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 PLA2G4A
Basic gene info.Gene symbolPLA2G4A
Gene namephospholipase A2, group IVA (cytosolic, calcium-dependent)
SynonymsPLA2G4|cPLA2-alpha
CytomapUCSC genome browser: 1q25
Genomic locationchr1 :186798031-186958113
Type of geneprotein-coding
RefGenesNM_024420.2,
Ensembl idENSG00000116711
DescriptioncPLA2calcium-dependent phospholipid-binding proteincytosolic phospholipase A2lysophospholipasephosphatidylcholine 2-acylhydrolasephospholipase A2 group IVA
Modification date20141207
dbXrefs MIM : 600522
HGNC : HGNC
Ensembl : ENSG00000116711
HPRD : 08986
Vega : OTTHUMG00000035512
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLA2G4A
BioGPS: 5321
Gene Expression Atlas: ENSG00000116711
The Human Protein Atlas: ENSG00000116711
PathwayNCI Pathway Interaction Database: PLA2G4A
KEGG: PLA2G4A
REACTOME: PLA2G4A
ConsensusPathDB
Pathway Commons: PLA2G4A
MetabolismMetaCyc: PLA2G4A
HUMANCyc: PLA2G4A
RegulationEnsembl's Regulation: ENSG00000116711
miRBase: chr1 :186,798,031-186,958,113
TargetScan: NM_024420
cisRED: ENSG00000116711
ContextiHOP: PLA2G4A
cancer metabolism search in PubMed: PLA2G4A
UCL Cancer Institute: PLA2G4A
Assigned class in ccmGDBC

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Phenotypic Information for PLA2G4A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLA2G4A
Familial Cancer Database: PLA2G4A
* 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: PLA2G4A
MedGen: PLA2G4A (Human Medical Genetics with Condition)
ClinVar: PLA2G4A
PhenotypeMGI: PLA2G4A (International Mouse Phenotyping Consortium)
PhenomicDB: PLA2G4A

Mutations for PLA2G4A
* 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
breastPLA2G4Achr1186866548186866548PLA2G4Achr1186867452186867452
ovaryPLA2G4Achr1186879599186879619MIR548F1chr1186404355186404375
pancreasPLA2G4Achr1186942620186942640chr1234701934234701954
pancreasPLA2G4Achr1186942883186942903chr1191110717191110737
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 PLA2G4A 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 # sample2211    1        
GAIN (# sample)2 11    1        
LOSS (# sample) 2               
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=100)
Stat. for Synonymous SNVs
(# total SNVs=29)
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
chr1:186919850-186919850p.H442Q3
chr1:186919851-186919851p.E443K3
chr1:186957600-186957600p.R737I2
chr1:186862165-186862165p.V46V2
chr1:186901934-186901934p.R200*2
chr1:186880450-186880450p.E163*2
chr1:186934719-186934719p.P586P2
chr1:186915773-186915773p.W346C2
chr1:186934649-186934649p.R563T2
chr1:186925423-186925423p.D509G2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample161123 3 4  1481 3105 15
# mutation171143 3 5  1581 3105 16
nonsynonymous SNV 61113 2 2  1361 283 11
synonymous SNV11 3  1 3  22  122 5
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
chr1:186919850p.Q270H2
chr1:186919851p.R563T2
chr1:186908254p.H442Q2
chr1:186957600p.E443K2
chr1:186934649p.R737I2
chr1:186901983p.A477G1
chr1:186925348p.F612I1
chr1:186862216p.F743L1
chr1:186909161p.M92I1
chr1:186934718p.Y213Y1

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 PLA2G4A 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 PLA2G4A

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

C1orf74,CALCA,CYSLTR2,FILIP1,GPR133,GUCY2GP,KLK5,
KLK7,LOC154822,MAPK4,MYBPHL,NMU,PLA2G2A,PLA2G4A,
PPARGC1A,PTGS2,SLAIN1,SLC22A2,SLC22A3,USH1C,WNT1
CLMP,ATP2B4,CAV1,DENND5A,DMGDH,DSEL,EHBP1,
EPB41L2,FAM69A,FERMT2,GLYAT,GNG2,LAMA4,LOC339524,
MARK1,MMD,PLA2G4A,PPP2R1B,SAR1A,TK2,VKORC1L1

AHR,BACE2,BARX2,VSTM5,MYRF,C1orf21,CDR2L,
DUSP4,ERI1,FAM115C,TVP23C,TVP23B,KCNK1,KIAA1211,
MTUS1,PLA2G4A,RNF125,SDR16C5,SERPINB5,TNFRSF10D,TSTA3
ARL4D,BAG2,PIFO,CFL2,DSTN,GUCY1B3,LOC728819,
MORN5,NECAB1,PEA15,PLA2G4A,PLN,PTBP2,PTPLA,
RASSF8,REEP1,SCRG1,SH3BGRL,ST3GAL3,TEAD2,TMEM55A
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 PLA2G4A
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
DB00588phospholipase A2, group IVA (cytosolic, calcium-dependent)approved; investigationalFluticasone Propionate
DB01103phospholipase A2, group IVA (cytosolic, calcium-dependent)approvedQuinacrine
DB04552phospholipase A2, group IVA (cytosolic, calcium-dependent)approvedNiflumic Acid
DB00945phospholipase A2, group IVA (cytosolic, calcium-dependent)approvedAcetylsalicylic acid
DB00482phospholipase A2, group IVA (cytosolic, calcium-dependent)approved; investigationalCelecoxib


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Cross referenced IDs for PLA2G4A
* 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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