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 DDOST

Basic gene info.	Gene symbol	DDOST
	Gene name	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)
	Synonyms	AGER1\|CDG1R\|OKSWcl45\|OST\|OST48\|WBP1
	Cytomap	UCSC genome browser: 1p36.1
	Genomic location	chr1 :20978259-20988037
	Type of gene	protein-coding
	RefGenes	NM_005216.4,
	Ensembl id	ENSG00000244038
	Description	advanced glycation endproduct receptor 1dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunitdolichyl-diphosphooligosaccharide-protein glycotransferaseoligosaccharyl transferase 48 kDa subunitoligosaccharyltransferase 48 kDa su
	Modification date	20141219
dbXrefs	MIM : 602202
	HGNC : HGNC
	Ensembl : ENSG00000244038
	HPRD : 03728
	Vega : OTTHUMG00000002844
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DDOST
	BioGPS: 1650
	Gene Expression Atlas: ENSG00000244038
	The Human Protein Atlas: ENSG00000244038
Pathway	NCI Pathway Interaction Database: DDOST
	KEGG: DDOST
	REACTOME: DDOST
	ConsensusPathDB
	Pathway Commons: DDOST
Metabolism	MetaCyc: DDOST
	HUMANCyc: DDOST
Regulation	Ensembl's Regulation: ENSG00000244038
	miRBase: chr1 :20,978,259-20,988,037
	TargetScan: NM_005216
	cisRED: ENSG00000244038
Context	iHOP: DDOST
	cancer metabolism search in PubMed: DDOST
	UCL Cancer Institute: DDOST
Assigned class in ccmGDB	C

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

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: DDOST
	MedGen: DDOST (Human Medical Genetics with Condition)
	ClinVar: DDOST
Phenotype	MGI: DDOST (International Mouse Phenotyping Consortium)
Phenotype	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.

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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	DDOST	chr1	20984914	20985114		chr4	106245716	106245916

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 DDOST 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
BF572086	DDOST	1	201	1	20978985	20979402	ITPKC	193	224	19	41227551	41227583
AW411410	SOX6	461	510	11	16249441	16249490	DDOST	508	590	1	20978812	20978894
AW411241	SOX6	479	528	11	16249441	16249490	DDOST	526	612	1	20978812	20978898
AW467499	LYZ	1	93	12	69747545	69747637	DDOST	83	380	1	20978613	20978909
AW614804	OSTC	1	312	4	109588663	109588974	DDOST	302	585	1	20978660	20978943
BF306134	TMEM56	163	185	1	95639943	95639966	DDOST	180	677	1	20978617	20979214

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

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

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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=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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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
chr1:20981988-20981988	p.A183S	2
chr1:20982261-20982261	p.R139*	1
chr1:20979149-20979149	p.R396R	1
chr1:20987829-20987829	p.T22T	1
chr1:20980831-20980831	p.I244V	1
chr1:20982631-20982631	p.G122G	1
chr1:20979188-20979188	p.D383N	1
chr1:20987835-20987835	p.P20P	1
chr1:20980854-20980854	p.A236V	1
chr1:20982660-20982660	p.V113M	1

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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=3

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				9					1			2	1	2			4	3		4
# mutation				10					1			2	1	2			4	3		4
nonsynonymous SNV				4					1			1	1				2			3
synonymous SNV				6								1		2			2	3		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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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
chr1:20980730	p.A277A	2
chr1:20981986	p.D383N	1
chr1:20979452	p.L74I	1
chr1:20982214	p.L340I	1
chr1:20980210	p.L34L	1
chr1:20982660	p.V336M	1
chr1:20987434	p.L33L	1
chr1:20980731	p.K301K	1
chr1:20987470	p.A24A	1
chr1:20980800	p.T22T	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 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

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


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

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 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