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 ALOX5
Basic gene info.Gene symbolALOX5
Gene namearachidonate 5-lipoxygenase
Synonyms5-LO|5-LOX|5LPG|LOG5
CytomapUCSC genome browser: 10q11.2
Genomic locationchr10 :45869623-45941567
Type of geneprotein-coding
RefGenesNM_000698.3,
NM_001256153.1,NM_001256154.1,
Ensembl idENSG00000262552
DescriptionLOX-5arachidonic 5-lipoxygenase alpha-10 isoformarachidonic 5-lipoxygenase delta-10-13 isoformarachidonic 5-lipoxygenase delta-13 isoformarachidonic 5-lipoxygenase delta-p10 isoformarachidonic acid 5-lipoxygenaseleukotriene A4 synthase
Modification date20141207
dbXrefs MIM : 152390
HGNC : HGNC
Ensembl : ENSG00000012779
HPRD : 01065
Vega : OTTHUMG00000018081
ProteinUniProt: P09917
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALOX5
BioGPS: 240
Gene Expression Atlas: ENSG00000262552
The Human Protein Atlas: ENSG00000262552
PathwayNCI Pathway Interaction Database: ALOX5
KEGG: ALOX5
REACTOME: ALOX5
ConsensusPathDB
Pathway Commons: ALOX5
MetabolismMetaCyc: ALOX5
HUMANCyc: ALOX5
RegulationEnsembl's Regulation: ENSG00000262552
miRBase: chr10 :45,869,623-45,941,567
TargetScan: NM_000698
cisRED: ENSG00000262552
ContextiHOP: ALOX5
cancer metabolism search in PubMed: ALOX5
UCL Cancer Institute: ALOX5
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for ALOX5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ALOX5
Familial Cancer Database: ALOX5
* 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 152390; gene.
Orphanet
DiseaseKEGG Disease: ALOX5
MedGen: ALOX5 (Human Medical Genetics with Condition)
ClinVar: ALOX5
PhenotypeMGI: ALOX5 (International Mouse Phenotyping Consortium)
PhenomicDB: ALOX5

Mutations for ALOX5
* 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
ovaryALOX5chr104593063045930650chr104584851545848535
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 ALOX5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF895730ALOX521274104592229245922547ABCA1325546574862683748654939

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  2 1     1  
GAIN (# sample)1             1  
LOSS (# sample)   1  2 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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=64)		Stat. for Synonymous SNVs
(# total SNVs=22)
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
chr10:45891350-45891350p.R133S3
chr10:45891356-45891356p.E135K3
chr10:45869748-45869748p.T7T3
chr10:45936008-45936008p.R371Q3
chr10:45938939-45938939p.F509F2
chr10:45891369-45891369p.R139Q2
chr10:45924111-45924111p.D294N2
chr10:45924146-45924146p.F305F2
chr10:45920488-45920488p.R248C2
chr10:45920489-45920489p.R248H2

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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
# sample1 2161 2 2111112  129 12
# mutation1 2161 2 2111112  1610 16
nonsynonymous SNV   101 2 21 9 2  97 10
synonymous SNV1 26      121   73 6
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
chr10:45935921p.D294N,ALOX52
chr10:45936008p.F305F,ALOX52
chr10:45907676p.D157N,ALOX52
chr10:45924111p.S342L,ALOX52
chr10:45924146p.S200F,ALOX52
chr10:45919533p.R371Q,ALOX52
chr10:45877968p.F556L,ALOX51
chr10:45919567p.G63G,ALOX51
chr10:45939260p.D114N,ALOX51
chr10:45878080p.V244E,ALOX51

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 ALOX5 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 ALOX5

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

ALOX5,ALOX5AP,APBB1IP,CD4,DOCK2,FMNL1,GAB3,
HLA-DMB,ITGAX,ITGB2,LAIR1,LAPTM5,LAT2,MNDA,
MYO1F,NCKAP1L,P2RY13,PIK3R5,PLCB2,PLEKHO2,SLCO2B1		ABCC3,ALOX5,ARID5A,CHI3L1,DGKA,EDN2,IL34,
KCNK13,KLK5,KRT6B,LRRC4C,RARRES1,RGS14,RHBDF2,
SFN,STAC2,TMEM51,TRIM17,VWA5A,WFDC2,WNT7B

ADAM28,AKAP13,ALOX5,ARHGAP22,ARHGAP24,TMEM263,CARD6,
DACT1,EFNA5,EPHA4,FGD6,MAPRE2,MYOF,PIAS3,
PLCL2,PTGER2,ARHGEF28,SHF,SWAP70,TNFAIP8,TRIM8		ACRBP,AGT,ALOX5,BLNK,NCMAP,CD209,CD68,
FUT8,GGT5,GPR114,IRF5,LCT,LGMN,PIK3CG,
PIK3R5,PLCG2,SLCO2B1,SYK,TK2,TRAM2,TTYH3
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 ALOX5
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P09917; -.
ChemistryChEMBL CHEMBL215; -.
ChemistryGuidetoPHARMACOLOGY 1385; -.
Organism-specific databasesPharmGKB PA46; -.
Organism-specific databasesCTD 240; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00163arachidonate 5-lipoxygenaseapproved; nutraceuticalVitamin E
DB00179arachidonate 5-lipoxygenaseapprovedMasoprocol
DB00233arachidonate 5-lipoxygenaseapprovedAminosalicylic Acid
DB00244arachidonate 5-lipoxygenaseapprovedMesalazine
DB00471arachidonate 5-lipoxygenaseapprovedMontelukast
DB00586arachidonate 5-lipoxygenaseapprovedDiclofenac
DB00711arachidonate 5-lipoxygenaseapprovedDiethylcarbamazine
DB00744arachidonate 5-lipoxygenaseapproved; investigationalZileuton
DB00795arachidonate 5-lipoxygenaseapprovedSulfasalazine
DB00939arachidonate 5-lipoxygenaseapprovedMeclofenamic acid
DB01014arachidonate 5-lipoxygenaseapproved; investigationalBalsalazide
DB01017arachidonate 5-lipoxygenaseapproved; investigationalMinocycline
DB01097arachidonate 5-lipoxygenaseapproved; investigationalLeflunomide
DB01892arachidonate 5-lipoxygenasenutraceuticalHyperforin
DB03014arachidonate 5-lipoxygenaseexperimentalHeme
DB00143arachidonate 5-lipoxygenaseapproved; nutraceuticalGlutathione
DB00145arachidonate 5-lipoxygenaseapproved; nutraceuticalGlycine
DB00917arachidonate 5-lipoxygenaseapprovedDinoprostone
DB01240arachidonate 5-lipoxygenaseapprovedEpoprostenol
DB00549arachidonate 5-lipoxygenaseapproved; investigationalZafirlukast


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Cross referenced IDs for ALOX5
* 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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