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 PLA2G15
Basic gene info.Gene symbolPLA2G15
Gene namephospholipase A2, group XV
SynonymsACS|GXVPLA2|LLPL|LPLA2|LYPLA3
CytomapUCSC genome browser: 16q22.1
Genomic locationchr16 :68279246-68294961
Type of geneprotein-coding
RefGenesNM_012320.3,
Ensembl idENSG00000103066
Description1-O-acylceramide synthaseLCAT-like lysophospholipasegroup XV phospholipase A2lysophospholipase 3 (lysosomal phospholipase A2)lysosomal phospholipase A2
Modification date20141207
dbXrefs MIM : 609362
HGNC : HGNC
Ensembl : ENSG00000103066
HPRD : 07128
Vega : OTTHUMG00000137554
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLA2G15
BioGPS: 23659
Gene Expression Atlas: ENSG00000103066
The Human Protein Atlas: ENSG00000103066
PathwayNCI Pathway Interaction Database: PLA2G15
KEGG: PLA2G15
REACTOME: PLA2G15
ConsensusPathDB
Pathway Commons: PLA2G15
MetabolismMetaCyc: PLA2G15
HUMANCyc: PLA2G15
RegulationEnsembl's Regulation: ENSG00000103066
miRBase: chr16 :68,279,246-68,294,961
TargetScan: NM_012320
cisRED: ENSG00000103066
ContextiHOP: PLA2G15
cancer metabolism search in PubMed: PLA2G15
UCL Cancer Institute: PLA2G15
Assigned class in ccmGDBC

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Phenotypic Information for PLA2G15(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLA2G15
Familial Cancer Database: PLA2G15
* 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_GLYCEROPHOSPHOLIPID_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PLA2G15
MedGen: PLA2G15 (Human Medical Genetics with Condition)
ClinVar: PLA2G15
PhenotypeMGI: PLA2G15 (International Mouse Phenotyping Consortium)
PhenomicDB: PLA2G15

Mutations for PLA2G15
* 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 PLA2G15 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ000365PLA2G1519278166829470768294965APBB227467344101581341016213
T11609SDF4484111592561159336PLA2G1570198166829426468294391
CN480826PLA2G1517564166829441368294961CD82559676114463825144638370

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
There's no copy number variation information in COSMIC data for this gene.

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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=27)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=2)

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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
chr16:68283280-68283280p.Y72C3
chr16:68293167-68293167p.F282F2
chr16:68293320-68293320p.G333G2
chr16:68288909-68288909p.L124L2
chr16:68293055-68293055p.N245S1
chr16:68283257-68283257p.L64L1
chr16:68293421-68293422p.A368fs*>451
chr16:68293468-68293468p.L383V1
chr16:68289239-68289239p.G153D1
chr16:68293091-68293091p.R257L1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2 71 3 2  112 1 8 2
# mutation 2 51 3 2  112 1 8 2
nonsynonymous SNV 1 4  3 1  111   5  
synonymous SNV 1 11   1    1 1 3 2
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
chr16:68283280p.Y72C3
chr16:68289682p.R296H1
chr16:68293405p.Y72Y1
chr16:68283257p.D306N1
chr16:68289698p.F73L1
chr16:68293433p.G333G1
chr16:68289850p.I94M1
chr16:68293500p.Y343C1
chr16:68283281p.R114C1
chr16:68289889p.T362A1

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 PLA2G15 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 PLA2G15

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

APOE,ATP6V0D1,CCM2,CHPF,CLEC11A,CRYBB1,CTSB,
DUS2,EMP3,FHOD1,GPX1,GRN,MGAT1,NAGK,
PLA2G15,PRMT7,TMEM208,TRADD,TYROBP,VAC14,VPS4A
ARRB2,C1QC,CD300C,CD68,CTSB,DOK2,DPEP2,
FERMT3,HK3,IFI30,ITGB2,LRRC25,NRROS,NFAM1,
PILRA,PLA2G15,PLD3,SLC15A3,SPI1,TRPV2,TYROBP

AEBP1,ARAP1,C16orf86,CMTM3,COL8A2,CTSZ,EFEMP2,
GLIS2,ISLR,ITGB5,MRAS,MXRA8,PLA2G15,PSAP,
RAB3IL1,RARRES2,RUSC2,SFRP4,THBS2,TNS3,VEGFB
C1QA,C2,M1AP,C3AR1,CD4,CMKLR1,CSF1R,
CYTH4,DISC1,GGTA1P,GIMAP1,LAIR1,NRROS,MAFB,
NFAM1,NPL,PLA2G15,RASGRP4,SIGLEC1,TMEM86A,TRIM50
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 PLA2G15
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
DB01992phospholipase A2, group XVexperimentalCoenzyme A
DB03230phospholipase A2, group XVexperimentalAdenosine-5'-Propylphosphate


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Cross referenced IDs for PLA2G15
* 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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