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 HS3ST3B1
Basic gene info.Gene symbolHS3ST3B1
Gene nameheparan sulfate (glucosamine) 3-O-sulfotransferase 3B1
Synonyms30ST3B1|3OST3B1
CytomapUCSC genome browser: 17p12
Genomic locationchr17 :14204505-14249492
Type of geneprotein-coding
RefGenesNM_006041.1,
Ensembl idENSG00000125430
Description3-OST-3Bh3-OST-3Bheparan sulfate 3-O-sulfotransferase 3B1heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3B1heparan sulfate glucosamine 3-O-sulfotransferase 3B1
Modification date20141207
dbXrefs MIM : 604058
HGNC : HGNC
HPRD : 04959
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HS3ST3B1
BioGPS: 9953
Gene Expression Atlas: ENSG00000125430
The Human Protein Atlas: ENSG00000125430
PathwayNCI Pathway Interaction Database: HS3ST3B1
KEGG: HS3ST3B1
REACTOME: HS3ST3B1
ConsensusPathDB
Pathway Commons: HS3ST3B1
MetabolismMetaCyc: HS3ST3B1
HUMANCyc: HS3ST3B1
RegulationEnsembl's Regulation: ENSG00000125430
miRBase: chr17 :14,204,505-14,249,492
TargetScan: NM_006041
cisRED: ENSG00000125430
ContextiHOP: HS3ST3B1
cancer metabolism search in PubMed: HS3ST3B1
UCL Cancer Institute: HS3ST3B1
Assigned class in ccmGDBC

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Phenotypic Information for HS3ST3B1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HS3ST3B1
Familial Cancer Database: HS3ST3B1
* 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: HS3ST3B1
MedGen: HS3ST3B1 (Human Medical Genetics with Condition)
ClinVar: HS3ST3B1
PhenotypeMGI: HS3ST3B1 (International Mouse Phenotyping Consortium)
PhenomicDB: HS3ST3B1

Mutations for HS3ST3B1
* 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
pancreasHS3ST3B1chr171420619914206219HS3ST3B1chr171420634814206368
pancreasHS3ST3B1chr171422900814229028ADORA2Bchr171587477715874797
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 HS3ST3B1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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)        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=14)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr17:14248393-14248393p.T201T3
chr17:14204946-14204946p.F37F2
chr17:14248423-14248423p.P211P2
chr17:14248369-14248369p.D193D1
chr17:14248462-14248462p.I224I1
chr17:14204913-14204913p.P26P1
chr17:14248381-14248381p.T197T1
chr17:14248469-14248469p.V227M1
chr17:14204920-14204920p.V29M1
chr17:14248383-14248383p.M198T1

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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   7  1    3  1 45 4
# mutation   7  1    3  1 45 5
nonsynonymous SNV   4  1    1    23 5
synonymous SNV   3       2  1 22  
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
chr17:14248381p.P26P1
chr17:14248727p.P211L1
chr17:14204913p.V29M1
chr17:14248383p.S215S1
chr17:14248875p.C41C1
chr17:14204920p.I224I1
chr17:14248392p.A58T1
chr17:14248938p.V227M1
chr17:14204958p.A92A1
chr17:14248393p.T255M1

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 HS3ST3B1 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 HS3ST3B1

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

ANKRD44,CD226,DOCK11,DOCK2,FAM89A,FMNL3,FPR2,
HS3ST3A1,HS3ST3B1,KCNAB2,KLHL6,MGC12916,NCKAP1L,PRDM1,
PRDM8,PTPRC,RAPGEF1,SNX20,TNFRSF9,WIPF1,ZEB2
BHLHA15,CD3G,FOXP3,GCSAM,GPR174,GSG2,HS3ST3A1,
HS3ST3B1,IKZF3,IL7R,ITGA4,KIAA0125,LAX1,MGC12916,
P2RY10,RASGRP1,RFX5,SCML4,SLAMF1,TCL6,TRAT1

AVPR1A,CD163,CD93,CEACAM4,COL15A1,COL4A1,COL5A3,
FCGR2A,FPR1,FPR2,GLT1D1,GPR176,GPR97,HRH2,
HS3ST3B1,IL7R,PDPN,PXDN,TLR2,TRPC6,WISP1
AMIGO3,ANGPTL6,ANKMY1,ANO7,C2CD4D,ERN1,HS3ST3B1,
ING5,KCNAB3,KIAA1024,KLHL36,LRIT2,MPPED1,PCDH19,
SCARNA12,SH3TC1,SPDYE3,TERT,TFCP2L1,TRIM41,ZNF497
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 HS3ST3B1


There's no related Drug.
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Cross referenced IDs for HS3ST3B1
* 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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