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 DAD1
Basic gene info.Gene symbolDAD1
Gene namedefender against cell death 1
SynonymsOST2
CytomapUCSC genome browser: 14q11.2
Genomic locationchr14 :23033806-23058143
Type of geneprotein-coding
RefGenesNM_001344.3,
Ensembl idENSG00000129562
DescriptionDAD-1dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1oligosaccharyl transferase subunit DAD1oligosaccharyltransferase 2 homologoligosaccharyltransferase subunit 2 (non-catalytic)
Modification date20141207
dbXrefs MIM : 600243
HGNC : HGNC
Ensembl : ENSG00000129562
HPRD : 02589
Vega : OTTHUMG00000028685
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DAD1
BioGPS: 1603
Gene Expression Atlas: ENSG00000129562
The Human Protein Atlas: ENSG00000129562
PathwayNCI Pathway Interaction Database: DAD1
KEGG: DAD1
REACTOME: DAD1
ConsensusPathDB
Pathway Commons: DAD1
MetabolismMetaCyc: DAD1
HUMANCyc: DAD1
RegulationEnsembl's Regulation: ENSG00000129562
miRBase: chr14 :23,033,806-23,058,143
TargetScan: NM_001344
cisRED: ENSG00000129562
ContextiHOP: DAD1
cancer metabolism search in PubMed: DAD1
UCL Cancer Institute: DAD1
Assigned class in ccmGDBC

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Phenotypic Information for DAD1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: DAD1
MedGen: DAD1 (Human Medical Genetics with Condition)
ClinVar: DAD1
PhenotypeMGI: DAD1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DAD1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI094624DAD128339142303380723044039YWHAE3375151712652411268269
BE537940GNB1199249117171041717154DAD1249575142304409323058136
BC013646GNB1215268117171011717154DAD1268959142303380523058136

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=2

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check002.gifSomatic 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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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
chr14:23058038-23058038p.I9S1
chr14:23044008-23044010p.V112delV1
chr14:23058043-23058044p.S7fs*891
chr14:23044032-23044032p.H105Y1
chr14:23044071-23044071p.R92*1
chr14:23044096-23044096p.A83A1
chr14:23044097-23044097p.A83V1
chr14:23057891-23057891p.S58L1
chr14:23057896-23057897p.F56fs*401
chr14:23057900-23057900p.S55Y1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# 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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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
chr14:23044032p.H105Y1
chr14:23057900p.S55Y1
chr14:23057909p.P52L1
chr14:23058005p.T20N1
chr14:23058021p.E15K1
chr14:23058038p.I9S1

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 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

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

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
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 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



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