS3ST3A1

Mutations for HS3ST3A1
* 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
pancreasHS3ST3A1chr171345581813455838chr171498842514988445
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 HS3ST3A1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BC082963HS3ST3A1222058171339948713505235GSTO12058285810106014662106027213

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 # sample2     1 1 1   1  
GAIN (# sample)1       1        
LOSS (# sample)1     1   1   1  
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=22)
Stat. for Synonymous SNVs
(# total SNVs=24)
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
chr17:13399583-13399583p.R384R4
chr17:13400018-13400018p.I239I3
chr17:13399616-13399616p.P373P3
chr17:13400123-13400123p.P204P2
chr17:13400087-13400087p.T216T2
chr17:13399862-13399862p.Y291Y2
chr17:13503904-13503904p.V181V2
chr17:13399967-13399967p.T256T2
chr17:13400102-13400102p.I211I2
chr17:13400111-13400111p.D208D2

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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
# sample   62 1 2  721  92 4
# mutation   62 1 2  721  92 4
nonsynonymous SNV   22   1  511  42 2
synonymous SNV   4  1 1  21   5  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
chr17:13504345p.T34T2
chr17:13400102p.I211I2
chr17:13503904p.V181V2
chr17:13399973p.D401N1
chr17:13400068p.V241L1
chr17:13399534p.A43A1
chr17:13504318p.G399W1
chr17:13399983p.I239I1
chr17:13400087p.T398T1
chr17:13399540p.T236P1

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 HS3ST3A1 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 HS3ST3A1

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

ALPK2,ARSI,C1R,CHST11,DPYSL3,FEZ1,GAS1,
GFPT2,HS3ST3A1,HS3ST3B1,IFFO1,ITGA5,PPP1R18,MGC12916,
MMP14,NTNG2,PDPN,SCARF2,ST3GAL2,SYDE1,TWIST2
BHLHA15,CARD11,CCR2,CCR5,CD48,CD6,CIITA,
COL22A1,CRTAM,HLA-DOA,HS3ST3A1,HS3ST3B1,ITGAL,ITGB7,
LCK,MAP4K1,RASAL3,SEL1L3,SLAMF7,TMC8,TRAF3IP3

ADAMTS12,ADAMTS7,ANTXR1,COL6A2,COL6A3,DKK3,EVC,
FAM101B,GPR176,HECW2,HS3ST3A1,LOXL2,MMP14,MRC2,
NID2,NTM,PCOLCE,PDGFRB,PRR16,SYDE1,THY1
ARAP3,ASXL1,ATM,CSNK1E,DENND4B,FBXO41,FCHSD2,
HS3ST3A1,KRI1,NFATC1,NLRP1,PHACTR1,PRR3,SEMA3F,
SLC23A2,SLC25A29,TGIF2,WDR91,ZBTB39,ZCCHC11,ZHX2
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 HS3ST3A1
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
DB01812heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1experimentalAdenosine-3'-5'-Diphosphate
DB02264heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1experimentalO2-Sulfo-Glucuronic Acid
DB03959heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1experimentalN,O6-Disulfo-Glucosamine
DB03981heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1experimental1,4-Dideoxy-5-Dehydro-O2-Sulfo-Glucuronic Acid
DB04272heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1experimentalCitric Acid


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Cross referenced IDs for HS3ST3A1
* 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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