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 DSE

Basic gene info.	Gene symbol	DSE
	Gene name	dermatan sulfate epimerase
	Synonyms	DSEP\|DSEPI\|EDSMC2\|SART-2\|SART2
	Cytomap	UCSC genome browser: 6q22
	Genomic location	chr6 :116601282-116759442
	Type of gene	protein-coding
	RefGenes	NM_001080976.1, NM_013352.2,
	Ensembl id	ENSG00000111817
	Description	DS epimerasechondroitin-glucuronate 5-epimerasedermatan-sulfate epimerasesquamous cell carcinoma antigen recognized by T-cells 2
	Modification date	20141207
dbXrefs	MIM : 605942
	HGNC : HGNC
	Ensembl : ENSG00000111817
	HPRD : 05807
	Vega : OTTHUMG00000015434
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DSE
	BioGPS: 29940
	Gene Expression Atlas: ENSG00000111817
	The Human Protein Atlas: ENSG00000111817
Pathway	NCI Pathway Interaction Database: DSE
	KEGG: DSE
	REACTOME: DSE
	ConsensusPathDB
	Pathway Commons: DSE
Metabolism	MetaCyc: DSE
	HUMANCyc: DSE
Regulation	Ensembl's Regulation: ENSG00000111817
	miRBase: chr6 :116,601,282-116,759,442
	TargetScan: NM_001080976
	cisRED: ENSG00000111817
Context	iHOP: DSE
	cancer metabolism search in PubMed: DSE
	UCL Cancer Institute: DSE
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: DSE
	Familial Cancer Database: DSE

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

Mutations for DSE

* 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	DSE	chr6	116628915	116628935	NT5DC1	chr6	116468060	116468080
pancreas	DSE	chr6	116617548	116617748	DSE	chr6	116615114	116615314
pancreas	DSE	chr6	116750820	116750840	DSE	chr6	116751140	116751160

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 DSE 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
BF577271	MYL2	2	377	12	111351075	111358383	DSE	373	649	6	116598255	116598542
BQ028298	DSE	9	263	6	116757992	116758246	LOC100130987	263	321	11	67120879	67120937
BQ340167	ELOVL7	10	113	5	60128753	60128856	DSE	109	191	6	116599271	116599354
AA557756	DSE	7	235	6	116599216	116599444	DSE	232	369	6	116599435	116599572
BF959216	DSE	2	101	6	116599260	116599359	DSE	96	260	6	116599103	116599267
M62263	DSE	1	180	6	116596548	116596727	CSNK1E	180	295	22	38689413	38689528

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=70)	Stat. for Synonymous SNVs (# total SNVs=25)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=0)
	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
chr6:116747852-116747852	p.L178I	3
chr6:116752203-116752203	p.G253C	3
chr6:116757777-116757777	p.R716C	3
chr6:116757259-116757259	p.G543E	2
chr6:116756873-116756873	p.F414F	2
chr6:116720492-116720492	p.E27K	2
chr6:116757537-116757537	p.P636S	2
chr6:116757959-116757959	p.R776R	2
chr6:116757070-116757070	p.F480S	2
chr6:116757438-116757438	p.H603Y	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=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	10	2	12	2				2			16	4				18	7	1	15
# mutation	1	10	2	12	2				2			16	4				23	7	1	22
nonsynonymous SNV	1	8	1	9	2				1			13	3				17	6	1	17
synonymous SNV		2	1	3					1			3	1				6	1		5

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
chr6:116747852	p.L178I,DSE	3
chr6:116756758	p.G376D,DSE	2
chr6:116757959	p.F414F,DSE	2
chr6:116756873	p.R716C,DSE	2
chr6:116757777	p.R776R,DSE	2
chr6:116757287	p.N167H,DSE	1
chr6:116758155	p.R335C,DSE	1
chr6:116747888	p.D516N,DSE	1
chr6:116754598	p.E626Q,DSE	1
chr6:116757507	p.K783M,DSE	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 DSE 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 DSE

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


ADAMTS2,ANTXR2,ARSB,CLMP,AXL,BICC1,DPYSL3, DSE,FAM26E,FBN1,FSTL1,HEG1,LATS2,LHFPL2, LOX,MXRA5,PLXNC1,RECK,TIMP2,VCAN,ZEB2	ABCA8,APOL6,C2CD2,CELF2,DOCK11,DSE,EPB41L2, EPS8,FAM26E,GPR116,LAMC1,MAN1A1,NRP1,PCOLCE2, PCSK5,PVRL3,SESTD1,SH3D19,TACC1,TLR4,ZEB2

C3AR1,CD86,CSF1R,DCN,DSE,FAM26E,FCGR1C, HCK,LAPTM5,LILRB2,LY96,MS4A4A,MS4A6A,MSR1, PDCD1LG2,PLEKHO2,SRGN,TYROBP,VCAN,WISP1,ZEB2	ACSL4,BRMS1L,CDADC1,DDX50,DNAJC24,DSE,DTWD1, GNB4,HIAT1,IGFBP7,IRAK1BP1,MSANTD4,LOC339524,MAD2L2, NBN,POT1,PPT1,RIPK2,SGTB,SLFN11,ZNF239

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 DSE

There's no related Drug.

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Cross referenced IDs for DSE

* 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