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 PLA2G7
Basic gene info.Gene symbolPLA2G7
Gene namephospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)
SynonymsLDL-PLA2|LP-PLA2|PAFAD|PAFAH
CytomapUCSC genome browser: 6p21.2-p12
Genomic locationchr6 :46672052-46703151
Type of geneprotein-coding
RefGenesNM_001168357.1,
NM_005084.3,
Ensembl idENSG00000146070
Description1-alkyl-2-acetylglycerophosphocholine esterase2-acetyl-1-alkylglycerophosphocholine esteraseLDL-PLA(2)LDL-associated phospholipase A2PAF 2-acylhydrolasePAF acetylhydrolasegVIIA-PLA2group-VIIA phospholipase A2lipoprotein-associated phospholipase A2
Modification date20141207
dbXrefs MIM : 601690
HGNC : HGNC
Ensembl : ENSG00000146070
HPRD : 03407
Vega : OTTHUMG00000014789
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLA2G7
BioGPS: 7941
Gene Expression Atlas: ENSG00000146070
The Human Protein Atlas: ENSG00000146070
PathwayNCI Pathway Interaction Database: PLA2G7
KEGG: PLA2G7
REACTOME: PLA2G7
ConsensusPathDB
Pathway Commons: PLA2G7
MetabolismMetaCyc: PLA2G7
HUMANCyc: PLA2G7
RegulationEnsembl's Regulation: ENSG00000146070
miRBase: chr6 :46,672,052-46,703,151
TargetScan: NM_001168357
cisRED: ENSG00000146070
ContextiHOP: PLA2G7
cancer metabolism search in PubMed: PLA2G7
UCL Cancer Institute: PLA2G7
Assigned class in ccmGDBC

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Phenotypic Information for PLA2G7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLA2G7
Familial Cancer Database: PLA2G7
* 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
Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PLA2G7
MedGen: PLA2G7 (Human Medical Genetics with Condition)
ClinVar: PLA2G7
PhenotypeMGI: PLA2G7 (International Mouse Phenotyping Consortium)
PhenomicDB: PLA2G7

Mutations for PLA2G7
* 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 PLA2G7 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 # sample      1          
GAIN (# sample)      1          
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=42)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr6:46679243-46679243p.R218Q3
chr6:46684166-46684166p.L111I2
chr6:46678360-46678361p.L233Q2
chr6:46690584-46690584p.C15C2
chr6:46684222-46684222p.R92H2
chr6:46678392-46678392p.R223R2
chr6:46675817-46675817p.I317I2
chr6:46682255-46682255p.L138V2
chr6:46684775-46684775p.I56I2
chr6:46679259-46679259p.E213*2

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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
# sample32 71 2 2  102   95 8
# mutation33 81 2 2  112   95 9
nonsynonymous SNV32 8  2 2  101   74 6
synonymous SNV 1  1      11   21 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
chr6:46678321p.K246N,PLA2G72
chr6:46684166p.L111I,PLA2G72
chr6:46679243p.R218Q,PLA2G72
chr6:46678293p.S435S,PLA2G71
chr6:46672318p.H272N,PLA2G71
chr6:46679322p.D192Y,PLA2G71
chr6:46675788p.M33I,PLA2G71
chr6:46684241p.F10V,PLA2G71
chr6:46678298p.Q427K,PLA2G71
chr6:46672344p.A268S,PLA2G71

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 PLA2G7 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 PLA2G7

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

CCR1,CD300LF,CD68,CTSS,FGR,HAVCR2,HK3,
IFI30,IGSF6,LILRB3,LILRB4,MS4A4A,NCF2,NCKAP1L,
NPL,PLA2G7,PLEK,SIGLEC7,SLAMF8,SLC7A7,TLR8
ACP5,CCL7,CD300LB,CD52,FGR,IFI30,ITGAX,
ITGB2,KCNAB2,LIPA,LOC653786,OSCAR,OTOA,PILRA,
PLA2G7,SIGLEC7,SLAMF9,SPOCD1,TM4SF19,DCSTAMP,TREM2

ACP5,C1QA,C1QB,C1QC,CD300LF,CD86,CYBB,
FCER1G,FPR3,GPNMB,HAVCR2,HCK,IGSF6,LILRB4,
LRRC25,MS4A4A,PDCD1LG2,PLA2G7,SIGLEC7,SLAMF8,TYROBP
ACP5,AOAH,CARD9,CCR2,CD300A,CD300LF,CLEC4A,
CSF2RA,CTSC,FPR3,HERPUD1,IGSF6,KCNK13,LILRB1,
MMP9,MPEG1,PLA2G7,SIGLEC7,SIGLEC9,TRPM2,WNT10A
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 PLA2G7
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
DB07821phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)experimental(1R)-1,2,2-TRIMETHYLPROPYL (R)-METHYLPHOSPHINATE


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Cross referenced IDs for PLA2G7
* 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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