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 EXT1

Basic gene info.	Gene symbol	EXT1
	Gene name	exostosin glycosyltransferase 1
	Synonyms	EXT\|LGCR\|LGS\|TRPS2\|TTV
	Cytomap	UCSC genome browser: 8q24.11
	Genomic location	chr8 :118811601-119124058
	Type of gene	protein-coding
	RefGenes	NM_000127.2,
	Ensembl id	ENSG00000182197
	Description	Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferaseLanger-Giedion syndrome chromosome regionN-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferaseexostoses (multiple) 1exostosin 1exostosin-1glucuronosyl-
	Modification date	20141219
dbXrefs	MIM : 608177
	HGNC : HGNC
	HPRD : 00598
Protein	UniProt: Q16394 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EXT1
	BioGPS: 2131
	Gene Expression Atlas: ENSG00000182197
	The Human Protein Atlas: ENSG00000182197
Pathway	NCI Pathway Interaction Database: EXT1
	KEGG: EXT1
	REACTOME: EXT1
	ConsensusPathDB
	Pathway Commons: EXT1
Metabolism	MetaCyc: EXT1
	HUMANCyc: EXT1
Regulation	Ensembl's Regulation: ENSG00000182197
	miRBase: chr8 :118,811,601-119,124,058
	TargetScan: NM_000127
	cisRED: ENSG00000182197
Context	iHOP: EXT1
	cancer metabolism search in PubMed: EXT1
	UCL Cancer Institute: EXT1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EXT1 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM	133700; phenotype. 150230; phenotype. 215300; phenotype. 608177; gene.
Orphanet	321; Multiple osteochondromas. 502; Langer-Giedion syndrome. 55880; Chondrosarcoma.
Disease	KEGG Disease: EXT1
	MedGen: EXT1 (Human Medical Genetics with Condition)
	ClinVar: EXT1
Phenotype	MGI: EXT1 (International Mouse Phenotyping Consortium)
Phenotype	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.

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
breast	EXT1	chr8	118977538	118977538		chr8	125303028	125303028
breast	EXT1	chr8	118979249	118979249		chr8	132514437	132514437
ovary	EXT1	chr8	118818150	118818170	ZFAT	chr8	135581203	135581223
ovary	EXT1	chr8	118859906	118859926	EXT1	chr8	118835869	118835889
ovary	EXT1	chr8	118948168	118948188	EXT1	chr8	118948233	118948253
ovary	EXT1	chr8	119089567	119089587	EXT1	chr8	119047397	119047417
pancreas	EXT1	chr8	118883454	118883474	EXT1	chr8	118907364	118907384
pancreas	EXT1	chr8	118887892	118887912		chr8	118717933	118717953
pancreas	EXT1	chr8	118940512	118940532		chr8	125906387	125906407
pancreas	EXT1	chr8	118981577	118981597	EXT1	chr8	119066782	119066802
pancreas	EXT1	chr8	119091432	119091452	EXT1	chr8	119091855	119091875

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 EXT1 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
AK128498	EXT1	1	851	8	118920852	118921703	CLUL1	849	3297	18	597674	645227
BE077260	EXT1	3	88	8	119086632	119086717	EXT1	89	288	8	119086384	119086585
AK130402	EXT1	1	404	8	118942307	118942709	FAM177A1	398	1340	14	35551657	35552600
BF749377	DSCAM	81	103	21	42162053	42162076	EXT1	99	120	8	118835645	118835666
AA868517	EXT1	16	134	8	118875219	118875337	EXT1	131	542	8	118875594	118876013
AI209006	EXT1	16	134	8	118875219	118875337	EXT1	131	456	8	118875594	118875928

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	12			2	1		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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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=7

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Somatic 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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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
chr8:118825129-118825129	p.T568T	3
chr8:118825130-118825130	p.T568M	3
chr8:118830694-118830694	p.V538I	3
chr8:118847766-118847766	p.S361R	2
chr8:119122395-119122395	p.T297T	2
chr8:119122833-119122833	p.A151A	2
chr8:119122691-119122691	p.T199A	2
chr8:118847782-118847782	p.C355C	2
chr8:119122978-119122978	p.C103Y	2
chr8:119122872-119122872	p.I138I	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=5

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	3	2		26			4		2			8	3	4		1	8	17	1	14
# mutation	3	2		23			4		2			9	3	4		1	8	19	1	17
nonsynonymous SNV	2	2		19			2		2			6	2	2		1	2	14		14
synonymous SNV	1			4			2					3	1	2			6	5	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
chr8:118830694	p.T568M	3
chr8:118825130	p.V538I	3
chr8:119122978	p.C103Y	2
chr8:119122833	p.A151A	2
chr8:118812030	p.Q721R	2
chr8:118830735	p.A594T	1
chr8:119122705	p.P524Q	1
chr8:118812096	p.A378A	1
chr8:118842475	p.N194S	1
chr8:119122873	p.F106I	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 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

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


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

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 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