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 EPHX1
Basic gene info.Gene symbolEPHX1
Gene nameepoxide hydrolase 1, microsomal (xenobiotic)
SynonymsEPHX|EPOX|HYL1|MEH
CytomapUCSC genome browser: 1q42.1
Genomic locationchr1 :226013001-226033262
Type of geneprotein-coding
RefGenesNM_000120.3,
NM_001136018.3,NM_001291163.1,
Ensembl idENSG00000143819
Descriptionepoxide hydrataseepoxide hydrolase 1
Modification date20141207
dbXrefs MIM : 132810
HGNC : HGNC
Ensembl : ENSG00000143819
HPRD : 00581
Vega : OTTHUMG00000037743
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EPHX1
BioGPS: 2052
Gene Expression Atlas: ENSG00000143819
The Human Protein Atlas: ENSG00000143819
PathwayNCI Pathway Interaction Database: EPHX1
KEGG: EPHX1
REACTOME: EPHX1
ConsensusPathDB
Pathway Commons: EPHX1
MetabolismMetaCyc: EPHX1
HUMANCyc: EPHX1
RegulationEnsembl's Regulation: ENSG00000143819
miRBase: chr1 :226,013,001-226,033,262
TargetScan: NM_000120
cisRED: ENSG00000143819
ContextiHOP: EPHX1
cancer metabolism search in PubMed: EPHX1
UCL Cancer Institute: EPHX1
Assigned class in ccmGDBC

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Phenotypic Information for EPHX1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EPHX1
Familial Cancer Database: EPHX1
* 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
KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: EPHX1
MedGen: EPHX1 (Human Medical Genetics with Condition)
ClinVar: EPHX1
PhenotypeMGI: EPHX1 (International Mouse Phenotyping Consortium)
PhenomicDB: EPHX1

Mutations for EPHX1
* 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
ovaryEPHX1chr1226032830226032850SRP9chr1225978033225978053
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 EPHX1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI636871C6orf478344629569102957246EPHX13404551226026353226026468
AW261826PHGDH194001120285616120286838EPHX13955531226016559226019583
BE613010RPL11149612402032324020406EPHX1976871226027547226033006
AI933022EPHX111801226033081226033260JPH3176452168773101787731294
BF513447HNRNPH315299107010174370102028EPHX12993491226033214226033264

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  
GAIN (# sample)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=51)
Stat. for Synonymous SNVs
(# total SNVs=23)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=2)

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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
chr1:226032229-226032229p.N357N3
chr1:226026406-226026406p.H139R3
chr1:226032209-226032209p.L351M2
chr1:226032903-226032903p.T408M2
chr1:226027015-226027015p.L230L2
chr1:226032262-226032262p.I368I2
chr1:226027028-226027028p.M235L2
chr1:226027031-226027031p.A236T2
chr1:226032273-226032273p.R372P2
chr1:226019633-226019633p.Y113H2

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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
# sample 1 92 215  513  74 4
# mutation 1 92 215  513  74 5
nonsynonymous SNV 1 71 114  4 3  23 2
synonymous SNV   21 1 1  11   51 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
chr1:226032903p.F268F,EPHX12
chr1:226027611p.T408K,EPHX12
chr1:226027630p.K23Q,EPHX11
chr1:226016460p.P240H,EPHX11
chr1:226032237p.R372C,EPHX11
chr1:226026435p.G32V,EPHX11
chr1:226027665p.G245R,EPHX11
chr1:226016497p.T384A,EPHX11
chr1:226032272p.T38T,EPHX11
chr1:226026455p.V392V,EPHX11

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 EPHX1 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 EPHX1

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

ARF1,ARV1,CD63,EPHX1,LYPLAL1,MFSD5,MRPL55,
NANS,NDUFB1,ORMDL2,PRR13,PYCR2,SLC50A1,RNF187,
LAMTOR2,SELENBP1,SQSTM1,SRA1,SRP9,TMEM9,UQCRQ
AIFM2,AKR1C3,AOC3,BTD,CALB2,CPNE2,EHD2,
EPHX1,FADS3,GPD1,ITGB1BP1,ITPK1,MCAM,MGLL,
MRAS,RETSAT,SERPINF1,TFE3,TK2,VEGFB,VTI1B

BMP7,CCDC115,CST7,CTNNA2,CYB5R1,DDIT4L,EPHX1,
GLP1R,HOTAIR,HOXC12,HRNR,HSPA12A,KIAA0087,LOC92973,
MME,NEURL3,OR13J1,PROM2,RGSL1,RPLP0P2,SMYD3
ABHD4,ATPAF1,BTBD2,NATD1,CDIPT,DBNDD1,EEF2,
EPHX1,FOXO4,GLTSCR2,HDAC11,HDAC5,KCNJ12,KIAA1107,
MYLIP,PGBD3,RNF208,SORBS3,WDTC1,WIPI2,ZNF395
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 EPHX1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00252epoxide hydrolase 1, microsomal (xenobiotic)approvedPhenytoin
DB01248epoxide hydrolase 1, microsomal (xenobiotic)approved; investigationalDocetaxel
DB00564epoxide hydrolase 1, microsomal (xenobiotic)approved; investigationalCarbamazepine
DB00313epoxide hydrolase 1, microsomal (xenobiotic)approved; investigationalValproic Acid
DB00917epoxide hydrolase 1, microsomal (xenobiotic)approvedDinoprostone
DB01240epoxide hydrolase 1, microsomal (xenobiotic)approvedEpoprostenol
DB00682epoxide hydrolase 1, microsomal (xenobiotic)approvedWarfarin


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Cross referenced IDs for EPHX1
* 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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