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 DSE
Basic gene info.Gene symbolDSE
Gene namedermatan sulfate epimerase
SynonymsDSEP|DSEPI|EDSMC2|SART-2|SART2
CytomapUCSC genome browser: 6q22
Genomic locationchr6 :116601282-116759442
Type of geneprotein-coding
RefGenesNM_001080976.1,
NM_013352.2,
Ensembl idENSG00000111817
DescriptionDS epimerasechondroitin-glucuronate 5-epimerasedermatan-sulfate epimerasesquamous cell carcinoma antigen recognized by T-cells 2
Modification date20141207
dbXrefs MIM : 605942
HGNC : HGNC
Ensembl : ENSG00000111817
HPRD : 05807
Vega : OTTHUMG00000015434
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DSE
BioGPS: 29940
Gene Expression Atlas: ENSG00000111817
The Human Protein Atlas: ENSG00000111817
PathwayNCI Pathway Interaction Database: DSE
KEGG: DSE
REACTOME: DSE
ConsensusPathDB
Pathway Commons: DSE
MetabolismMetaCyc: DSE
HUMANCyc: DSE
RegulationEnsembl's Regulation: ENSG00000111817
miRBase: chr6 :116,601,282-116,759,442
TargetScan: NM_001080976
cisRED: ENSG00000111817
ContextiHOP: DSE
cancer metabolism search in PubMed: DSE
UCL Cancer Institute: DSE
Assigned class in ccmGDBC

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Phenotypic Information for DSE(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: DSE
MedGen: DSE (Human Medical Genetics with Condition)
ClinVar: DSE
PhenotypeMGI: DSE (International Mouse Phenotyping Consortium)
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.

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
ovaryDSEchr6116628915116628935NT5DC1chr6116468060116468080
pancreasDSEchr6116617548116617748DSEchr6116615114116615314
pancreasDSEchr6116750820116750840DSEchr6116751140116751160
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 DSE related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF577271MYL2237712111351075111358383DSE3736496116598255116598542
BQ028298DSE92636116757992116758246LOC100130987263321116712087967120937
BQ340167ELOVL71011356012875360128856DSE1091916116599271116599354
AA557756DSE72356116599216116599444DSE2323696116599435116599572
BF959216DSE21016116599260116599359DSE962606116599103116599267
M62263DSE11806116596548116596727CSNK1E180295223868941338689528

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 # sample41    1          
GAIN (# sample)4                
LOSS (# sample) 1    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=3

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check002.gifSomatic 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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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
chr6:116757777-116757777p.R716C3
chr6:116747852-116747852p.L178I3
chr6:116752203-116752203p.G253C3
chr6:116757959-116757959p.R776R2
chr6:116757070-116757070p.F480S2
chr6:116757438-116757438p.H603Y2
chr6:116757259-116757259p.G543E2
chr6:116756873-116756873p.F414F2
chr6:116720492-116720492p.E27K2
chr6:116757537-116757537p.P636S2

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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
# sample1102122   2  164   187115
# mutation1102122   2  164   237122
nonsynonymous SNV18192   1  133   176117
synonymous SNV 213    1  31   61 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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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
chr6:116747852p.L178I,DSE3
chr6:116756873p.R776R,DSE2
chr6:116757777p.G376D,DSE2
chr6:116756758p.R716C,DSE2
chr6:116757959p.F414F,DSE2
chr6:116720666p.F749V,DSE1
chr6:116756814p.A883V,DSE1
chr6:116757740p.F112L,DSE1
chr6:116747819p.R248W,DSE1
chr6:116757177p.Y473Y,DSE1

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 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

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

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
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 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



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