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 SULT2B1

Basic gene info.	Gene symbol	SULT2B1
	Gene name	sulfotransferase family, cytosolic, 2B, member 1
	Synonyms	HSST2
	Cytomap	UCSC genome browser: 19q13.3
	Genomic location	chr19 :49078992-49102684
	Type of gene	protein-coding
	RefGenes	NM_004605.2, NM_177973.1,
	Ensembl id	ENSG00000088002
	Description	ST2B1alcohol sulfotransferasehydroxysteroid sulfotransferase 2sulfotransferase 2B1sulfotransferase family cytosolic 2B member 1
	Modification date	20141207
dbXrefs	MIM : 604125
	HGNC : HGNC
	Ensembl : ENSG00000088002
	HPRD : 04991
	Vega : OTTHUMG00000183314
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SULT2B1
	BioGPS: 6820
	Gene Expression Atlas: ENSG00000088002
	The Human Protein Atlas: ENSG00000088002
Pathway	NCI Pathway Interaction Database: SULT2B1
	KEGG: SULT2B1
	REACTOME: SULT2B1
	ConsensusPathDB
	Pathway Commons: SULT2B1
Metabolism	MetaCyc: SULT2B1
	HUMANCyc: SULT2B1
Regulation	Ensembl's Regulation: ENSG00000088002
	miRBase: chr19 :49,078,992-49,102,684
	TargetScan: NM_004605
	cisRED: ENSG00000088002
Context	iHOP: SULT2B1
	cancer metabolism search in PubMed: SULT2B1
	UCL Cancer Institute: SULT2B1
Assigned class in ccmGDB	C

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Phenotypic Information for SULT2B1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SULT2B1
	Familial Cancer Database: SULT2B1

* 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
KEGG_SULFUR_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: SULT2B1
	MedGen: SULT2B1 (Human Medical Genetics with Condition)
	ClinVar: SULT2B1
Phenotype	MGI: SULT2B1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SULT2B1

Mutations for SULT2B1

* 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

There's no inter-chromosomal structural variation.

- 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	SULT2B1	chr19	49080487	49080687	SULT2B1	chr19	49086294	49086494
ovary	SULT2B1	chr19	49080590	49080610	SULT2B1	chr19	49086383	49086403

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 SULT2B1 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

There's no copy number variation information in COSMIC data for this gene.

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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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=26)	Stat. for Synonymous SNVs (# total SNVs=15)

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
chr19:49096065-49096065	p.L198L	2
chr19:49096081-49096081	p.?	2
chr19:49090527-49090527	p.E71K	2
chr19:49102399-49102399	p.C263C	2
chr19:49102445-49102445	p.D279N	2
chr19:49079250-49079250	p.G27S	2
chr19:49090613-49090613	p.P99P	1
chr19:49102458-49102458	p.R283H	1
chr19:49094988-49094988	p.G167G	1
chr19:49079294-49079294	p.Q41H	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	2		1	4	1				2			2		1			8		1	5
# mutation	2		1	4	1				2			2		1			9		1	7
nonsynonymous SNV	1		1	4	1							2		1			6			4
synonymous SNV	1								2								3		1	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])

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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
chr19:49100007	p.D279N,SULT2B1	2
chr19:49102445	p.G204G,SULT2B1	2
chr19:49094988	p.E32K,SULT2B1	1
chr19:49102458	p.F257F,SULT2B1	1
chr19:49079174	p.I62I,SULT2B1	1
chr19:49096055	p.K267N,SULT2B1	1
chr19:49102508	p.E71K,SULT2B1	1
chr19:49079265	p.P74T,SULT2B1	1
chr19:49096070	p.R280C,SULT2B1	1
chr19:49102616	p.L106P,SULT2B1	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 SULT2B1 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 SULT2B1

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


BLVRB,CHMP2A,COX6A1,GAMT,HSPB1,KRT18,KRT8, LMTK3,LOC113230,MFSD5,MRFAP1,NDUFA2,PLA2G4F,PPDPF, PTOV1,SERTAD3,SIGIRR,SPR,SULT2B1,VAMP8,WIBG	ANXA9,AP1M2,ARFIP2,ATP2C2,KDF1,CRB3,FAM174B, GOLT1A,GPR39,GRTP1,IRX3,LRRC48,MRPL49,PHYHD1, PRRG2,RAB17,SPDEF,SPINT2,SULT2B1,TMEM25,ZBTB42

AIM1L,CHMP2A,COPZ1,DNAJC15,EFNB1,GRTP1,H2AFY, KRT18,KRT8,LMTK3,METTL7B,NDUFA1,NSDHL,PNKD, PRAP1,PRR13,RAB20,SSR4,SULT2B1,TMEM117,WDR13	ABCG5,ABCG8,ALDOB,ERICH4,TMEM252,DEFA5,DHDH, DPEP1,GLTPD2,GSTA2,HAPLN4,MEP1B,MGAM,NAT8, NTS,SLC10A2,SLC6A4,SP8,SULT2B1,TMEM229A,TREH

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 SULT2B1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB01708	sulfotransferase family, cytosolic, 2B, member 1	nutraceutical	Dehydroepiandrosterone
DB01812	sulfotransferase family, cytosolic, 2B, member 1	experimental	Adenosine-3'-5'-Diphosphate
DB02789	sulfotransferase family, cytosolic, 2B, member 1	experimental	Pregnenolone
DB03309	sulfotransferase family, cytosolic, 2B, member 1	experimental	N-Cyclohexyltaurine
DB00988	sulfotransferase family, cytosolic, 2B, member 1	approved	Dopamine
DB00655	sulfotransferase family, cytosolic, 2B, member 1	approved	Estrone
DB03255	sulfotransferase family, cytosolic, 2B, member 1	experimental	Phenol
DB00783	sulfotransferase family, cytosolic, 2B, member 1	approved; investigational	Estradiol
DB00675	sulfotransferase family, cytosolic, 2B, member 1	approved	Tamoxifen

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Cross referenced IDs for SULT2B1

* 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