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 EBP
Basic gene info.Gene symbolEBP
Gene nameemopamil binding protein (sterol isomerase)
SynonymsCDPX2|CHO2|CPX|CPXD
CytomapUCSC genome browser: Xp11.23-p11.22
Genomic locationchrX :48380163-48387104
Type of geneprotein-coding
RefGenesNM_006579.2,
Ensembl idENSG00000268394
Description3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase3-beta-hydroxysteroid-delta-8,delta-7-isomeraseChondrodysplasia punctata-2, X-linked dominant (Happle syndrome)D8-D7 sterol isomerasecholestenol Delta-isomerasedelta(8)-Delta(7) sterol isomeraseemopam
Modification date20141222
dbXrefs MIM : 300205
HGNC : HGNC
HPRD : 02192
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EBP
BioGPS: 10682
Gene Expression Atlas: ENSG00000268394
The Human Protein Atlas: ENSG00000268394
PathwayNCI Pathway Interaction Database: EBP
KEGG: EBP
REACTOME: EBP
ConsensusPathDB
Pathway Commons: EBP
MetabolismMetaCyc: EBP
HUMANCyc: EBP
RegulationEnsembl's Regulation: ENSG00000268394
miRBase: chrX :48,380,163-48,387,104
TargetScan: NM_006579
cisRED: ENSG00000268394
ContextiHOP: EBP
cancer metabolism search in PubMed: EBP
UCL Cancer Institute: EBP
Assigned class in ccmGDBC

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Phenotypic Information for EBP(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EBP
Familial Cancer Database: EBP
* 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_LIPIDS_AND_LIPOPROTEINS

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

Mutations for EBP
* 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 EBP related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=15)
Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr23:48382321-48382321p.A54A5
chr23:48382320-48382320p.A54V3
chr23:48386663-48386663p.R171C2
chr23:48382174-48382174p.A5A2
chr23:48386774-48386774p.V208fs*11
chr23:48382228-48382228p.P23P1
chr23:48382420-48382420p.Y87Y1
chr23:48386821-48386821p.T223T1
chr23:48382237-48382237p.R26R1
chr23:48385382-48385382p.E103*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=8

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2 10       1 2   1 5
# mutation 2 5       1 2   1 5
nonsynonymous SNV 1 3       1 2   1 2
synonymous SNV 1 2               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
chrX:48382321p.A54A5
chrX:48382320p.A54V3
chrX:48382237p.H181R1
chrX:48386821p.L205F1
chrX:48382289p.T223T1
chrX:48382317p.G6V1
chrX:48382367p.H15Y1
chrX:48382377p.P23P1
chrX:48385405p.R26R1
chrX:48382176p.V44M1

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 EBP 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 EBP

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

ATP5J2,CCDC22,CDK16,COX6B1,COX7B,EBP,FDPS,
FTSJ1,GPKOW,HSD17B10,MVD,NDUFB11,PLP2,PQBP1,
RPP21,SHFM1,SUV39H1,TIMM17B,TMSB10,UXT,WDR13
AKR1A1,ALDH3B2,CYB561D2,DHCR7,EBP,FDPS,G6PD,
GALE,GGT1,GGTLC2,GSS,HIST1H3D,HRASLS2,CERS4,
MFSD7,MMAB,MVD,MVK,QPRT,SLC50A1,REEP6

AIFM1,APOO,COX7B,EBP,EMD,FAM58A,HAUS7,
HSD17B10,IDH3G,MCTS1,MMAB,NAA10,NDUFA1,NDUFB11,
NSDHL,PDHA1,PDZD11,PQBP1,SUV39H1,TIMM17B,UXT
ATP6V0A2,BRI3BP,C1GALT1,EBP,FDFT1,FDPS,GSR,
H2AFY,IDI1,MGST2,MMAB,MPDU1,NSDHL,NUDT8,
PCYT2,PI4K2B,PLEK2,S100A14,STARD4,TALDO1,TXNDC17
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 EBP


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