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 HS3ST4
Basic gene info.Gene symbolHS3ST4
Gene nameheparan sulfate (glucosamine) 3-O-sulfotransferase 4
Synonyms3-OST-4|30ST4|3OST4|h3-OST-4
CytomapUCSC genome browser: 16p11.2
Genomic locationchr16 :25703346-26149009
Type of geneprotein-coding
RefGenesNM_006040.2,
Ensembl idENSG00000182601
Descriptionheparan sulfate 3-O-sulfotransferase 4heparan sulfate 3-O-sulfotransferase-4heparan sulfate D-glucosaminyl 3-O-sulfotransferase 4heparan sulfate glucosamine 3-O-sulfotransferase 4
Modification date20141207
dbXrefs MIM : 604059
HGNC : HGNC
Ensembl : ENSG00000182601
HPRD : 04960
Vega : OTTHUMG00000059978
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HS3ST4
BioGPS: 9951
Gene Expression Atlas: ENSG00000182601
The Human Protein Atlas: ENSG00000182601
PathwayNCI Pathway Interaction Database: HS3ST4
KEGG: HS3ST4
REACTOME: HS3ST4
ConsensusPathDB
Pathway Commons: HS3ST4
MetabolismMetaCyc: HS3ST4
HUMANCyc: HS3ST4
RegulationEnsembl's Regulation: ENSG00000182601
miRBase: chr16 :25,703,346-26,149,009
TargetScan: NM_006040
cisRED: ENSG00000182601
ContextiHOP: HS3ST4
cancer metabolism search in PubMed: HS3ST4
UCL Cancer Institute: HS3ST4
Assigned class in ccmGDBC

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Phenotypic Information for HS3ST4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HS3ST4
Familial Cancer Database: HS3ST4
* 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: HS3ST4
MedGen: HS3ST4 (Human Medical Genetics with Condition)
ClinVar: HS3ST4
PhenotypeMGI: HS3ST4 (International Mouse Phenotyping Consortium)
PhenomicDB: HS3ST4

Mutations for HS3ST4
* 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
breastHS3ST4chr162585127225851272GSG1Lchr162781154227811542
pancreasHS3ST4chr162573875425738774HS3ST4chr162573863325738653
pancreasHS3ST4chr162583525825835278HS3ST4chr162583589325835913
pancreasHS3ST4chr162591915425919174HS3ST4chr162592153625921556
pancreasHS3ST4chr162601515026015170HS3ST4chr162601830726018327
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 HS3ST4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
T05820CDK14810979083885190838952HS3ST4110312162584792625848126
CX755679HS3ST4171162570439125704461ATP5G265743125406507454065762
BC019599HS3ST44640162604302626043662FEN16412257116156309461564710

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 # sample42 14 2 7 1  2 43
GAIN (# sample)4  1  1 6    1 43
LOSS (# sample) 2  4 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=53)
Stat. for Synonymous SNVs
(# total SNVs=21)
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
chr16:26147192-26147192p.R332*4
chr16:26147507-26147507p.L437V4
chr16:26147193-26147193p.R332Q3
chr16:26147409-26147409p.S404N3
chr16:26147239-26147239p.F347F3
chr16:26147297-26147297p.E367K2
chr16:26147382-26147382p.P395H2
chr16:26147408-26147408p.S404G2
chr16:26147076-26147076p.R293T2
chr16:26147315-26147315p.D373N2

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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
# sample16 162 4    662  21717
# mutation16 142 4    662  20718
nonsynonymous SNV 4 111 3    441  11515
synonymous SNV12 31 1    221  92 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
chr16:26147239p.F347F3
chr16:26147507p.L437L2
chr16:26147408p.S404G2
chr16:26147315p.R273H2
chr16:26147076p.D325N2
chr16:26147171p.D373N2
chr16:26147016p.R293T2
chr16:26147193p.R332Q2
chr16:26147293p.Y387Y1
chr16:26147026p.A225V1

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 HS3ST4 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 HS3ST4

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

B3GALT1,C10orf90,CA6,EPHB1,ETV5,GNG7,HS3ST4,
ID4,IL36B,LOC286094,MFGE8,MGC16025,MSMP,NDRG2,
NES,PTPRZ1,RGS2,SFRP1,SNX22,SOX10,TPPP2
ACTR3B,CELF5,CHKA,CHRM1,DTNB,ELF5,ETV6,
FAM3D,FOLH1,FZD1,HS3ST4,KCNN4,PDCD4,ROPN1,
ROPN1B,SFRP1,SLC13A2,SOX8,TMEM87A,TMPRSS2,UCK2

ACSM2B,ADAMTS18,AHSG,BANF2,LINC00293,SPATA31E1,CPN2,
CYP11B2,FLJ16779,GLDC,HIST1H2AA,HS3ST4,LECT2,LINC01512,
LOC151300,LOC286359,RNASE11,RSPO4,SLC6A2,TMEM207,TPTE2P3
CA11,CFAP58,CCK,DGKB,EXTL1,FSTL5,HS3ST4,
HTR2B,LOC255167,LPPR5,OPRK1,PENK,PPP2R2B,RGS2,
SH3BGR,SLITRK1,SNAP25,SNCB,SYT4,THSD7B,UNC13C
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 HS3ST4


There's no related Drug.
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Cross referenced IDs for HS3ST4
* 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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