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 LTA4H
Basic gene info.Gene symbolLTA4H
Gene nameleukotriene A4 hydrolase
Synonyms-
CytomapUCSC genome browser: 12q22
Genomic locationchr12 :96394530-96437298
Type of geneprotein-coding
RefGenesNM_000895.2,
NM_001256643.1,NM_001256644.1,
Ensembl idENSG00000111144
DescriptionLTA-4 hydrolaseleukotriene A-4 hydrolase
Modification date20141207
dbXrefs MIM : 151570
HGNC : HGNC
Ensembl : ENSG00000111144
HPRD : 01056
Vega : OTTHUMG00000170355
ProteinUniProt: P09960
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LTA4H
BioGPS: 4048
Gene Expression Atlas: ENSG00000111144
The Human Protein Atlas: ENSG00000111144
PathwayNCI Pathway Interaction Database: LTA4H
KEGG: LTA4H
REACTOME: LTA4H
ConsensusPathDB
Pathway Commons: LTA4H
MetabolismMetaCyc: LTA4H
HUMANCyc: LTA4H
RegulationEnsembl's Regulation: ENSG00000111144
miRBase: chr12 :96,394,530-96,437,298
TargetScan: NM_000895
cisRED: ENSG00000111144
ContextiHOP: LTA4H
cancer metabolism search in PubMed: LTA4H
UCL Cancer Institute: LTA4H
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of LTA4H in cancer cell metabolism1. Guo Y, Wang X, Zhang X, Sun Z, Chen X (2011) Ethanol promotes chemically induced oral cancer in mice through activation of the 5-lipoxygenase pathway of arachidonic acid metabolism. Cancer Prev Res (Phila) 4: 1863-1872. doi: 10.1158/1940-6207.CAPR-11-0206. pmid: 3208736. go to article
2. Sun Z, Sood S, Li N, Ramji D, Yang P, et al. (2006) Involvement of the 5-lipoxygenase/leukotriene A4 hydrolase pathway in 7,12-dimethylbenz[a]anthracene (DMBA)-induced oral carcinogenesis in hamster cheek pouch, and inhibition of carcinogenesis by its inhibitors. Carcinogenesis 27: 1902-1908. doi: 10.1093/carcin/bgl039. go to article

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Phenotypic Information for LTA4H(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LTA4H
Familial Cancer Database: LTA4H
* 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 151570; gene.
Orphanet
DiseaseKEGG Disease: LTA4H
MedGen: LTA4H (Human Medical Genetics with Condition)
ClinVar: LTA4H
PhenotypeMGI: LTA4H (International Mouse Phenotyping Consortium)
PhenomicDB: LTA4H

Mutations for LTA4H
* 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 LTA4H related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ335002LTA4H4114129639485696396821RPLP210437111810308812822
BE875453LTA4H10179129640014596407038ADCY21733341152004982152005144

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 # sample11           11  
GAIN (# sample) 1           11  
LOSS (# sample)1                
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=22)		Stat. for Synonymous SNVs
(# total SNVs=4)
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
chr12:96421313-96421313p.F107S3
chr12:96421314-96421314p.F107L2
chr12:96394809-96394809p.P598P2
chr12:96412987-96412987p.E224Q2
chr12:96397644-96397644p.A529T1
chr12:96409430-96409430p.C330C1
chr12:96414878-96414879p.G208fs*161
chr12:96397680-96397680p.H517N1
chr12:96421316-96421316p.S106Y1
chr12:96409440-96409440p.R327H1

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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
# sample11 3    5 1321  54 3
# mutation11 3    4 1321  54 3
nonsynonymous SNV1  2    3 1221  44 3
synonymous SNV 1 1    1  1    1   
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
chr12:96421313p.F107S,LTA4H2
chr12:96421314p.F107L,LTA4H2
chr12:96397680p.A447T,LTA4H1
chr12:96410827p.N441S,LTA4H1
chr12:96421316p.V437A,LTA4H1
chr12:96400102p.S106Y,LTA4H1
chr12:96412590p.A410T,LTA4H1
chr12:96400166p.L366R,LTA4H1
chr12:96412600p.C330C,LTA4H1
chr12:96402917p.P598P,LTA4H1

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 LTA4H 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 LTA4H

