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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 HS3ST4

Basic gene info.	Gene symbol	HS3ST4
	Gene name	heparan sulfate (glucosamine) 3-O-sulfotransferase 4
	Synonyms	3-OST-4\|30ST4\|3OST4\|h3-OST-4
	Cytomap	UCSC genome browser: 16p11.2
	Genomic location	chr16 :25703346-26149009
	Type of gene	protein-coding
	RefGenes	NM_006040.2,
	Ensembl id	ENSG00000182601
	Description	heparan sulfate 3-O-sulfotransferase 4heparan sulfate 3-O-sulfotransferase-4heparan sulfate D-glucosaminyl 3-O-sulfotransferase 4heparan sulfate glucosamine 3-O-sulfotransferase 4
	Modification date	20141207
dbXrefs	MIM : 604059
	HGNC : HGNC
	Ensembl : ENSG00000182601
	HPRD : 04960
	Vega : OTTHUMG00000059978
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HS3ST4
	BioGPS: 9951
	Gene Expression Atlas: ENSG00000182601
	The Human Protein Atlas: ENSG00000182601
Pathway	NCI Pathway Interaction Database: HS3ST4
	KEGG: HS3ST4
	REACTOME: HS3ST4
	ConsensusPathDB
	Pathway Commons: HS3ST4
Metabolism	MetaCyc: HS3ST4
	HUMANCyc: HS3ST4
Regulation	Ensembl's Regulation: ENSG00000182601
	miRBase: chr16 :25,703,346-26,149,009
	TargetScan: NM_006040
	cisRED: ENSG00000182601
Context	iHOP: HS3ST4
	cancer metabolism search in PubMed: HS3ST4
	UCL Cancer Institute: HS3ST4
Assigned class in ccmGDB	C

Top

Phenotypic Information for HS3ST4(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: HS3ST4
	Familial Cancer Database: HS3ST4

* 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: HS3ST4
	MedGen: HS3ST4 (Human Medical Genetics with Condition)
	ClinVar: HS3ST4
Phenotype	MGI: HS3ST4 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: HS3ST4

Mutations for HS3ST4

* 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

Top

- 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
breast	HS3ST4	chr16	25851272	25851272	GSG1L	chr16	27811542	27811542
pancreas	HS3ST4	chr16	25738754	25738774	HS3ST4	chr16	25738633	25738653
pancreas	HS3ST4	chr16	25835258	25835278	HS3ST4	chr16	25835893	25835913
pancreas	HS3ST4	chr16	25919154	25919174	HS3ST4	chr16	25921536	25921556
pancreas	HS3ST4	chr16	26015150	26015170	HS3ST4	chr16	26018307	26018327

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 HS3ST4 related fusion information.

ID	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
T05820	CDK14	8	109	7	90838851	90838952	HS3ST4	110	312	16	25847926	25848126
CX755679	HS3ST4	1	71	16	25704391	25704461	ATP5G2	65	743	12	54065074	54065762
BC019599	HS3ST4	4	640	16	26043026	26043662	FEN1	641	2257	11	61563094	61564710

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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

Mutation type/ Tissue ID	brca	cns	cerv	endome	haematopo	kidn	Lintest	liver	lung	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	4	2		1	4		2		7		1			2		4	3
GAIN (# sample)	4			1			1		6					1		4	3
LOSS (# sample)		2			4		1		1		1			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)

Top

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=5

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=53)	Stat. for Synonymous SNVs (# total SNVs=21)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

Top

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
chr16:26147192-26147192	p.R332*	4
chr16:26147507-26147507	p.L437V	4
chr16:26147239-26147239	p.F347F	3
chr16:26147193-26147193	p.R332Q	3
chr16:26147409-26147409	p.S404N	3
chr16:26147110-26147110	p.K304N	2
chr16:26147171-26147171	p.D325N	2
chr16:26147297-26147297	p.E367K	2
chr16:26147382-26147382	p.P395H	2
chr16:26147408-26147408	p.S404G	2

Top

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	6		16	2		4					6	6	2			21	7	1	7
# mutation	1	6		14	2		4					6	6	2			20	7	1	8
nonsynonymous SNV		4		11	1		3					4	4	1			11	5	1	5
synonymous SNV	1	2		3	1		1					2	2	1			9	2		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])

Top

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
chr16:26147239	p.F347F	3
chr16:26147507	p.S404G	2
chr16:26147408	p.R273H	2
chr16:26147076	p.D325N	2
chr16:26147315	p.R293T	2
chr16:26147171	p.D373N	2
chr16:26147016	p.R332Q	2
chr16:26147193	p.L437L	2
chr16:26147026	p.P230P	1
chr16:26147293	p.P306P	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 HS3ST4 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]

Top

Gene Expression for HS3ST4

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


B3GALT1,C10orf90,CA6,EPHB1,ETV5,GNG7,HS3ST4, ID4,IL36B,LOC286094,MFGE8,MGC16025,MSMP,NDRG2, NES,PTPRZ1,RGS2,SFRP1,SNX22,SOX10,TPPP2	ACTR3B,CELF5,CHKA,CHRM1,DTNB,ELF5,ETV6, FAM3D,FOLH1,FZD1,HS3ST4,KCNN4,PDCD4,ROPN1, ROPN1B,SFRP1,SLC13A2,SOX8,TMEM87A,TMPRSS2,UCK2

ACSM2B,ADAMTS18,AHSG,BANF2,LINC00293,SPATA31E1,CPN2, CYP11B2,FLJ16779,GLDC,HIST1H2AA,HS3ST4,LECT2,LINC01512, LOC151300,LOC286359,RNASE11,RSPO4,SLC6A2,TMEM207,TPTE2P3	CA11,CFAP58,CCK,DGKB,EXTL1,FSTL5,HS3ST4, HTR2B,LOC255167,LPPR5,OPRK1,PENK,PPP2R2B,RGS2, SH3BGR,SLITRK1,SNAP25,SNCB,SYT4,THSD7B,UNC13C

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for HS3ST4

There's no related Drug.

Top

Cross referenced IDs for HS3ST4

* 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