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 EXT1
Basic gene info.Gene symbolEXT1
Gene nameexostosin glycosyltransferase 1
SynonymsEXT|LGCR|LGS|TRPS2|TTV
CytomapUCSC genome browser: 8q24.11
Genomic locationchr8 :118811601-119124058
Type of geneprotein-coding
RefGenesNM_000127.2,
Ensembl idENSG00000182197
DescriptionGlucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferaseLanger-Giedion syndrome chromosome regionN-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferaseexostoses (multiple) 1exostosin 1exostosin-1glucuronosyl-
Modification date20141219
dbXrefs MIM : 608177
HGNC : HGNC
HPRD : 00598
ProteinUniProt: Q16394
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EXT1
BioGPS: 2131
Gene Expression Atlas: ENSG00000182197
The Human Protein Atlas: ENSG00000182197
PathwayNCI Pathway Interaction Database: EXT1
KEGG: EXT1
REACTOME: EXT1
ConsensusPathDB
Pathway Commons: EXT1
MetabolismMetaCyc: EXT1
HUMANCyc: EXT1
RegulationEnsembl's Regulation: ENSG00000182197
miRBase: chr8 :118,811,601-119,124,058
TargetScan: NM_000127
cisRED: ENSG00000182197
ContextiHOP: EXT1
cancer metabolism search in PubMed: EXT1
UCL Cancer Institute: EXT1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EXT1 in cancer cell metabolism1. Julien S, Ivetic A, Grigoriadis A, QiZe D, Burford B, et al. (2011) Selectin ligand sialyl-Lewis x antigen drives metastasis of hormone-dependent breast cancers. Cancer Res 71: 7683-7693. doi: 10.1158/0008-5472.CAN-11-1139. go to article
2. Suhovskih AV, Tsidulko AY, Kutsenko OS, Kovner AV, Aidagulova SV, et al. (2014) Transcriptional Activity of Heparan Sulfate Biosynthetic Machinery is Specifically Impaired in Benign Prostate Hyperplasia and Prostate Cancer. Front Oncol 4: 79. doi: 10.3389/fonc.2014.00079. pmid: 3995048. go to article
3. 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
4. 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

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Phenotypic Information for EXT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EXT1
Familial Cancer Database: EXT1
* 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 133700; phenotype.
150230; phenotype.
215300; phenotype.
608177; gene.
Orphanet 321; Multiple osteochondromas.
502; Langer-Giedion syndrome.
55880; Chondrosarcoma.
DiseaseKEGG Disease: EXT1
MedGen: EXT1 (Human Medical Genetics with Condition)
ClinVar: EXT1
PhenotypeMGI: EXT1 (International Mouse Phenotyping Consortium)
PhenomicDB: EXT1

Mutations for EXT1
* 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
breastEXT1chr8118977538118977538chr8125303028125303028
breastEXT1chr8118979249118979249chr8132514437132514437
ovaryEXT1chr8118818150118818170ZFATchr8135581203135581223
ovaryEXT1chr8118859906118859926EXT1chr8118835869118835889
ovaryEXT1chr8118948168118948188EXT1chr8118948233118948253
ovaryEXT1chr8119089567119089587EXT1chr8119047397119047417
pancreasEXT1chr8118883454118883474EXT1chr8118907364118907384
pancreasEXT1chr8118887892118887912chr8118717933118717953
pancreasEXT1chr8118940512118940532chr8125906387125906407
pancreasEXT1chr8118981577118981597EXT1chr8119066782119066802
pancreasEXT1chr8119091432119091452EXT1chr8119091855119091875
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 EXT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK128498EXT118518118920852118921703CLUL1849329718597674645227
BE077260EXT13888119086632119086717EXT1892888119086384119086585
AK130402EXT114048118942307118942709FAM177A13981340143555165735552600
BF749377DSCAM81103214216205342162076EXT1991208118835645118835666
AA868517EXT1161348118875219118875337EXT11315428118875594118876013
AI209006EXT1161348118875219118875337EXT11314568118875594118875928

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 # sample12  21 10 3 9 1 4 1
GAIN (# sample)12  2  3 3 9 1 3 1
LOSS (# sample)    1 8       1  
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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=88)
Stat. for Synonymous SNVs
(# total SNVs=21)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=1)

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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
chr8:118830694-118830694p.V538I3
chr8:118825129-118825129p.T568T3
chr8:118825130-118825130p.T568M3
chr8:119122872-119122872p.I138I2
chr8:118819472-118819472p.A623T2
chr8:118819479-118819479p.L620L2
chr8:118819578-118819578p.E587E2
chr8:119122768-119122768p.N173S2
chr8:118812006-118812006p.F729S2
chr8:119122907-119122907p.I127V2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample32 26  4 2  834 1817114
# mutation32 23  4 2  934 1819117
nonsynonymous SNV22 19  2 2  622 1214 14
synonymous SNV1  4  2    312  6513
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
chr8:118830694p.V538I3
chr8:118825130p.T568M3
chr8:119122978p.Q721R2
chr8:119122833p.C103Y2
chr8:118812030p.A151A2
chr8:119122970p.K261E1
chr8:118819559p.I138I1
chr8:118847713p.L17L1
chr8:119123272p.A623T1
chr8:118825189p.R549C1

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 EXT1 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 EXT1

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

MSANTD3,CDH3,CHST11,CORO1C,ENO1,EPHB2,EXT1,
EVA1A,FNDC3B,COLGALT1,GSDMC,LRP12,MAP4K4,MED30,
MSN,MYO1E,PLS3,RAP2B,RNF145,S100A3,TMEM65
ADAMTS2,CALU,CAMKK2,CARD6,CCDC80,CD248,CORO1C,
EFEMP1,EXT1,EXT2,FKBP9,FSTL1,FYN,GAS7,
GFPT2,GPR176,KDELR3,LOXL2,MSN,SRPX2,VCAN

BDKRB1,BDKRB2,BMP2,CDR2L,DERL1,EXT1,GCNT3,
HOOK3,KIAA1211,MYO1E,NCOA2,NDRG1,NFKBIA,PAG1,
PLEC,RAB2A,RNF19A,RRM2B,SEC24D,TPD52,TRAM1
EPS8L3,EXT1,EZR,HECTD3,KIF3B,LASP1,LRRC16A,
MMP15,MYH14,MYO5B,MYO7B,NHSL1,PLXNA2,PTPN3,
RAB11FIP1,RAB11FIP4,RAB8A,TJP2,TMEM164,VIL1,ZZEF1
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 EXT1


There's no related Drug.
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Cross referenced IDs for EXT1
* 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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