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 EXT2

Basic gene info.	Gene symbol	EXT2
	Gene name	exostosin glycosyltransferase 2
	Synonyms	SOTV
	Cytomap	UCSC genome browser: 11p12-p11
	Genomic location	chr11 :44117098-44266980
	Type of gene	protein-coding
	RefGenes	NM_000401.3, NM_001178083.1,NM_207122.1,
	Ensembl id	ENSG00000151348
	Description	N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferaseexostosin-2glucuronosyl-N-acetylglucosaminyl-proteoglycan/N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferasemultiple exostoses protein 2putative tumor suppressor pr
	Modification date	20141219
dbXrefs	MIM : 608210
	HGNC : HGNC
	Ensembl : ENSG00000151348
	HPRD : 00599
	Vega : OTTHUMG00000166498
Protein	UniProt: Q93063 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EXT2
	BioGPS: 2132
	Gene Expression Atlas: ENSG00000151348
	The Human Protein Atlas: ENSG00000151348
Pathway	NCI Pathway Interaction Database: EXT2
	KEGG: EXT2
	REACTOME: EXT2
	ConsensusPathDB
	Pathway Commons: EXT2
Metabolism	MetaCyc: EXT2
	HUMANCyc: EXT2
Regulation	Ensembl's Regulation: ENSG00000151348
	miRBase: chr11 :44,117,098-44,266,980
	TargetScan: NM_000401
	cisRED: ENSG00000151348
Context	iHOP: EXT2
	cancer metabolism search in PubMed: EXT2
	UCL Cancer Institute: EXT2
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EXT2 in cancer cell metabolism	1. Suhovskih AV, Domanitskaya NV, Tsidulko AY, Prudnikova TY, Kashuba VI, et al. (2015) Tissue-specificity of heparan sulfate biosynthetic machinery in cancer. Cell Adh Migr: 0. doi: 10.1080/19336918.2015.1049801. go to article 2. Jones KB, Piombo V, Searby C, Kurriger G, Yang B, et al. (2010) A mouse model of osteochondromagenesis from clonal inactivation of Ext1 in chondrocytes. Proc Natl Acad Sci U S A 107: 2054-2059. doi: 10.1073/pnas.0910875107. pmid: 2836675. go to article 3. Busse-Wicher M, Wicher KB, Kusche-Gullberg M (2014) The exostosin family: proteins with many functions. Matrix Biol 35: 25-33. doi: 10.1016/j.matbio.2013.10.001. go to article

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Phenotypic Information for EXT2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: EXT2
	Familial Cancer Database: EXT2

* 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	133701; phenotype. 601224; phenotype. 608210; gene.
Orphanet	321; Multiple osteochondromas. 52022; Potocki-Shaffer syndrome.
Disease	KEGG Disease: EXT2
	MedGen: EXT2 (Human Medical Genetics with Condition)
	ClinVar: EXT2
Phenotype	MGI: EXT2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: EXT2

Mutations for EXT2

* 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	EXT2	chr11	44173451	44173471	EXT2	chr11	44173533	44173553
pancreas	EXT2	chr11	44259822	44259842		chr11	47885222	47885242

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 EXT2 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
AA554222	CSTB	2	148	21	45193831	45193977	EXT2	144	254	11	44200528	44200638
T17444	SBF2	186	207	11	10061641	10061662	EXT2	190	459	11	44266705	44266974

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=49)	Stat. for Synonymous SNVs (# total SNVs=16)

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
chr11:44129289-44129289	p.I9I	2
chr11:44129312-44129312	p.R17K	2
chr11:44129545-44129545	p.R95C	2
chr11:44151688-44151688	p.Q391Q	2
chr11:44255775-44255775	p.T639T	2
chr11:44193237-44193237	p.R417Q	2
chr11:44228397-44228397	p.N517I	2
chr11:44130751-44130751	p.R182*	2
chr11:44254017-44254017	p.V593L	2
chr11:44129667-44129667	p.M135I	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	6		4	1		2		2			5	2		1	2	8	10		11
# mutation	1	6		4	1		2		2			7	2		1	2	9	10		12
nonsynonymous SNV		6		2	1		2		2			6	1		1	2	5	6		8
synonymous SNV	1			2								1	1				4	4		4

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
chr11:44255775	p.T672T,EXT2	2
chr11:44130830	p.L221W,EXT2	1
chr11:44253919	p.P374R,EXT2	1
chr11:44148448	p.Y559C,EXT2	1
chr11:44129690	p.G227E,EXT2	1
chr11:44219521	p.P399A,EXT2	1
chr11:44135753	p.I562I,EXT2	1
chr11:44254029	p.R50I,EXT2	1
chr11:44151611	p.P229L,EXT2	1
chr11:44129312	p.V406M,EXT2	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 EXT2 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 EXT2

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


ACAN,BGN,CALU,DEPDC7,DYSF,ENPEP,EXT2, FKBP9,FXYD4,GALNS,GLG1,COLGALT1,LCTL,NOS2, PANX3,PHOSPHO1,PLXNA1,PRELP,SNAI2,TMEM43,TPST1	XXYLT1,CALU,CAPN5,EXT1,EXT2,FBXL7,FKBP9, FSTL1,FUCA2,GNB1,GPX8,HEXA,HTRA1,KDELR3, LPAR1,PGAM1,CPQ,PPIC,SEPN1,TPST1,TRAM2

ALKBH3,AMBRA1,ATP6AP2,CD151,CD59,CEACAM5,EXT2, FNDC3B,HARBI1,IFT46,MAGED2,MICAL2,NEU1,NFE2L1, PARVA,SMPD1,SRPX2,ST14,TMEM158,TRAF6,UXS1	C9orf64,CANX,EPB41L2,ERO1L,EXT2,HNRNPH2,INPP4B, LDHA,LONP2,PCYT1A,PIGX,PIR,PSMD1,RAB6A, RAD23B,SDCBP,SERPINB6,SSR1,SURF4,VAPB,XRCC5

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 EXT2

There's no related Drug.

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Cross referenced IDs for EXT2

* 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