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 EPHX2
Basic gene info.Gene symbolEPHX2
Gene nameepoxide hydrolase 2, cytoplasmic
SynonymsCEH|SEH
CytomapUCSC genome browser: 8p21
Genomic locationchr8 :27348684-27402439
Type of geneprotein-coding
RefGenesNM_001256482.1,
NM_001256483.1,NM_001256484.1,NM_001979.5,
Ensembl idENSG00000120915
Descriptionbifunctional epoxide hydrolase 2epoxide hydrataseepoxide hydrolase 2, cytosolicepoxide hydrolase, soluble
Modification date20141207
dbXrefs MIM : 132811
HGNC : HGNC
Ensembl : ENSG00000120915
HPRD : 00582
Vega : OTTHUMG00000102115
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EPHX2
BioGPS: 2053
Gene Expression Atlas: ENSG00000120915
The Human Protein Atlas: ENSG00000120915
PathwayNCI Pathway Interaction Database: EPHX2
KEGG: EPHX2
REACTOME: EPHX2
ConsensusPathDB
Pathway Commons: EPHX2
MetabolismMetaCyc: EPHX2
HUMANCyc: EPHX2
RegulationEnsembl's Regulation: ENSG00000120915
miRBase: chr8 :27,348,684-27,402,439
TargetScan: NM_001256482
cisRED: ENSG00000120915
ContextiHOP: EPHX2
cancer metabolism search in PubMed: EPHX2
UCL Cancer Institute: EPHX2
Assigned class in ccmGDBC

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Phenotypic Information for EPHX2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EPHX2
Familial Cancer Database: EPHX2
* 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_ARACHIDONIC_ACID_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: EPHX2
MedGen: EPHX2 (Human Medical Genetics with Condition)
ClinVar: EPHX2
PhenotypeMGI: EPHX2 (International Mouse Phenotyping Consortium)
PhenomicDB: EPHX2

Mutations for EPHX2
* 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
* 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
liverEPHX2chr82738985927389859SCARA5chr82783091027830910
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 EPHX2 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1                
GAIN (# sample)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=41)
Stat. for Synonymous SNVs
(# total SNVs=19)
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
chr8:27382971-27382971p.Q384L3
chr8:27382881-27382881p.A354V3
chr8:27382957-27382957p.P379P3
chr8:27398124-27398124p.E444K2
chr8:27364474-27364474p.T208M2
chr8:27358512-27358512p.E57E2
chr8:27362584-27362584p.S153L2
chr8:27369368-27369368p.A226T2
chr8:27396186-27396186p.S418F2
chr8:27379945-27379945p.L326L2

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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
# sample31121 4 1  443  95 12
# mutation31121 4 1  443  95 13
nonsynonymous SNV2 12  4 1  133  54 8
synonymous SNV11  1      31   41 5
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
chr8:27364474p.T142M,EPHX22
chr8:27396186p.S352F,EPHX22
chr8:27373267p.A29V,EPHX21
chr8:27361194p.S172T,EPHX21
chr8:27396187p.N365D,EPHX21
chr8:27364405p.L40L,EPHX21
chr8:27401308p.G174G,EPHX21
chr8:27373843p.P370H,EPHX21
chr8:27361207p.R47S,EPHX21
chr8:27398071p.V176M,EPHX21

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 EPHX2 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 EPHX2

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

ALDH6A1,BNIP3L,CCDC25,ELP3,EPHX2,FBXO16,FBXO25,
HMGCL,INTS9,CCAR2,KIF13B,NEK11,NOSTRIN,NUDT18,
PHYHD1,RORC,SH2D4A,SIAE,TMEM25,UBXN8,ZNF395
AGBL5,CIRBP,EPHX2,GNG7,HSD17B8,IL17RC,ING5,
LGTN,LOC100286793,MKS1,POLR1E,RPL3,RPL4,RPL5,
RPL7A,RPS18,RPS6,SNHG8,TMCO4,VIPR1,ZNF821

AGPAT5,BIN3,CCDC25,CNOT7,ELP3,DMTN,EPHX2,
ERICH1,FBXO25,INTS10,INTS9,KBTBD11,CCAR2,LONRF1,
MCPH1,NAT1,NAT2,TRIM35,TTC38,VPS37A,XPO7
ACY1,CCDC108,CHN2,CLDN15,CYP2J2,DAK,DDC,
DEGS2,DGAT1,EPHX2,FBP1,IYD,MACC1,MMEL1,
MARC2,MYO1A,PCK2,PKLR,SLC37A4,SLC39A5,TM4SF5
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 EPHX2
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
DB01248epoxide hydrolase 2, cytoplasmicapproved; investigationalDocetaxel


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Cross referenced IDs for EPHX2
* 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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