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 EDEM3
Basic gene info.Gene symbolEDEM3
Gene nameER degradation enhancer, mannosidase alpha-like 3
SynonymsC1orf22
CytomapUCSC genome browser: 1q25
Genomic locationchr1 :184659624-184724041
Type of geneprotein-coding
RefGenesNM_025191.3,
Ensembl idENSG00000116406
DescriptionER degradation-enhancing -mannosidase-like protein 3ER degradation-enhancing alpha-mannosidase-like 3ER degradation-enhancing alpha-mannosidase-like protein 3alpha-1,2-mannosidase EDEM3
Modification date20141207
dbXrefs MIM : 610214
HGNC : HGNC
Ensembl : ENSG00000116406
HPRD : 10724
Vega : OTTHUMG00000035387
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EDEM3
BioGPS: 80267
Gene Expression Atlas: ENSG00000116406
The Human Protein Atlas: ENSG00000116406
PathwayNCI Pathway Interaction Database: EDEM3
KEGG: EDEM3
REACTOME: EDEM3
ConsensusPathDB
Pathway Commons: EDEM3
MetabolismMetaCyc: EDEM3
HUMANCyc: EDEM3
RegulationEnsembl's Regulation: ENSG00000116406
miRBase: chr1 :184,659,624-184,724,041
TargetScan: NM_025191
cisRED: ENSG00000116406
ContextiHOP: EDEM3
cancer metabolism search in PubMed: EDEM3
UCL Cancer Institute: EDEM3
Assigned class in ccmGDBC

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Phenotypic Information for EDEM3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EDEM3
Familial Cancer Database: EDEM3
* 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: EDEM3
MedGen: EDEM3 (Human Medical Genetics with Condition)
ClinVar: EDEM3
PhenotypeMGI: EDEM3 (International Mouse Phenotyping Consortium)
PhenomicDB: EDEM3

Mutations for EDEM3
* 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
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasEDEM3chr1184691261184691281ASTN1chr1176989263176989283
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 EDEM3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF919684TBPL1273006134274374134301303EDEM32924251184662691184662824
M16328EDEM343471184664188184664531GBAP134825871155204244155210991
CV569883EDEM3102851184660956184661234EDEM32785231184662192184662437

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  1   
GAIN (# sample)2         1  1   
LOSS (# sample)                 
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=55)
Stat. for Synonymous SNVs
(# total SNVs=23)
Stat. for Deletions
(# total SNVs=2)
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
chr1:184663581-184663581p.Q762Q3
chr1:184681639-184681639p.I445I2
chr1:184703759-184703759p.E79*2
chr1:184663418-184663418p.P817S2
chr1:184680954-184680954p.Q489K2
chr1:184706771-184706771p.R50R2
chr1:184680990-184680990p.D477N2
chr1:184677464-184677464p.I577I2
chr1:184663537-184663537p.I777S2
chr1:184695455-184695455p.A184A1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22 10  1 1  751  9515
# mutation22 9  1 1  751  9716
nonsynonymous SNV22 4  1 1  451  5513
synonymous SNV   5       3    42 3
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
chr1:184681639p.I488I3
chr1:184706771p.R93R2
chr1:184706786p.G88G2
chr1:184677474p.A617V2
chr1:184718701p.F194F1
chr1:184679666p.F766F1
chr1:184688331p.R394T1
chr1:184663564p.F393L1
chr1:184695461p.D139N1
chr1:184723669p.L747L1

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 EDEM3 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 EDEM3

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

ACBD3,ANGEL2,ASH1L,BLZF1,SWT1,C1orf27,BROX,
CD46,CDC73,CEP350,EDEM3,MIA3,POLK,RAB3GAP2,
RALGPS2,TOR1AIP1,TOR1AIP2,UHMK1,ZBTB41,ZNF281,ZNF678
ACAP2,ANKIB1,BMPR2,CAMSAP2,CDC73,CLOCK,CPD,
DICER1,DMXL1,DNAJB14,EDEM3,FRYL,INTS2,ITCH,
MAP3K2,PIK3C2A,RAB3GAP2,SEL1L,SLC30A6,TNPO1,UBR1

ACBD3,ARNT,ATF6,BLZF1,CEP350,COPA,EDEM3,
EGLN1,F11R,FAM177B,FAM20B,FBXO28,GNAQ,GOLPH3L,
KCTD3,KDM5B,MIA3,RNASEL,TM9SF3,UAP1,WDR26
APAF1,ARFGEF2,ATP11B,CFTR,DOPEY2,EDEM3,FAM102B,
FGD4,FNBP1L,FRYL,GALNT3,KIAA1468,KIAA1598,MCTP2,
MYO5C,PAWR,SATB2,SLC9A2,TM9SF3,TOX3,UTP14C
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 EDEM3


There's no related Drug.
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Cross referenced IDs for EDEM3
* 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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