Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	EPHX1
	Gene name	epoxide hydrolase 1, microsomal (xenobiotic)
	Synonyms	EPHX\|EPOX\|HYL1\|MEH
	Cytomap	UCSC genome browser: 1q42.1
	Genomic location	chr1 :226013001-226033262
	Type of gene	protein-coding
	RefGenes	NM_000120.3, NM_001136018.3,NM_001291163.1,
	Ensembl id	ENSG00000143819
	Description	epoxide hydrataseepoxide hydrolase 1
	Modification date	20141207
dbXrefs	MIM : 132810
	HGNC : HGNC
	Ensembl : ENSG00000143819
	HPRD : 00581
	Vega : OTTHUMG00000037743
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EPHX1
	BioGPS: 2052
	Gene Expression Atlas: ENSG00000143819
	The Human Protein Atlas: ENSG00000143819
Pathway	NCI Pathway Interaction Database: EPHX1
	KEGG: EPHX1
	REACTOME: EPHX1
	ConsensusPathDB
	Pathway Commons: EPHX1
Metabolism	MetaCyc: EPHX1
	HUMANCyc: EPHX1
Regulation	Ensembl's Regulation: ENSG00000143819
	miRBase: chr1 :226,013,001-226,033,262
	TargetScan: NM_000120
	cisRED: ENSG00000143819
Context	iHOP: EPHX1
	cancer metabolism search in PubMed: EPHX1
	UCL Cancer Institute: EPHX1
Assigned class in ccmGDB	C

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Phenotypic Information for EPHX1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450

Others
OMIM
Orphanet
Disease	KEGG Disease: EPHX1
	MedGen: EPHX1 (Human Medical Genetics with Condition)
	ClinVar: EPHX1
Phenotype	MGI: EPHX1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	EPHX1	chr1	226032830	226032850	SRP9	chr1	225978033	225978053

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EPHX1 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
AI636871	C6orf47	8	344	6	2956910	2957246	EPHX1	340	455	1	226026353	226026468
AW261826	PHGDH	19	400	1	120285616	120286838	EPHX1	395	553	1	226016559	226019583
BE613010	RPL11	14	96	1	24020323	24020406	EPHX1	97	687	1	226027547	226033006
AI933022	EPHX1	1	180	1	226033081	226033260	JPH3	176	452	16	87731017	87731294
BF513447	HNRNPH3	15	299	10	70101743	70102028	EPHX1	299	349	1	226033214	226033264

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr1:226026406-226026406	p.H139R	3
chr1:226032229-226032229	p.N357N	3
chr1:226032262-226032262	p.I368I	2
chr1:226027015-226027015	p.L230L	2
chr1:226027028-226027028	p.M235L	2
chr1:226032273-226032273	p.R372P	2
chr1:226027031-226027031	p.A236T	2
chr1:226019633-226019633	p.Y113H	2
chr1:226016439-226016439	p.L3L	2
chr1:226032877-226032877	p.S399S	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		1		9	2		2	1	5			5	1	3			7	4		4
# mutation		1		9	2		2	1	5			5	1	3			7	4		5
nonsynonymous SNV		1		7	1		1	1	4			4		3			2	3		2
synonymous SNV				2	1		1		1			1	1				5	1		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr1:226032903	p.F268F,EPHX1	2
chr1:226027611	p.T408K,EPHX1	2
chr1:226027678	p.F415L,EPHX1	1
chr1:226016525	p.I67I,EPHX1	1
chr1:226032308	p.T275A,EPHX1	1
chr1:226026479	p.I421I,EPHX1	1
chr1:226027685	p.F70F,EPHX1	1
chr1:226016544	p.K286K,EPHX1	1
chr1:226032856	p.R428H,EPHX1	1
chr1:226026529	p.R71R,EPHX1	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00252	epoxide hydrolase 1, microsomal (xenobiotic)	approved	Phenytoin
DB01248	epoxide hydrolase 1, microsomal (xenobiotic)	approved; investigational	Docetaxel
DB00564	epoxide hydrolase 1, microsomal (xenobiotic)	approved; investigational	Carbamazepine
DB00313	epoxide hydrolase 1, microsomal (xenobiotic)	approved; investigational	Valproic Acid
DB00917	epoxide hydrolase 1, microsomal (xenobiotic)	approved	Dinoprostone
DB01240	epoxide hydrolase 1, microsomal (xenobiotic)	approved	Epoprostenol
DB00682	epoxide hydrolase 1, microsomal (xenobiotic)	approved	Warfarin

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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