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 DDOST
Basic gene info.Gene symbolDDOST
Gene namedolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)
SynonymsAGER1|CDG1R|OKSWcl45|OST|OST48|WBP1
CytomapUCSC genome browser: 1p36.1
Genomic locationchr1 :20978259-20988037
Type of geneprotein-coding
RefGenesNM_005216.4,
Ensembl idENSG00000244038
Descriptionadvanced glycation endproduct receptor 1dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunitdolichyl-diphosphooligosaccharide-protein glycotransferaseoligosaccharyl transferase 48 kDa subunitoligosaccharyltransferase 48 kDa su
Modification date20141219
dbXrefs MIM : 602202
HGNC : HGNC
Ensembl : ENSG00000244038
HPRD : 03728
Vega : OTTHUMG00000002844
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DDOST
BioGPS: 1650
Gene Expression Atlas: ENSG00000244038
The Human Protein Atlas: ENSG00000244038
PathwayNCI Pathway Interaction Database: DDOST
KEGG: DDOST
REACTOME: DDOST
ConsensusPathDB
Pathway Commons: DDOST
MetabolismMetaCyc: DDOST
HUMANCyc: DDOST
RegulationEnsembl's Regulation: ENSG00000244038
miRBase: chr1 :20,978,259-20,988,037
TargetScan: NM_005216
cisRED: ENSG00000244038
ContextiHOP: DDOST
cancer metabolism search in PubMed: DDOST
UCL Cancer Institute: DDOST
Assigned class in ccmGDBC

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Phenotypic Information for DDOST(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DDOST
Familial Cancer Database: DDOST
* 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_PROTEINS

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

Mutations for DDOST
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryDDOSTchr12098491420985114chr4106245716106245916
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 DDOST related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF572086DDOST120112097898520979402ITPKC193224194122755141227583
AW411410SOX6461510111624944116249490DDOST50859012097881220978894
AW411241SOX6479528111624944116249490DDOST52661212097881220978898
AW467499LYZ193126974754569747637DDOST8338012097861320978909
AW614804OSTC13124109588663109588974DDOST30258512097866020978943
BF306134TMEM5616318519563994395639966DDOST18067712097861720979214

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
There's no copy number variation information in COSMIC data for this gene.

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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=20)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=1)
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
chr1:20981988-20981988p.A183S2
chr1:20979452-20979452p.V336M1
chr1:20981985-20981985p.P184T1
chr1:20978950-20978950p.S431S1
chr1:20987720-20987720p.T59A1
chr1:20980210-20980210p.K301K1
chr1:20981986-20981986p.A183A1
chr1:20978956-20978956p.Y429Y1
chr1:20987752-20987752p.L48S1
chr1:20980730-20980730p.A277A1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   9    1  212  43 4
# mutation   10    1  212  43 4
nonsynonymous SNV   4    1  11   2  3
synonymous SNV   6       1 2  23 1
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
chr1:20980730p.A277A2
chr1:20981953p.A425T1
chr1:20987823p.V113M1
chr1:20978970p.S405F1
chr1:20981967p.L86F1
chr1:20987829p.D383N1
chr1:20979121p.L74I1
chr1:20981983p.L340I1
chr1:20987835p.L34L1
chr1:20979188p.V336M1

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 DDOST 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 DDOST

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

PITHD1,SZRD1,CALR,DDOST,DNAJB11,ENO1,KDM1A,
EMC1,KIAA2013,LYPLA2,MRTO4,P4HB,PDIA4,PDIA5,
PDIA6,PLOD1,PPIB,RCC2,RPN1,SEC61A1,SRM
AP1S1,APH1A,C11orf49,CAPN1,DDOST,EBNA1BP2,ERGIC3,
GMDS,H2AFY2,MBOAT7,NIPSNAP1,NPM3,PAFAH1B3,PRPF19,
RFC2,RNASEH2A,RUVBL1,SCAMP4,SLC35B2,STAP2,TMED3

AKR7A2,APITD1,C19orf10,PITHD1,SZRD1,MINOS1,KDF1,
CDC42,DDOST,EIF3I,ENO1,GPN2,HMGN2,EMC1,
MANF,MED18,MRTO4,NUDC,PPP1R8,SDF4,SDHB
APRT,BID,C19orf10,COPZ1,DDOST,ILF2,MTHFD2,
NPM3,NUDT5,NUF2,NUP37,PCNA,PDIA6,PPIB,
PRDX4,PYCR1,SNRPD3,SYNGR2,TMED3,TMED9,ZDHHC16
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 DDOST


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