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 HS6ST1
Basic gene info.Gene symbolHS6ST1
Gene nameheparan sulfate 6-O-sulfotransferase 1
SynonymsHH15|HS6ST
CytomapUCSC genome browser: 2q21
Genomic locationchr2 :129023053-129076171
Type of geneprotein-coding
RefGenesNM_004807.2,
Ensembl idENSG00000136720
DescriptionHS6ST-1heparan-sulfate 6-O-sulfotransferase 1heparan-sulfate 6-sulfotransferase
Modification date20141207
dbXrefs MIM : 604846
HGNC : HGNC
Ensembl : ENSG00000136720
HPRD : 07274
Vega : OTTHUMG00000153542
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HS6ST1
BioGPS: 9394
Gene Expression Atlas: ENSG00000136720
The Human Protein Atlas: ENSG00000136720
PathwayNCI Pathway Interaction Database: HS6ST1
KEGG: HS6ST1
REACTOME: HS6ST1
ConsensusPathDB
Pathway Commons: HS6ST1
MetabolismMetaCyc: HS6ST1
HUMANCyc: HS6ST1
RegulationEnsembl's Regulation: ENSG00000136720
miRBase: chr2 :129,023,053-129,076,171
TargetScan: NM_004807
cisRED: ENSG00000136720
ContextiHOP: HS6ST1
cancer metabolism search in PubMed: HS6ST1
UCL Cancer Institute: HS6ST1
Assigned class in ccmGDBC

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Phenotypic Information for HS6ST1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HS6ST1
Familial Cancer Database: HS6ST1
* 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: HS6ST1
MedGen: HS6ST1 (Human Medical Genetics with Condition)
ClinVar: HS6ST1
PhenotypeMGI: HS6ST1 (International Mouse Phenotyping Consortium)
PhenomicDB: HS6ST1

Mutations for HS6ST1
* 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
breastHS6ST1chr2129028833129028833chr2129182142129182142
ovaryHS6ST1chr2129056092129056112HS6ST1chr2129064226129064246
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 HS6ST1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ375227PEBP178912118577253118577336HS6ST1823562129023995129024269

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=9

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=46)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr2:129075877-129075877p.D87E9
chr2:129025860-129025860p.R371H8
chr2:129026227-129026227p.R249S6
chr2:129075961-129075961p.T59T4
chr2:129026419-129026419p.R185*4
chr2:129026421-129026421p.L184P4
chr2:129075797-129075797p.V114G4
chr2:129025928-129025928p.Y348Y3
chr2:129075939-129075939p.K67*3
chr2:129025758-129025758p.S405I3

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample15 2  2    33   35 7
# mutation12 2  2    33   25 6
nonsynonymous SNV12 2  1    33   12 3
synonymous SNV      1         13 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
chr2:129075877p.D87E4
chr2:129026218p.R252C2
chr2:129026412p.T228T2
chr2:129026288p.R371H2
chr2:129025860p.P187R2
chr2:129025925p.Q318R1
chr2:129026332p.F308L1
chr2:129025948p.P269P1
chr2:129026338p.P222P1
chr2:129025949p.T215T1

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 HS6ST1 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 HS6ST1

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

AAMP,ABHD8,AGAP3,BAG1,DNAJB2,DVL1,ERCC3,
GRAMD4,HS6ST1,IMP4,MTCL1,NACC1,NSMF,OBSL1,
POMGNT1,SLC4A3,SMPD4,STK25,THAP4,TMEM177,WDR33
AGRN,ARVCF,CADM4,CAPN1,CHST10,EPS8L2,EVPL,
FAM129B,FBXL19,H2AFY2,HS6ST1,ITGB4,LSR,NGFR,
NKD2,PKP3,RTKN,SEPT9,SMARCA4,ST14,U2AF2

ASXL1,CEP250,CLASP1,DNAJC5,ELMO2,FMNL2,HS6ST1,
LRP3,LSM14B,MYO7A,NCOA6,NOD2,OGFR,PLCG1,
SLC5A6,SNRNP200,SNX21,TAF4,UGGT1,ZGPAT,ZNF319
ARHGAP17,ATG2A,CACFD1,CLCN2,CLDN4,CLSTN1,CYTH2,
GBA,GBAP1,GMIP,HS6ST1,JUP,LRP10,MARK2,
NR2F6,OSBPL2,PCSK7,SLC9A1,TMEM127,TMEM8A,WWP2
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 HS6ST1


There's no related Drug.
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Cross referenced IDs for HS6ST1
* 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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