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

METTL25,C12orf29,CEP83,EIF4B,LTA4H,METAP2,MRPL42,
NAP1L1,NEDD1,NR2C1,POC1B,PPP1CC,RPL15,RPL17,
RPL6,RPS12,RPS23,SLC25A3,SNRPF,STX7,UBE2N		BTF3,CCNB1IP1,CCT4,CLNS1A,DPH5,EIF2S3,EIF3E,
EIF3L,EIF3M,LTA4H,NIFK,NPM1,RPL15,RPL22,
RPL35A,RPS15A,RPS24,RPS3A,RPS4X,RPS7,TIMM9

ATP5G2,DDX54,DENR,EIF4B,HNRNPA1,LTA4H,METAP2,
NACA,NACAP1,NAP1L1,PA2G4,PCBP2,POLR3B,PPP1CC,
PWP1,RPL13A,RPL3,RPL6,RPLP0,SLC25A3,SNRPF		ABCB7,ACRBP,AZGP1,CDC14B,CLPX,CREBL2,EIF2S3,
EIF3H,EIF4B,FGGY,IGBP1,LETMD1,LTA4H,PCBP2,
ECI2,PLAG1,RAG1,RMND1,RPL22,TMEM19,WDR48
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 LTA4H
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P09960; -.
ChemistryChEMBL CHEMBL4618; -.
ChemistryGuidetoPHARMACOLOGY 1395; -.
Organism-specific databasesPharmGKB PA24345; -.
Organism-specific databasesCTD 4048; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02062leukotriene A4 hydrolaseexperimentalN-[3-[(1-Aminoethyl)(Hydroxy)Phosphoryl]-2-(1,1'-Biphenyl-4-Ylmethyl)Propanoyl]Alanine
DB02352leukotriene A4 hydrolaseexperimental3-(Benzyloxy)Pyridin-2-Amine
DB03424leukotriene A4 hydrolaseexperimentalBestatin
DB06828leukotriene A4 hydrolaseexperimental5-[2-(1H-pyrrol-1-yl)ethoxy]-1H-indole
DB06851leukotriene A4 hydrolaseexperimentalN-(pyridin-3-ylmethyl)aniline
DB06917leukotriene A4 hydrolaseexperimental(4-fluorophenyl)(pyridin-4-yl)methanone
DB07094leukotriene A4 hydrolaseexperimental1-(2,2'-bithiophen-5-yl)methanamine
DB07099leukotriene A4 hydrolaseexperimentalN-[4-(benzyloxy)phenyl]glycinamide
DB07102leukotriene A4 hydrolaseexperimental(2S)-2-amino-5-oxo-5-[(4-phenylmethoxyphenyl)amino]pentanoic acid
DB07104leukotriene A4 hydrolaseexperimental4-amino-N-[4-(benzyloxy)phenyl]butanamide
DB07196leukotriene A4 hydrolaseexperimentalN-methyl-1-(2-thiophen-2-ylphenyl)methanamine
DB07237leukotriene A4 hydrolaseexperimental{4-[(2R)-pyrrolidin-2-ylmethoxy]phenyl}(4-thiophen-3-ylphenyl)methanone
DB07258leukotriene A4 hydrolaseexperimental(R)-pyridin-4-yl[4-(2-pyrrolidin-1-ylethoxy)phenyl]methanol
DB07259leukotriene A4 hydrolaseexperimental1-(4-thiophen-2-ylphenyl)methanamine
DB07260leukotriene A4 hydrolaseexperimentalN-benzyl-4-[(2R)-pyrrolidin-2-ylmethoxy]aniline
DB07292leukotriene A4 hydrolaseexperimental4-(2-amino-1,3-thiazol-4-yl)phenol
DB08040leukotriene A4 hydrolaseexperimentalN-[(2R)-2-benzyl-4-(hydroxyamino)-4-oxobutanoyl]-L-alanine
DB08466leukotriene A4 hydrolaseexperimental5-[2-(4-hydroxyphenyl)ethyl]benzene-1,3-diol
DB00143leukotriene A4 hydrolaseapproved; nutraceuticalGlutathione
DB00145leukotriene A4 hydrolaseapproved; nutraceuticalGlycine
DB00471leukotriene A4 hydrolaseapprovedMontelukast


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Cross referenced IDs for LTA4H
* 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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