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 HS2ST1
Basic gene info.Gene symbolHS2ST1
Gene nameheparan sulfate 2-O-sulfotransferase 1
SynonymsdJ604K5.2
CytomapUCSC genome browser: 1p22.3
Genomic locationchr1 :87380334-87575681
Type of geneprotein-coding
RefGenesNM_001134492.1,
NM_012262.3,
Ensembl idENSG00000153936
Description2-O-sulfotransferase2OST
Modification date20141207
dbXrefs MIM : 604844
HGNC : HGNC
Ensembl : ENSG00000153936
HPRD : 09215
Vega : OTTHUMG00000010255
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HS2ST1
BioGPS: 9653
Gene Expression Atlas: ENSG00000153936
The Human Protein Atlas: ENSG00000153936
PathwayNCI Pathway Interaction Database: HS2ST1
KEGG: HS2ST1
REACTOME: HS2ST1
ConsensusPathDB
Pathway Commons: HS2ST1
MetabolismMetaCyc: HS2ST1
HUMANCyc: HS2ST1
RegulationEnsembl's Regulation: ENSG00000153936
miRBase: chr1 :87,380,334-87,575,681
TargetScan: NM_001134492
cisRED: ENSG00000153936
ContextiHOP: HS2ST1
cancer metabolism search in PubMed: HS2ST1
UCL Cancer Institute: HS2ST1
Assigned class in ccmGDBC

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Phenotypic Information for HS2ST1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HS2ST1
Familial Cancer Database: HS2ST1
* 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: HS2ST1
MedGen: HS2ST1 (Human Medical Genetics with Condition)
ClinVar: HS2ST1
PhenotypeMGI: HS2ST1 (International Mouse Phenotyping Consortium)
PhenomicDB: HS2ST1

Mutations for HS2ST1
* 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
ovaryHS2ST1chr18738187787381897SH3GLB1chr18720789487207914
ovaryHS2ST1chr18751157287511592HS2ST1chr18750583287505852
ovaryHS2ST1chr18757539787575417HS2ST1chr18756978587569805
pancreasHS2ST1chr18745142787451447NBEAchr133578557635785596
pancreasHS2ST1chr18750294387502963HS2ST1chr18750287187502891
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 HS2ST1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE156347CENPF141421214822145214825155HS2ST113215118761312487613143
BF947708HS2ST1111918738065187380768KCNJ2-AS1116522176816474768165150
AW086208HS2ST117520218748384987483876PCGF31964004763719763922
BF223279HS2ST120022218751269387512716SSX2IP21152418511195585112268
BP376296UBA28463193494536334955033HS2ST146458218751180887511926
BF917753HS2ST11020318738161887381811RUNX218962664542143445421870

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 # sample          1      
GAIN (# sample)          1      
LOSS (# sample)                 
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=24)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr1:87538859-87538859p.?2
chr1:87538643-87538643p.R51*2
chr1:87549881-87549881p.R123H2
chr1:87538679-87538679p.R63W2
chr1:87563588-87563588p.P219L2
chr1:87558333-87558333p.R190Q2
chr1:87570197-87570197p.T297A1
chr1:87380819-87380819p.L34M1
chr1:87563566-87563566p.E212Q1
chr1:87570261-87570261p.E318G1

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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
# sample1214  4 21 1 2  25 5
# mutation1214  4 21 1 2  25 5
nonsynonymous SNV1213  4 21 1 1  13 5
synonymous SNV   1         1  12  
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
chr1:87563588p.P219L,HS2ST12
chr1:87538634p.G61G,HS2ST11
chr1:87558290p.E277K1
chr1:87570197p.N79S,HS2ST11
chr1:87538659p.T281I1
chr1:87558299p.S86N,HS2ST11
chr1:87570261p.L287L1
chr1:87538675p.P114L,HS2ST11
chr1:87558326p.T297A1
chr1:87570349p.D120D,HS2ST11

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 HS2ST1 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 HS2ST1

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

ADAM17,ANKRD13C,CTTNBP2NL,DBT,DR1,EVI5,EXTL2,
HIAT1,HS2ST1,LRRC40,LRRC8B,PKN2,RBMXL1,ROCK2,
RRAGC,SEP15,SH3GLB1,SLC30A7,ZFR,ZNF644,ZYG11B
CREB1,CTDSPL2,FNDC3A,G2E3,HS2ST1,CFAP97,LMBR1,
LRRC58,MIB1,PDS5A,PPIP5K2,PRRC1,QSER1,SENP1,
SLC39A10,SMARCAD1,SMC2,SUZ12,TMTC3,UBXN4,ZNF148

ARL15,CSDE1,EDNRA,FNBP1L,GLCE,HIAT1,HOOK1,
HS2ST1,MTF2,NRAS,PIGK,SCARB2,SH3GLB1,SSX2IP,
ST13,STAU2,TMED5,TRIM33,ZNF644,ZNHIT6,ZZZ3
ADNP,APPL1,ARID1B,NDNF,CAPN7,CNOT6L,CPD,
DENND4C,FAM73A,HS2ST1,MIA3,PGAP1,POFUT1,PTENP1,
PTK2,RAD50,ST18,TCF12,TNKS,ZNF318,ZNF395
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 HS2ST1


There's no related Drug.
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Cross referenced IDs for HS2ST1
* 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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