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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PLA2G4A |
Basic gene info. | Gene symbol | PLA2G4A |
Gene name | phospholipase A2, group IVA (cytosolic, calcium-dependent) | |
Synonyms | PLA2G4|cPLA2-alpha | |
Cytomap | UCSC genome browser: 1q25 | |
Genomic location | chr1 :186798031-186958113 | |
Type of gene | protein-coding | |
RefGenes | NM_024420.2, | |
Ensembl id | ENSG00000116711 | |
Description | cPLA2calcium-dependent phospholipid-binding proteincytosolic phospholipase A2lysophospholipasephosphatidylcholine 2-acylhydrolasephospholipase A2 group IVA | |
Modification date | 20141207 | |
dbXrefs | MIM : 600522 | |
HGNC : HGNC | ||
Ensembl : ENSG00000116711 | ||
HPRD : 08986 | ||
Vega : OTTHUMG00000035512 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PLA2G4A | |
BioGPS: 5321 | ||
Gene Expression Atlas: ENSG00000116711 | ||
The Human Protein Atlas: ENSG00000116711 | ||
Pathway | NCI Pathway Interaction Database: PLA2G4A | |
KEGG: PLA2G4A | ||
REACTOME: PLA2G4A | ||
ConsensusPathDB | ||
Pathway Commons: PLA2G4A | ||
Metabolism | MetaCyc: PLA2G4A | |
HUMANCyc: PLA2G4A | ||
Regulation | Ensembl's Regulation: ENSG00000116711 | |
miRBase: chr1 :186,798,031-186,958,113 | ||
TargetScan: NM_024420 | ||
cisRED: ENSG00000116711 | ||
Context | iHOP: PLA2G4A | |
cancer metabolism search in PubMed: PLA2G4A | ||
UCL Cancer Institute: PLA2G4A | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PLA2G4A(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PLA2G4A |
Familial Cancer Database: PLA2G4A |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
Metabolic 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 |
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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
breast | PLA2G4A | chr1 | 186866548 | 186866548 | PLA2G4A | chr1 | 186867452 | 186867452 |
ovary | PLA2G4A | chr1 | 186879599 | 186879619 | MIR548F1 | chr1 | 186404355 | 186404375 |
pancreas | PLA2G4A | chr1 | 186942620 | 186942640 | chr1 | 234701934 | 234701954 | |
pancreas | PLA2G4A | chr1 | 186942883 | 186942903 | chr1 | 191110717 | 191110737 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PLA2G4A related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 2 | 2 | 1 | 1 |   |   |   |   | 1 |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 2 |   | 1 | 1 |   |   |   |   | 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=100) | (# total SNVs=29) |
(# total SNVs=1) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr1:186919850-186919850 | p.H442Q | 3 |
chr1:186919851-186919851 | p.E443K | 3 |
chr1:186934649-186934649 | p.R563T | 2 |
chr1:186925423-186925423 | p.D509G | 2 |
chr1:186946751-186946751 | p.A597A | 2 |
chr1:186946892-186946892 | p.N644N | 2 |
chr1:186862236-186862236 | p.V70E | 2 |
chr1:186915834-186915834 | p.L367I | 2 |
chr1:186946900-186946900 | p.F647Y | 2 |
chr1:186915853-186915853 | p.F373C | 2 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 | 6 | 1 | 12 | 3 |   | 3 |   | 4 |   |   | 14 | 8 | 1 |   | 3 | 10 | 5 |   | 15 |
# mutation | 1 | 7 | 1 | 14 | 3 |   | 3 |   | 5 |   |   | 15 | 8 | 1 |   | 3 | 10 | 5 |   | 16 |
nonsynonymous SNV |   | 6 | 1 | 11 | 3 |   | 2 |   | 2 |   |   | 13 | 6 | 1 |   | 2 | 8 | 3 |   | 11 |
synonymous SNV | 1 | 1 |   | 3 |   |   | 1 |   | 3 |   |   | 2 | 2 |   |   | 1 | 2 | 2 |   | 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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr1:186919851 | p.Q270H | 2 |
chr1:186908254 | p.R563T | 2 |
chr1:186957600 | p.H442Q | 2 |
chr1:186934649 | p.E443K | 2 |
chr1:186919850 | p.R737I | 2 |
chr1:186934597 | p.I429T | 1 |
chr1:186823505 | p.V548V | 1 |
chr1:186908212 | p.E658G | 1 |
chr1:186946809 | p.E13E | 1 |
chr1:186863259 | p.F157F | 1 |
Other DBs for Point Mutations |
Copy 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 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for PLA2G4A |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00588 | phospholipase A2, group IVA (cytosolic, calcium-dependent) | approved; investigational | Fluticasone Propionate | ||
DB01103 | phospholipase A2, group IVA (cytosolic, calcium-dependent) | approved | Quinacrine | ||
DB04552 | phospholipase A2, group IVA (cytosolic, calcium-dependent) | approved | Niflumic Acid | ||
DB00945 | phospholipase A2, group IVA (cytosolic, calcium-dependent) | approved | Acetylsalicylic acid | ||
DB00482 | phospholipase A2, group IVA (cytosolic, calcium-dependent) | approved; investigational | Celecoxib |
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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 |
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