Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 PLA2G6
Basic gene info.Gene symbolPLA2G6
Gene namephospholipase A2, group VI (cytosolic, calcium-independent)
SynonymsCaI-PLA2|GVI|INAD1|IPLA2-VIA|NBIA2|NBIA2A|NBIA2B|PARK14|PLA2|PNPLA9|iPLA2|iPLA2beta
CytomapUCSC genome browser: 22q13.1
Genomic locationchr22 :38507501-38577761
Type of geneprotein-coding
RefGenesNM_001004426.1,
NM_001199562.1,NM_003560.2,
Ensembl idENSG00000184381
Description85 kDa calcium-independent phospholipase A285/88 kDa calcium-independent phospholipase A2GVI PLA2calcium-independent phospholipase A2cytosolic, calcium-independent phospholipase A2group VI phospholipase A2iPLA2-betaintracellular membrane-associated
Modification date20141219
dbXrefs MIM : 603604
HGNC : HGNC
Ensembl : ENSG00000184381
HPRD : 04675
Vega : OTTHUMG00000151246
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLA2G6
BioGPS: 8398
Gene Expression Atlas: ENSG00000184381
The Human Protein Atlas: ENSG00000184381
PathwayNCI Pathway Interaction Database: PLA2G6
KEGG: PLA2G6
REACTOME: PLA2G6
ConsensusPathDB
Pathway Commons: PLA2G6
MetabolismMetaCyc: PLA2G6
HUMANCyc: PLA2G6
RegulationEnsembl's Regulation: ENSG00000184381
miRBase: chr22 :38,507,501-38,577,761
TargetScan: NM_001004426
cisRED: ENSG00000184381
ContextiHOP: PLA2G6
cancer metabolism search in PubMed: PLA2G6
UCL Cancer Institute: PLA2G6
Assigned class in ccmGDBC

Top
Phenotypic Information for PLA2G6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLA2G6
Familial Cancer Database: PLA2G6
* 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
KEGG_ARACHIDONIC_ACID_METABOLISM
KEGG_LINOLEIC_ACID_METABOLISM
KEGG_ALPHA_LINOLENIC_ACID_METABOLISM
KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PLA2G6
MedGen: PLA2G6 (Human Medical Genetics with Condition)
ClinVar: PLA2G6
PhenotypeMGI: PLA2G6 (International Mouse Phenotyping Consortium)
PhenomicDB: PLA2G6

Mutations for PLA2G6
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
skinPLA2G6chr223851451138514511TMEM184Bchr223864361638643616
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 PLA2G6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CV375307PLA2G6299223856056538560662CLTCL197240221922836819228511
BQ300191PLA2G610229223852388938524110MAP421736034791717447917317
BF871762SYT71301116130011161300411PLA2G6291373223852225138522333
CV375347CLTCL183226221922836819228511PLA2G6223248223856051638560541

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample          1  2   
GAIN (# sample)          1  2   
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)

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=51)
Stat. for Synonymous SNVs
(# total SNVs=14)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
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
chr22:38539282-38539282p.A147T3
chr22:38508290-38508290p.D767H2
chr22:38536013-38536013p.S258L2
chr22:38509556-38509556p.P714S2
chr22:38524296-38524296p.P443L2
chr22:38531004-38531004p.K295N2
chr22:38512182-38512182p.P593P2
chr22:38512189-38512189p.R591Q1
chr22:38528935-38528935p.R327H1
chr22:38565252-38565252p.N61S1

Top
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
# sample22 91 113  451  165 12
# mutation22 91 123  451  175 13
nonsynonymous SNV11 81 112  251  95 10
synonymous SNV11 1   11  2    8  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])

Top
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
chr22:38509556p.P660S,PLA2G62
chr22:38536013p.S258L,PLA2G62
chr22:38522429p.P51S,PLA2G61
chr22:38541528p.P539P,PLA2G61
chr22:38509509p.A401A1
chr22:38528987p.I248I,PLA2G61
chr22:38512212p.R39W,PLA2G61
chr22:38536074p.D536D,PLA2G61
chr22:38524296p.I393I,PLA2G61
chr22:38541618p.N243K,PLA2G61

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 PLA2G6 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]

Top
Gene Expression for PLA2G6

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

LMNTD2,CAPN10,CCNL2,CDK10,CHKB-CPT1B,CPT1B,DENND6B,
FLJ37453,GGA1,HDAC10,LOC338799,NEIL1,PILRB,PLA2G6,
RNF215,SCNN1D,SELO,SFI1,TRMT2A,TUBGCP6,WASH7P
APBB3,ENTHD2,CCNL2,CSAD,ECHDC2,ENGASE,FAM193B,
GIGYF1,HDAC6,HEMK1,HSF4,LENG8,LPIN3,MAN2C1,
MYO15B,NSUN5P2,PILRB,PLA2G6,PNPLA7,TUBGCP6,WASH7P

ZNF436-AS1,CCNL2,CDK10,CDK5RAP3,CHKB-CPT1B,CROCCP2,CYP2D7,
GGA1,HDAC10,LOC100131434,LOC91316,NOL12,PAN2,PI4KAP1,
PICK1,PLA2G6,SFI1,SH2B1,TMEM175,TOP3B,TUBGCP6
ACAD10,VPS51___IFT46,LMNTD2,CCDC61,CNKSR1,COX19,DGKQ,
DMAP1,FUK,HDAC10,HDAC6,MIB2,MYPOP,OPLAH,
PLA2G6,PNPLA7,RNF44,SPPL2B,SPSB3,STK11,TPCN1
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for PLA2G6
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
DB01103phospholipase A2, group VI (cytosolic, calcium-independent)approvedQuinacrine


Top
Cross referenced IDs for PLA2G6
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas