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 PLA2G4D
Basic gene info.Gene symbolPLA2G4D
Gene namephospholipase A2, group IVD (cytosolic)
SynonymscPLA2delta
CytomapUCSC genome browser: 15q15.1
Genomic locationchr15 :42359880-42386752
Type of geneprotein-coding
RefGenesNM_178034.3,
Ensembl idENSG00000159337
DescriptioncPLA2-deltacytosolic phospholipase A2 deltaphospholipase A2 delta, cytosolicphospholipase A2 group IVD
Modification date20141207
dbXrefs MIM : 612864
HGNC : HGNC
Ensembl : ENSG00000159337
HPRD : 07145
Vega : OTTHUMG00000172587
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLA2G4D
BioGPS: 283748
Gene Expression Atlas: ENSG00000159337
The Human Protein Atlas: ENSG00000159337
PathwayNCI Pathway Interaction Database: PLA2G4D
KEGG: PLA2G4D
REACTOME: PLA2G4D
ConsensusPathDB
Pathway Commons: PLA2G4D
MetabolismMetaCyc: PLA2G4D
HUMANCyc: PLA2G4D
RegulationEnsembl's Regulation: ENSG00000159337
miRBase: chr15 :42,359,880-42,386,752
TargetScan: NM_178034
cisRED: ENSG00000159337
ContextiHOP: PLA2G4D
cancer metabolism search in PubMed: PLA2G4D
UCL Cancer Institute: PLA2G4D
Assigned class in ccmGDBC

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Phenotypic Information for PLA2G4D(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLA2G4D
Familial Cancer Database: PLA2G4D
* 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_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PLA2G4D
MedGen: PLA2G4D (Human Medical Genetics with Condition)
ClinVar: PLA2G4D
PhenotypeMGI: PLA2G4D (International Mouse Phenotyping Consortium)
PhenomicDB: PLA2G4D

Mutations for PLA2G4D
* 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 PLA2G4D 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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=61)
Stat. for Synonymous SNVs
(# total SNVs=19)
Stat. for Deletions
(# total SNVs=2)
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
chr15:42371752-42371752p.S434T8
chr15:42375496-42375496p.G191E2
chr15:42363462-42363462p.L579L2
chr15:42363991-42363991p.P518P2
chr15:42373291-42373291p.R333Q2
chr15:42377688-42377688p.?2
chr15:42374547-42374547p.G238A2
chr15:42374580-42374580p.R227K2
chr15:42362967-42362967p.R664L2
chr15:42361123-42361123p.P749P2

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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
# sample12192 1 7 1631  174 12
# mutation12192 1 7 1631  224 15
nonsynonymous SNV12191 1 3 16 1  102 10
synonymous SNV    1   4   3   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
chr15:42361123p.P749P2
chr15:42374005p.S226S1
chr15:42363337p.H69Y1
chr15:42375956p.E775K1
chr15:42364006p.A586V1
chr15:42379558p.A450V1
chr15:42371771p.Q443H1
chr15:42374525p.R222C1
chr15:42363357p.D66G1
chr15:42375969p.G761G1

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 PLA2G4D 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 PLA2G4D

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

APCS,APOA4,APOB,APOC3,ARG1,C8A,C9,
CRP,DUOXA2,F11,FABP1,FGF23,GLTPD2,MT1DP,
ORM1,PLA2G4D,PLG,PRAP1,SERPINA10,SERPINC1,SLC17A2
KIAA1549L,MYRF,DCAF4,GGA2,LOC154761,NCAPD2,PDCD11,
PLA2G4D,SEMA4A,SEMA4G,SETDB1,SF3B3,SLC12A8,SLC4A11,
SMARCC1,SNRNP200,SREBF2,UBAP2L,ZG16B,ZNF317,ZNF496

ANO7,B3GNT6,LINC00469,CACNA2D2,CCDC60,CLCA1,DLL1,
GP9,HEPACAM2,KLK3,LRRC26,LRRIQ4,OR52R1,PLA2G4D,
RASD1,REP15,RETNLB,RHBDL3,SLITRK6,TBC1D2,WISP3
AACS,ACSL3,SYNE4,C1QTNF6,CATSPERB,CKAP4,DHCR7,
DMBT1,GALNT5,GNA14,KIAA1244,LRIG3,LSS,MUC5B,
PCSK9,PKP4,PLA2G4D,QSOX1,SLC10A7,SRD5A3,USP17L2
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 PLA2G4D


There's no related Drug.
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Cross referenced IDs for PLA2G4D
* 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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