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 EDEM1
Basic gene info.Gene symbolEDEM1
Gene nameER degradation enhancer, mannosidase alpha-like 1
SynonymsEDEM
CytomapUCSC genome browser: 3p26.1
Genomic locationchr3 :5229358-5261650
Type of geneprotein-coding
RefGenesNM_014674.2,
Ensembl idENSG00000134109
DescriptionER degradation-enhancing alpha-mannosidase-like 1ER degradation-enhancing alpha-mannosidase-like protein 1
Modification date20141207
dbXrefs MIM : 607673
HGNC : HGNC
Ensembl : ENSG00000134109
HPRD : 09644
Vega : OTTHUMG00000154896
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EDEM1
BioGPS: 9695
Gene Expression Atlas: ENSG00000134109
The Human Protein Atlas: ENSG00000134109
PathwayNCI Pathway Interaction Database: EDEM1
KEGG: EDEM1
REACTOME: EDEM1
ConsensusPathDB
Pathway Commons: EDEM1
MetabolismMetaCyc: EDEM1
HUMANCyc: EDEM1
RegulationEnsembl's Regulation: ENSG00000134109
miRBase: chr3 :5,229,358-5,261,650
TargetScan: NM_014674
cisRED: ENSG00000134109
ContextiHOP: EDEM1
cancer metabolism search in PubMed: EDEM1
UCL Cancer Institute: EDEM1
Assigned class in ccmGDBC

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Phenotypic Information for EDEM1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EDEM1
Familial Cancer Database: EDEM1
* 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: EDEM1
MedGen: EDEM1 (Human Medical Genetics with Condition)
ClinVar: EDEM1
PhenotypeMGI: EDEM1 (International Mouse Phenotyping Consortium)
PhenomicDB: EDEM1

Mutations for EDEM1
* 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 EDEM1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BX487661ANP32E31811150208282150208460EDEM1178639352596315260091
R93121RAPGEF519872235215522352252EDEM195395352419035242197
AW372554CHM9224X8512820485128421EDEM1217293352599645260040

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 # sample2       1        
GAIN (# sample)1       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=31)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr3:5241287-5241287p.N198I2
chr3:5229491-5229491p.M1V2
chr3:5249807-5249807p.I456I2
chr3:5229643-5229643p.G51G2
chr3:5229970-5229970p.C160C1
chr3:5248946-5248946p.F442L1
chr3:5243503-5243503p.M251T1
chr3:5251877-5251877p.F509L1
chr3:5246762-5246762p.V351V1
chr3:5255213-5255213p.?1

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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
# sample6117  3    422  5524
# mutation7118  3    422  5525
nonsynonymous SNV4118  1    211  1324
synonymous SNV3     2    211  42 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
chr3:5243458p.S236F2
chr3:5251877p.F509L2
chr3:5241340p.S398I1
chr3:5252828p.K570T1
chr3:5244745p.D250D1
chr3:5249778p.R404I1
chr3:5241372p.P594S1
chr3:5255023p.M251T1
chr3:5244822p.F441L1
chr3:5249779p.P615P1

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 EDEM1 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 EDEM1

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

AFF4,ARL8B,AZI2,CREBRF,DMXL1,DNAJB14,EDEM1,
GCC2,GIGYF2,GOLGB1,IBTK,KIAA1109,PHC3,PJA2,
RAPGEF6,SCAF11,SPG11,TGOLN2,TMF1,UBR1,XIAP
AFTPH,EDEM1,EIF2AK3,ETNK1,FAM122B,FAM91A1,GSTCD,
MGAT4A,MOB1B,PARP11,PARP8,GSAP,PPIP5K2,PRPF40A,
RALGPS2,PTBP3,SLC30A7,SUZ12,TLK1,TMEM67,UBXN4

AKAP13,C10orf54,CEP85L,DOCK5,EDEM1,ENTPD4,EVI2B,
FAM114A1,FUT11,HIF1A,RIC1,LHFPL2,PFKFB3,PLCL2,
SEC24A,SEC24D,SETX,PEAK1,SNRK,TLR6,UGCG
ADRBK1,ARHGEF16,ARID3B,CSF2RB,CYTH1,DENND1C,DOCK2,
DOCK8,EDEM1,EIF2AK3,ELL,GMIP,GPR114,HMHA1,
HSH2D,PTK2B,PTPRE,SEL1L3,SYNRG,TXNDC11,ZFYVE28
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 EDEM1


There's no related Drug.
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Cross referenced IDs for EDEM1
* 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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