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 HS6ST3
Basic gene info.Gene symbolHS6ST3
Gene nameheparan sulfate 6-O-sulfotransferase 3
SynonymsHS6ST-3
CytomapUCSC genome browser: 13q32.1
Genomic locationchr13 :96743092-97491816
Type of geneprotein-coding
RefGenesNM_153456.3,
Ensembl idENSG00000185352
Descriptionheparan-sulfate 6-O-sulfotransferase 3
Modification date20141207
dbXrefs MIM : 609401
HGNC : HGNC
Ensembl : ENSG00000185352
HPRD : 11030
Vega : OTTHUMG00000017232
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HS6ST3
BioGPS: 266722
Gene Expression Atlas: ENSG00000185352
The Human Protein Atlas: ENSG00000185352
PathwayNCI Pathway Interaction Database: HS6ST3
KEGG: HS6ST3
REACTOME: HS6ST3
ConsensusPathDB
Pathway Commons: HS6ST3
MetabolismMetaCyc: HS6ST3
HUMANCyc: HS6ST3
RegulationEnsembl's Regulation: ENSG00000185352
miRBase: chr13 :96,743,092-97,491,816
TargetScan: NM_153456
cisRED: ENSG00000185352
ContextiHOP: HS6ST3
cancer metabolism search in PubMed: HS6ST3
UCL Cancer Institute: HS6ST3
Assigned class in ccmGDBC

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Phenotypic Information for HS6ST3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HS6ST3
Familial Cancer Database: HS6ST3
* 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: HS6ST3
MedGen: HS6ST3 (Human Medical Genetics with Condition)
ClinVar: HS6ST3
PhenotypeMGI: HS6ST3 (International Mouse Phenotyping Consortium)
PhenomicDB: HS6ST3

Mutations for HS6ST3
* 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
ovaryHS6ST3chr139674681596746835HS6ST3chr139674692496746944
ovaryHS6ST3chr139689506396895083HS6ST3chr139689512496895144
ovaryHS6ST3chr139735346297353482HS6ST3chr139735371497353734
pancreasHS6ST3chr139714521797145237ITGA11chr156871457768714597
pancreasHS6ST3chr139714580597145825ITGA11chr156871161168711631
pancreasHS6ST3chr139714944697149466HS6ST3chr139714952797149547
pancreasHS6ST3chr139720514697205166HS6ST3chr139720718097207200
pancreasHS6ST3chr139720884097208860HS6ST3chr139721741697217436
pancreasHS6ST3chr139721707897217098chr1951765955176615
pancreasHS6ST3chr139740895297408972HS6ST3chr139741082797410847
prostateHS6ST3chr139688422596884225HS6ST3chr139688498096884980
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 HS6ST3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA783707RPL4197156679514966795245HS6ST397594139748748897487986

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 # sample6     4 5 2     1
GAIN (# sample)4     4 3        
LOSS (# sample)2       2 2     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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=60)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr13:97485261-97485261p.E409K3
chr13:97484827-97484827p.W264*3
chr13:97485288-97485288p.R418S3
chr13:97484830-97484830p.K265T3
chr13:97485106-97485106p.Q357P2
chr13:97484984-97484984p.D316E2
chr13:96743811-96743811p.H232P2
chr13:97485053-97485053p.Q339H2
chr13:97485246-97485246p.D404Y2
chr13:97485076-97485076p.N347S2

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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
# sample11 8  311  1051  157 3
# mutation11 8  311  1251  188 3
nonsynonymous SNV 1 5  111  1131  126 3
synonymous SNV1  3  2    12   62  
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
chr13:97485261p.E409K2
chr13:97484999p.R442Q1
chr13:97485376p.R236R1
chr13:96743641p.V320M1
chr13:97485093p.S374P1
chr13:97484870p.R445W1
chr13:97485020p.F238L1
chr13:97485409p.V320V1
chr13:96743704p.P375H1
chr13:97485095p.H447L1

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 HS6ST3 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 HS6ST3

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

BPTF,C17orf58,CRYBA1,DEFB127,CCSER1,GAB1,HELZ,
HS6ST3,LOC651250,MBTD1,KAT6B,N4BP2,NUPL1,NXPH1,
PPFIA2,SLC23A2,TMEM150C,TMTC4,TRIM36,ZFHX3,ZNF804B
ABCA12,ALDH3B2,APOF,BRI3BP,LINC00589,CCDC64,CNTNAP2,
DHCR24,EGLN3,HIST1H2BC,HS6ST3,KIAA1467,LPCAT3,PTPLAD1,
RASGRF1,SEPHS2,SLC7A5,SQLE,SRMS,TCERG1L,WNT7B

C1orf61,CABS1,DNMT3L,FAM19A4,GRID2,GRIK5,HS6ST3,
KCNK3,NWD2,KRT76,MT1B,NPTX1,NRXN1,OR4C15,
PDZD4,SFRP5,SLC10A2,SLC7A3,SV2A,TRIM67,ZNF536
ALK,ANO3,APLP1,ATCAY,CACNA1B,CHD5,DPYSL5,
ELAVL3,FGF14,GARNL3,HS6ST3,KIF1A,KIF5A,MYT1L,
NDRG4,PRPH,PTPRN,RET,SLC7A14,SYT1,UNC80
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 HS6ST3


There's no related Drug.
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Cross referenced IDs for HS6ST3
* 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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