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 PLA2G2C
Basic gene info.Gene symbolPLA2G2C
Gene namephospholipase A2, group IIC
Synonyms-
CytomapUCSC genome browser: 1p36.12
Genomic locationchr1 :20490483-20501687
Type of geneprotein-coding
RefGenesNM_001105572.1,
Ensembl idENSG00000187980
Descriptionphosphatidylcholine 2-acylhydrolase-like protein GIICphospholipase A2, group IIC (possible pseudogene)putative inactive group IIC secretory phospholipase A2
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000187980
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLA2G2C
BioGPS: 391013
Gene Expression Atlas: ENSG00000187980
The Human Protein Atlas: ENSG00000187980
PathwayNCI Pathway Interaction Database: PLA2G2C
KEGG: PLA2G2C
REACTOME: PLA2G2C
ConsensusPathDB
Pathway Commons: PLA2G2C
MetabolismMetaCyc: PLA2G2C
HUMANCyc: PLA2G2C
RegulationEnsembl's Regulation: ENSG00000187980
miRBase: chr1 :20,490,483-20,501,687
TargetScan: NM_001105572
cisRED: ENSG00000187980
ContextiHOP: PLA2G2C
cancer metabolism search in PubMed: PLA2G2C
UCL Cancer Institute: PLA2G2C
Assigned class in ccmGDBC

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Phenotypic Information for PLA2G2C(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLA2G2C
Familial Cancer Database: PLA2G2C
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PLA2G2C
MedGen: PLA2G2C (Human Medical Genetics with Condition)
ClinVar: PLA2G2C
PhenotypeMGI: PLA2G2C (International Mouse Phenotyping Consortium)
PhenomicDB: PLA2G2C

Mutations for PLA2G2C
* 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 PLA2G2C 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=13)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr1:20490512-20490512p.R142K2
chr1:20501650-20501650p.S13L2
chr1:20501656-20501656p.F11fs*632
chr1:20490601-20490601p.A112A2
chr1:20499280-20499280p.?1
chr1:20501550-20501550p.G46G1
chr1:20499296-20499296p.A93T1
chr1:20501571-20501571p.F39L1
chr1:20499297-20499297p.G92G1
chr1:20501582-20501582p.R36*1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 3    1  111  32 4
# mutation 1 3    1  111  32 4
nonsynonymous SNV 1 1    1  1 1  21 3
synonymous SNV   2        1   11 1
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
chr1:20490512p.R142K2
chr1:20501520p.T34M1
chr1:20501525p.S13S1
chr1:20501539p.S13L1
chr1:20501550p.P128P1
chr1:20490553p.P128H1
chr1:20501586p.R109M1
chr1:20490554p.G92G1
chr1:20501587p.V90I1
chr1:20490611p.I89L1

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 PLA2G2C 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 PLA2G2C

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

CCDC176,C9orf135,AK8,CAPN8,CCDC24,CNKSR3,D2HGDH,
DLX1,DLX2,CRACR2B,GHRH,GPC3,HPN,LOC728606,
MAMDC4,MYL5,PDZK1,PLA2G2C,SCNN1D,UBXN10,UBXN11
ADAM3A,C9orf135,DNAI2,FGF20,FOXB2,LMNTD1,MAGEA11,
MAGEA9B,NPSR1,OR2AE1,PABPC1P2,PLA2G2C,PLG,PPIAL4E,
PRSS54,RTP1,SLC17A4,SLC30A10,SNORA18,SNORA56,STRA8

ADRB3,C14orf132,CCNA1,CDH19,CHRNA3,CSDC2,MT1M,
NEFH,NEFM,NGB,NOS1,NPAS3,PHOX2B,PLA2G2C,
PPP2R2B,SEL1L2,SLC18A3,SLC5A7,SOX10,ST8SIA3,STMN4
C1orf95,C9orf9,CACNA2D1,COPZ2,DRP2,EPHA6,ESYT3,
GDF5,GPR155,KLHL5,NEK10,PLA2G2C,RASSF3,SFTPD,
SHISA4,SLC22A2,TCF15,TULP2,VIPR2,WDR17,ZEB1
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 PLA2G2C


There's no related Drug.
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Cross referenced IDs for PLA2G2C
* 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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