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 PLA2G3
Basic gene info.Gene symbolPLA2G3
Gene namephospholipase A2, group III
SynonymsGIII-SPLA2|SPLA2III|sPLA2-III
CytomapUCSC genome browser: 22q12.2
Genomic locationchr22 :31530792-31536469
Type of geneprotein-coding
RefGenesNM_015715.4,
Ensembl idENSG00000100078
Descriptiongroup 3 secretory phospholipase A2group III secreted phospholipase A2phosphatidylcholine 2-acylhydrolase 3phosphatidylcholine 2-acylhydrolase GIII
Modification date20141207
dbXrefs MIM : 611651
HGNC : HGNC
Ensembl : ENSG00000100078
HPRD : 07144
Vega : OTTHUMG00000151255
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLA2G3
BioGPS: 50487
Gene Expression Atlas: ENSG00000100078
The Human Protein Atlas: ENSG00000100078
PathwayNCI Pathway Interaction Database: PLA2G3
KEGG: PLA2G3
REACTOME: PLA2G3
ConsensusPathDB
Pathway Commons: PLA2G3
MetabolismMetaCyc: PLA2G3
HUMANCyc: PLA2G3
RegulationEnsembl's Regulation: ENSG00000100078
miRBase: chr22 :31,530,792-31,536,469
TargetScan: NM_015715
cisRED: ENSG00000100078
ContextiHOP: PLA2G3
cancer metabolism search in PubMed: PLA2G3
UCL Cancer Institute: PLA2G3
Assigned class in ccmGDBC

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Phenotypic Information for PLA2G3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLA2G3
Familial Cancer Database: PLA2G3
* 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
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PLA2G3
MedGen: PLA2G3 (Human Medical Genetics with Condition)
ClinVar: PLA2G3
PhenotypeMGI: PLA2G3 (International Mouse Phenotyping Consortium)
PhenomicDB: PLA2G3

Mutations for PLA2G3
* 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 PLA2G3 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
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=43)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr22:31536133-31536133p.S70A4
chr22:31534698-31534698p.R201Q4
chr22:31533796-31533796p.S322R3
chr22:31536050-31536050p.I97I3
chr22:31535982-31535982p.A120V3
chr22:31535997-31535997p.W115*2
chr22:31535827-31535827p.G172R2
chr22:31532953-31532953p.I380I2
chr22:31534368-31534368p.D226N2
chr22:31535924-31535924p.V139V2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22141 2    521  1511 5
# mutation22141 2    621  2111 5
nonsynonymous SNV12 31 2    611  148 5
synonymous SNV1 11        1   73  
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
chr22:31534698p.R201Q5
chr22:31535929p.G138R2
chr22:31532705p.L108L1
chr22:31534744p.G350G1
chr22:31533797p.P269P1
chr22:31536060p.Q105Q1
chr22:31533881p.G344C1
chr22:31532738p.G233G1
chr22:31534755p.G101E1
chr22:31533801p.S335Y1

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 PLA2G3 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 PLA2G3

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

CCL14-CCL15,CEL,CSN1S1,CSN1S2AP,CSN2,CYSLTR1,EGF,
TMEM236,FBXO47,INPP5J,KRT12,LALBA,LOC126536,LYPD6,
MRC1,OR8U1,PLA2G3,PPP1R3C,SLC6A4,SMCP,SSX3
DRC1,C2orf70,CCR6,CLCN2,DAGLA,FUT2,IGFALS,
IGSF9,IPO4,KRT83,MUC4,MYH16,PLA2G3,PLCZ1,
ProSAPiP1,QSOX1,RNF43,SLC9A1,ST8SIA2,TMEM163,ZDHHC23

ACADS,ATP5A1,ATP5B,C11orf85,DEFB136,DLST,FRG2B,
KRTAP9-9,LOC149620,ME2,MVK,PADI3,PCSK9,PGAM1,
PLA2G3,PNPLA3,SCO1,SERPINB11,SHMT2,SLC25A3,SPINK2
APOL4,CD274,CXCL10,CXCL5,FCGR1A,FCGR1B,GSTA3,
HAPLN3,IDO1,IL15RA,LHX8,LOC400759,PAQR9,PER4,
PLA2G2A,PLA2G3,RIMS1,SCGB1D4,SEPT14,TNFSF13B,VAMP5
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 PLA2G3


There's no related Drug.
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Cross referenced IDs for PLA2G3
* 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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