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 DAD1

Basic gene info.	Gene symbol	DAD1
	Gene name	defender against cell death 1
	Synonyms	OST2
	Cytomap	UCSC genome browser: 14q11.2
	Genomic location	chr14 :23033806-23058143
	Type of gene	protein-coding
	RefGenes	NM_001344.3,
	Ensembl id	ENSG00000129562
	Description	DAD-1dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1oligosaccharyl transferase subunit DAD1oligosaccharyltransferase 2 homologoligosaccharyltransferase subunit 2 (non-catalytic)
	Modification date	20141207
dbXrefs	MIM : 600243
	HGNC : HGNC
	Ensembl : ENSG00000129562
	HPRD : 02589
	Vega : OTTHUMG00000028685
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DAD1
	BioGPS: 1603
	Gene Expression Atlas: ENSG00000129562
	The Human Protein Atlas: ENSG00000129562
Pathway	NCI Pathway Interaction Database: DAD1
	KEGG: DAD1
	REACTOME: DAD1
	ConsensusPathDB
	Pathway Commons: DAD1
Metabolism	MetaCyc: DAD1
	HUMANCyc: DAD1
Regulation	Ensembl's Regulation: ENSG00000129562
	miRBase: chr14 :23,033,806-23,058,143
	TargetScan: NM_001344
	cisRED: ENSG00000129562
Context	iHOP: DAD1
	cancer metabolism search in PubMed: DAD1
	UCL Cancer Institute: DAD1
Assigned class in ccmGDB	C

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Phenotypic Information for DAD1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: DAD1
	Familial Cancer Database: DAD1

* 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: DAD1
	MedGen: DAD1 (Human Medical Genetics with Condition)
	ClinVar: DAD1
Phenotype	MGI: DAD1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: DAD1

Mutations for DAD1

* 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

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DAD1 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
AI094624	DAD1	28	339	14	23033807	23044039	YWHAE	337	515	17	1265241	1268269
BE537940	GNB1	199	249	1	1717104	1717154	DAD1	249	575	14	23044093	23058136
BC013646	GNB1	215	268	1	1717101	1717154	DAD1	268	959	14	23033805	23058136

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=6)	Stat. for Synonymous SNVs (# total SNVs=0)
	There's no s-snv.
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
chr14:23058005-23058005	p.T20N	1
chr14:23058021-23058021	p.E15K	1
chr14:23058038-23058038	p.I9S	1
chr14:23044008-23044010	p.V112delV	1
chr14:23058043-23058044	p.S7fs*89	1
chr14:23044032-23044032	p.H105Y	1
chr14:23044071-23044071	p.R92*	1
chr14:23044096-23044096	p.A83A	1
chr14:23044097-23044097	p.A83V	1
chr14:23057891-23057891	p.S58L	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=1

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				2								1					1			1
# mutation				2								1					1			1
nonsynonymous SNV				2								1					1			1
synonymous SNV

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
chr14:23044032	p.H105Y	1
chr14:23057900	p.S55Y	1
chr14:23057909	p.P52L	1
chr14:23058005	p.T20N	1
chr14:23058021	p.E15K	1
chr14:23058038	p.I9S	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 DAD1 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 DAD1

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


C14orf119,C14orf2,CHMP4A,COX16,DAD1,DHRS4,DHRS4L2, EMC9,FKBP3,MRPL52,NEDD8,NGDN,ORMDL2,OXA1L, PRMT5,PSMB5,PSMC1,RABGGTA,RNF181,RPL36AL,TM9SF1	ATP6V0E1,C14orf119,BRK1,COMMD6,DAD1,DYNLRB1,GABARAP, GTF2A2,JAGN1,KRTCAP2,LAPTM4A,MPV17,MYL12B,NOP10, RAC1,SPCS1,SUMO1,TMEM60,TOMM5,TOMM6,TXNDC12

C14orf119,GSKIP,APOPT1,C14orf166,C14orf2,CINP,CNIH1, DAD1,ERH,GMPR2,ISCA2,MRPL52,NEDD8,OSGEP, PNP,PSMA6,PSMB5,PSMC6,RPL36AL,SCFD1,SIVA1	C14orf119,SLIRP,C14orf166,EMC7,COA6,COX7A2,DAD1, LAMTOR5,MMADHC,MRPL22,NDUFB4,NDUFB6,NDUFV2,PSMB1, PSMC6,PSMD13,PSMD8,RBX1,TXNL1,UBL5,YWHAE

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 DAD1

There's no related Drug.

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Cross referenced IDs for DAD1

* 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