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 HS2ST1

Basic gene info.	Gene symbol	HS2ST1
	Gene name	heparan sulfate 2-O-sulfotransferase 1
	Synonyms	dJ604K5.2
	Cytomap	UCSC genome browser: 1p22.3
	Genomic location	chr1 :87380334-87575681
	Type of gene	protein-coding
	RefGenes	NM_001134492.1, NM_012262.3,
	Ensembl id	ENSG00000153936
	Description	2-O-sulfotransferase2OST
	Modification date	20141207
dbXrefs	MIM : 604844
	HGNC : HGNC
	Ensembl : ENSG00000153936
	HPRD : 09215
	Vega : OTTHUMG00000010255
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HS2ST1
	BioGPS: 9653
	Gene Expression Atlas: ENSG00000153936
	The Human Protein Atlas: ENSG00000153936
Pathway	NCI Pathway Interaction Database: HS2ST1
	KEGG: HS2ST1
	REACTOME: HS2ST1
	ConsensusPathDB
	Pathway Commons: HS2ST1
Metabolism	MetaCyc: HS2ST1
	HUMANCyc: HS2ST1
Regulation	Ensembl's Regulation: ENSG00000153936
	miRBase: chr1 :87,380,334-87,575,681
	TargetScan: NM_001134492
	cisRED: ENSG00000153936
Context	iHOP: HS2ST1
	cancer metabolism search in PubMed: HS2ST1
	UCL Cancer Institute: HS2ST1
Assigned class in ccmGDB	C

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Phenotypic Information for HS2ST1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM
Orphanet
Disease	KEGG Disease: HS2ST1
	MedGen: HS2ST1 (Human Medical Genetics with Condition)
	ClinVar: HS2ST1
Phenotype	MGI: HS2ST1 (International Mouse Phenotyping Consortium)
Phenotype	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.

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	HS2ST1	chr1	87381877	87381897	SH3GLB1	chr1	87207894	87207914
ovary	HS2ST1	chr1	87511572	87511592	HS2ST1	chr1	87505832	87505852
ovary	HS2ST1	chr1	87575397	87575417	HS2ST1	chr1	87569785	87569805
pancreas	HS2ST1	chr1	87451427	87451447	NBEA	chr13	35785576	35785596
pancreas	HS2ST1	chr1	87502943	87502963	HS2ST1	chr1	87502871	87502891

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 HS2ST1 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
BE156347	CENPF	14	142	1	214822145	214825155	HS2ST1	132	151	1	87613124	87613143
BF947708	HS2ST1	1	119	1	87380651	87380768	KCNJ2-AS1	116	522	17	68164747	68165150
AW086208	HS2ST1	175	202	1	87483849	87483876	PCGF3	196	400	4	763719	763922
BF223279	HS2ST1	200	222	1	87512693	87512716	SSX2IP	211	524	1	85111955	85112268
BP376296	UBA2	8	463	19	34945363	34955033	HS2ST1	464	582	1	87511808	87511926
BF917753	HS2ST1	10	203	1	87381618	87381811	RUNX2	189	626	6	45421434	45421870

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=3

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Somatic 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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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
chr1:87558333-87558333	p.R190Q	2
chr1:87538859-87538859	p.?	2
chr1:87538643-87538643	p.R51*	2
chr1:87549881-87549881	p.R123H	2
chr1:87538679-87538679	p.R63W	2
chr1:87563588-87563588	p.P219L	2
chr1:87380793-87380793	p.L25R	1
chr1:87569257-87569257	p.E277K	1
chr1:87538749-87538749	p.S86N	1
chr1:87558325-87558325	p.L187L	1

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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=2

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	2	1	4			4		2	1		1		2			2	5		5
# mutation	1	2	1	4			4		2	1		1		2			2	5		5
nonsynonymous SNV	1	2	1	3			4		2	1		1		1			1	3		5
synonymous SNV				1										1			1	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
chr1:87563588	p.P219L,HS2ST1	2
chr1:87380793	p.Q30E,HS2ST1	1
chr1:87549881	p.R188W,HS2ST1	1
chr1:87380807	p.Q32R,HS2ST1	1
chr1:87549891	p.R188R,HS2ST1	1
chr1:87569257	p.A46T,HS2ST1	1
chr1:87380814	p.G206G,HS2ST1	1
chr1:87549897	p.H48Y,HS2ST1	1
chr1:87569270	p.E212Q,HS2ST1	1
chr1:87538628	p.R56Q,HS2ST1	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 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

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


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

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 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