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 HS3ST2

Basic gene info.	Gene symbol	HS3ST2
	Gene name	heparan sulfate (glucosamine) 3-O-sulfotransferase 2
	Synonyms	30ST2\|3OST2
	Cytomap	UCSC genome browser: 16p12
	Genomic location	chr16 :22825859-22927659
	Type of gene	protein-coding
	RefGenes	NM_006043.1,
	Ensembl id	ENSG00000122254
	Description	3-OST-2h3-OST-2heparan sulfate 3-O-sulfotransferase 2heparan sulfate D-glucosaminyl 3-O-sulfotransferase 2heparan sulfate glucosamine 3-O-sulfotransferase 2heparin-glucosamine 3-O-sulfotransferase
	Modification date	20141207
dbXrefs	MIM : 604056
	HGNC : HGNC
	Ensembl : ENSG00000122254
	HPRD : 04957
	Vega : OTTHUMG00000094785
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HS3ST2
	BioGPS: 9956
	Gene Expression Atlas: ENSG00000122254
	The Human Protein Atlas: ENSG00000122254
Pathway	NCI Pathway Interaction Database: HS3ST2
	KEGG: HS3ST2
	REACTOME: HS3ST2
	ConsensusPathDB
	Pathway Commons: HS3ST2
Metabolism	MetaCyc: HS3ST2
	HUMANCyc: HS3ST2
Regulation	Ensembl's Regulation: ENSG00000122254
	miRBase: chr16 :22,825,859-22,927,659
	TargetScan: NM_006043
	cisRED: ENSG00000122254
Context	iHOP: HS3ST2
	cancer metabolism search in PubMed: HS3ST2
	UCL Cancer Institute: HS3ST2
Assigned class in ccmGDB	C

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Phenotypic Information for HS3ST2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: HS3ST2
	Familial Cancer Database: HS3ST2

* 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: HS3ST2
	MedGen: HS3ST2 (Human Medical Genetics with Condition)
	ClinVar: HS3ST2
Phenotype	MGI: HS3ST2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: HS3ST2

Mutations for HS3ST2

* 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
haematopoietic_and_lymphoid_tissue	HS3ST2	chr16	22904605	22904605	HS3ST2	chr16	22904605	22904605
pancreas	HS3ST2	chr16	22846927	22846947		chr16	4224173	4224193
pancreas	HS3ST2	chr16	22861630	22861650		chr16	5373631	5373651
pancreas	HS3ST2	chr16	22893967	22893987	HS3ST2	chr16	22896410	22896430

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 HS3ST2 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

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=50)	Stat. for Synonymous SNVs (# total SNVs=22)

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
chr16:22926524-22926524	p.R249C	4
chr16:22826339-22826339	p.V136V	4
chr16:22926393-22926393	p.R205Q	3
chr16:22826294-22826294	p.G121G	3
chr16:22926818-22926818	p.E347*	2
chr16:22926605-22926605	p.R276*	2
chr16:22926525-22926525	p.R249L	2
chr16:22926609-22926609	p.L277H	2
chr16:22926750-22926750	p.R324Q	2
chr16:22926383-22926383	p.V202M	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=4

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	4		8	1		1		1	1		8	2	2	1		10	11	1	6
# mutation	1	4		8	1		1		1	1		8	2	2	1		11	10	1	6
nonsynonymous SNV		2		5			1		1	1		6	2	1	1		5	8	1	4
synonymous SNV	1	2		3	1							2		1			6	2		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
chr16:22926539	p.V254M	3
chr16:22926408	p.R210H	3
chr16:22926524	p.R249C	2
chr16:22926572	p.P265S	2
chr16:22926609	p.L277H	2
chr16:22926300	p.T216T	1
chr16:22926778	p.G283G	1
chr16:22926517	p.I119V	1
chr16:22926611	p.T227T	1
chr16:22826201	p.E284K	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 HS3ST2 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 HS3ST2

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


AJAP1,ARNT2,CST5,CYP2A13,CYP2A7,EDIL3,ESRRG, GOLIM4,GRIA1,HAPLN1,HS3ST2,LOC653786,P2RX6P,PTPRD, RASSF8,RNF152,SERPINI1,SLC14A2,TRPA1,USP14,VIPR2	APOC1,APOC2,ATP6V0D2,CELA1,CHIT1,DNAJC5B,FUCA1, HS3ST2,HTRA4,IGSF6,ITGAD,LILRA4,LILRB4,NKX2-6, NPL,OSCAR,PKD2L1,RAB42,SCN10A,SDS,SPATA12

ACP5,ALK,APOC1,APOE,C1QB,C1QC,CD68, DPEP2,FCGR1A,FCGR1B,GPNMB,HS3ST2,HTRA4,KCNJ5, LOC653786,LRRC25,MS4A4A,PSAP,RAB42,SDS,TREM2	ACTBL2,CCL18,CHIT1,DEFB103B,DEFB4A,DUOX1,FAM74A1, FAM92A1P2,FLJ25758,HS3ST2,HTRA4,KRT6B,KRTAP13-1,LY6D, MMP10,OR1J2,PRAMEF12,RBMXL3,TM4SF19,TRIM42,XKRY2

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 HS3ST2

There's no related Drug.

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Cross referenced IDs for HS3ST2

* 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