Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolEXT2
Gene nameexostosin glycosyltransferase 2
SynonymsSOTV
CytomapUCSC genome browser: 11p12-p11
Genomic locationchr11 :44117098-44266980
Type of geneprotein-coding
RefGenesNM_000401.3,
NM_001178083.1,NM_207122.1,
Ensembl idENSG00000151348
DescriptionN-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferaseexostosin-2glucuronosyl-N-acetylglucosaminyl-proteoglycan/N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferasemultiple exostoses protein 2putative tumor suppressor pr
Modification date20141219
dbXrefs MIM : 608210
HGNC : HGNC
Ensembl : ENSG00000151348
HPRD : 00599
Vega : OTTHUMG00000166498
ProteinUniProt: Q93063
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EXT2
BioGPS: 2132
Gene Expression Atlas: ENSG00000151348
The Human Protein Atlas: ENSG00000151348
PathwayNCI Pathway Interaction Database: EXT2
KEGG: EXT2
REACTOME: EXT2
ConsensusPathDB
Pathway Commons: EXT2
MetabolismMetaCyc: EXT2
HUMANCyc: EXT2
RegulationEnsembl's Regulation: ENSG00000151348
miRBase: chr11 :44,117,098-44,266,980
TargetScan: NM_000401
cisRED: ENSG00000151348
ContextiHOP: EXT2
cancer metabolism search in PubMed: EXT2
UCL Cancer Institute: EXT2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EXT2 in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 133701; phenotype.
601224; phenotype.
608210; gene.
Orphanet 321; Multiple osteochondromas.
52022; Potocki-Shaffer syndrome.
DiseaseKEGG Disease: EXT2
MedGen: EXT2 (Human Medical Genetics with Condition)
ClinVar: EXT2
PhenotypeMGI: EXT2 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryEXT2chr114417345144173471EXT2chr114417353344173553
pancreasEXT2chr114425982244259842chr114788522247885242
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EXT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA554222CSTB2148214519383145193977EXT2144254114420052844200638
T17444SBF2186207111006164110061662EXT2190459114426670544266974

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1       1 1      
GAIN (# sample)1       1 1      
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr11:44193237-44193237p.R417Q2
chr11:44228397-44228397p.N517I2
chr11:44130751-44130751p.R182*2
chr11:44254017-44254017p.V593L2
chr11:44129289-44129289p.I9I2
chr11:44129312-44129312p.R17K2
chr11:44129545-44129545p.R95C2
chr11:44151688-44151688p.Q391Q2
chr11:44255775-44255775p.T639T2
chr11:44135735-44135735p.R209R1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample16 41 2 2  52 12810 11
# mutation16 41 2 2  72 12910 12
nonsynonymous SNV 6 21 2 2  61 1256 8
synonymous SNV1  2       11   44 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr11:44255775p.T672T,EXT22
chr11:44193237p.W253C,EXT21
chr11:44129598p.S472S,EXT21
chr11:44228424p.L640L,EXT21
chr11:44130770p.S154S,EXT21
chr11:44146485p.D260N,EXT21
chr11:44193272p.V473M,EXT21
chr11:44129611p.C659F,EXT21
chr11:44228434p.Y163Y,EXT21
chr11:44130788p.D301G,EXT21

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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



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