Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	HS6ST3
	Gene name	heparan sulfate 6-O-sulfotransferase 3
	Synonyms	HS6ST-3
	Cytomap	UCSC genome browser: 13q32.1
	Genomic location	chr13 :96743092-97491816
	Type of gene	protein-coding
	RefGenes	NM_153456.3,
	Ensembl id	ENSG00000185352
	Description	heparan-sulfate 6-O-sulfotransferase 3
	Modification date	20141207
dbXrefs	MIM : 609401
	HGNC : HGNC
	Ensembl : ENSG00000185352
	HPRD : 11030
	Vega : OTTHUMG00000017232
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HS6ST3
	BioGPS: 266722
	Gene Expression Atlas: ENSG00000185352
	The Human Protein Atlas: ENSG00000185352
Pathway	NCI Pathway Interaction Database: HS6ST3
	KEGG: HS6ST3
	REACTOME: HS6ST3
	ConsensusPathDB
	Pathway Commons: HS6ST3
Metabolism	MetaCyc: HS6ST3
	HUMANCyc: HS6ST3
Regulation	Ensembl's Regulation: ENSG00000185352
	miRBase: chr13 :96,743,092-97,491,816
	TargetScan: NM_153456
	cisRED: ENSG00000185352
Context	iHOP: HS6ST3
	cancer metabolism search in PubMed: HS6ST3
	UCL Cancer Institute: HS6ST3
Assigned class in ccmGDB	C

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Phenotypic Information for HS6ST3(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM
Orphanet
Disease	KEGG Disease: HS6ST3
	MedGen: HS6ST3 (Human Medical Genetics with Condition)
	ClinVar: HS6ST3
Phenotype	MGI: HS6ST3 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	HS6ST3	chr13	96746815	96746835	HS6ST3	chr13	96746924	96746944
ovary	HS6ST3	chr13	96895063	96895083	HS6ST3	chr13	96895124	96895144
ovary	HS6ST3	chr13	97353462	97353482	HS6ST3	chr13	97353714	97353734
pancreas	HS6ST3	chr13	97145217	97145237	ITGA11	chr15	68714577	68714597
pancreas	HS6ST3	chr13	97145805	97145825	ITGA11	chr15	68711611	68711631
pancreas	HS6ST3	chr13	97149446	97149466	HS6ST3	chr13	97149527	97149547
pancreas	HS6ST3	chr13	97205146	97205166	HS6ST3	chr13	97207180	97207200
pancreas	HS6ST3	chr13	97208840	97208860	HS6ST3	chr13	97217416	97217436
pancreas	HS6ST3	chr13	97217078	97217098		chr19	5176595	5176615
pancreas	HS6ST3	chr13	97408952	97408972	HS6ST3	chr13	97410827	97410847
prostate	HS6ST3	chr13	96884225	96884225	HS6ST3	chr13	96884980	96884980

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HS6ST3 related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

DA783707

RPL4

66795149

66795245

HS6ST3

594

97487488

97487986

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr13:97485261-97485261	p.E409K	3
chr13:97484827-97484827	p.W264*	3
chr13:97485288-97485288	p.R418S	3
chr13:97484830-97484830	p.K265T	3
chr13:97485246-97485246	p.D404Y	2
chr13:97485076-97485076	p.N347S	2
chr13:97485207-97485207	p.E391K	2
chr13:96743785-96743785	p.M223I	2
chr13:97485106-97485106	p.Q357P	2
chr13:97484984-97484984	p.D316E	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		8			3	1	1			10	5	1			15	7		3
# mutation	1	1		8			3	1	1			12	5	1			18	8		3
nonsynonymous SNV		1		5			1	1	1			11	3	1			12	6		3
synonymous SNV	1			3			2					1	2				6	2

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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr13:97485261	p.E409K	2
chr13:97485030	p.D246N	1
chr13:97485146	p.G321G	1
chr13:96743747	p.Q378E	1
chr13:97484897	p.H447L	1
chr13:97485276	p.G261G	1
chr13:97485036	p.M328I	1
chr13:97485156	p.S385F	1
chr13:97484744	p.G458E	1
chr13:97484941	p.K265T	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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