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 EDEM2
Basic gene info.Gene symbolEDEM2
Gene nameER degradation enhancer, mannosidase alpha-like 2
SynonymsC20orf31|C20orf49|bA4204.1
CytomapUCSC genome browser: 20q11.22
Genomic locationchr20 :33703159-33735161
Type of geneprotein-coding
RefGenesNM_001145025.1,
NM_018217.2,NR_026728.1,
Ensembl idENSG00000088298
DescriptionER degradation-enhancing alpha-mannosidase-like 2ER degradation-enhancing alpha-mannosidase-like protein 2ER degradation-enhancing-mannosidase-like protein 2
Modification date20141207
dbXrefs MIM : 610302
HGNC : HGNC
Ensembl : ENSG00000088298
HPRD : 09841
Vega : OTTHUMG00000032322
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EDEM2
BioGPS: 55741
Gene Expression Atlas: ENSG00000088298
The Human Protein Atlas: ENSG00000088298
PathwayNCI Pathway Interaction Database: EDEM2
KEGG: EDEM2
REACTOME: EDEM2
ConsensusPathDB
Pathway Commons: EDEM2
MetabolismMetaCyc: EDEM2
HUMANCyc: EDEM2
RegulationEnsembl's Regulation: ENSG00000088298
miRBase: chr20 :33,703,159-33,735,161
TargetScan: NM_001145025
cisRED: ENSG00000088298
ContextiHOP: EDEM2
cancer metabolism search in PubMed: EDEM2
UCL Cancer Institute: EDEM2
Assigned class in ccmGDBC

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Phenotypic Information for EDEM2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EDEM2
Familial Cancer Database: EDEM2
* 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: EDEM2
MedGen: EDEM2 (Human Medical Genetics with Condition)
ClinVar: EDEM2
PhenotypeMGI: EDEM2 (International Mouse Phenotyping Consortium)
PhenomicDB: EDEM2

Mutations for EDEM2
* 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
pancreasEDEM2chr203370681133706831chr176238087162380891
pancreasEDEM2chr203372143633721456PRKCAchr176433325164333271
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 EDEM2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK128432BIRC61289623272091332723809EDEM228933032203386513033865269
BQ015907EDEM218195203385638933856566CTSS1926791150705384150722629
BE938093NAPB12316202335543923356179EDEM2311415203370335033703454

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 # sample1  1    1    11 1
GAIN (# sample)1       1    11 1
LOSS (# sample)   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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=35)
Stat. for Synonymous SNVs
(# total SNVs=8)
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
chr20:33703611-33703611p.F454F2
chr20:33711741-33711741p.P356S2
chr20:33703408-33703408p.S522L2
chr20:33725697-33725697p.R159Q2
chr20:33722565-33722565p.W226C2
chr20:33703607-33703607p.A456T1
chr20:33722705-33722705p.H180Y1
chr20:33706505-33706505p.M378V1
chr20:33734964-33734964p.A33V1
chr20:33703284-33703284p.F563L1

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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
# sample32 6    1  62   73 4
# mutation32 6    1  82   73 4
nonsynonymous SNV12 5       61   51 4
synonymous SNV2  1    1  21   22  
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
chr20:33703611p.F417F,EDEM22
chr20:33703674p.P522P,EDEM21
chr20:33719456p.T323K,EDEM21
chr20:33703296p.R122Q,EDEM21
chr20:33725697p.L519L,EDEM21
chr20:33703686p.P319S,EDEM21
chr20:33719520p.S49R1
chr20:33703305p.T496T,EDEM21
chr20:33734701p.R297W,EDEM21
chr20:33706412p.F3F,EDEM21

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 EDEM2 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 EDEM2

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

ACSS2,C20orf24,AAR2,CEP250,CPNE1,DLGAP4,DSN1,
DYNLRB1,EDEM2,EIF2S2,EIF6,ERGIC3,GSS,MAP1LC3A,
MMP24,NFS1,PIGU,RALY,ROMO1,TRPC4AP,UQCC1
ARHGDIA,ARPC4,C17orf62,C19orf10,CALR,CLIC1,CNPY3,
CRELD2,DBNL,DNASE2,EDEM2,GNPTG,HM13,NECAP2,
NUDT18,OS9,PPIB,SHISA5,SNX17,TMSB10,TRADD

ACOT8,AHCY,C20orf24,AAR2,COMMD7,CTNNBL1,DYNLRB1,
EDEM2,EIF6,ERGIC3,NFS1,PDRG1,PIGU,PSMA7,
RALY,ROMO1,SYS1,TP53RK,TPD52L2,TRPC4AP,UQCC1
APH1A,ATPIF1,PTRHD1,CCDC71,EDEM2,ERGIC3,IMP3,
ISCA2,JTB,KRTCAP3,MAPKAPK3,NUDT16L1,RAB25,RPS29,
STAMBP,STK16,TMEM179B,TXN2,UBAC2,UXT,YDJC
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 EDEM2


There's no related Drug.
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Cross referenced IDs for EDEM2
* 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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