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 PLA2G16
Basic gene info.Gene symbolPLA2G16
Gene namephospholipase A2, group XVI
SynonymsAdPLA|H-REV107-1|HRASLS3|HREV107|HREV107-1|HREV107-3|HRSL3
CytomapUCSC genome browser: 11q12.3
Genomic locationchr11 :63341943-63381909
Type of geneprotein-coding
RefGenesNM_001128203.1,
NM_007069.3,
Ensembl idENSG00000176485
DescriptionCa-independent phospholipase A1/2H-rev 107 protein homologHRAS-like suppressor 1HRAS-like suppressor 3adipose-specific PLA2adipose-specific phospholipase A2group XVI phospholipase A1/A2group XVI phospholipase A2renal carcinoma antigen NY-REN-65
Modification date20141207
dbXrefs MIM : 613867
HGNC : HGNC
Ensembl : ENSG00000176485
HPRD : 13671
ProteinUniProt: P53816
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLA2G16
BioGPS: 11145
Gene Expression Atlas: ENSG00000176485
The Human Protein Atlas: ENSG00000176485
PathwayNCI Pathway Interaction Database: PLA2G16
KEGG: PLA2G16
REACTOME: PLA2G16
ConsensusPathDB
Pathway Commons: PLA2G16
MetabolismMetaCyc: PLA2G16
HUMANCyc: PLA2G16
RegulationEnsembl's Regulation: ENSG00000176485
miRBase: chr11 :63,341,943-63,381,909
TargetScan: NM_001128203
cisRED: ENSG00000176485
ContextiHOP: PLA2G16
cancer metabolism search in PubMed: PLA2G16
UCL Cancer Institute: PLA2G16
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PLA2G16 in cancer cell metabolism1. Wang C-H, Shyu R-Y, Wu C-C, Tsai T-C, Wang L-K, et al. (2014) Phospholipase A/Acyltransferase enzyme activity of H-rev107 inhibits the H-RAS signaling pathway. Journal of biomedical science 21: 1-9. go to article

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Phenotypic Information for PLA2G16(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLA2G16
Familial Cancer Database: PLA2G16
* 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
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 613867; gene.
Orphanet
DiseaseKEGG Disease: PLA2G16
MedGen: PLA2G16 (Human Medical Genetics with Condition)
ClinVar: PLA2G16
PhenotypeMGI: PLA2G16 (International Mouse Phenotyping Consortium)
PhenomicDB: PLA2G16

Mutations for PLA2G16
* 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
breastPLA2G16chr116335071563350715PLA2G16chr116335286463352864
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 PLA2G16 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE166188PLA2G16197116334205763342153PLA2G1690471116334218063342560

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 # sample        2     1  
GAIN (# sample)        1     1  
LOSS (# sample)        1        
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=8)
Stat. for Synonymous SNVs
(# total SNVs=3)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr11:63357803-63357803p.S52S2
chr11:63342429-63342429p.R159R1
chr11:63357705-63357705p.S85L1
chr11:63342430-63342430p.R159Q1
chr11:63357739-63357739p.Y74H1
chr11:63342504-63342504p.I134M1
chr11:63357753-63357753p.A69V1
chr11:63357582-63357582p.R126H1
chr11:63357621-63357621p.C113Y1
chr11:63357818-63357818p.A47A1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   21   2  1 1  51 1
# mutation   21   2  1 1  51 1
nonsynonymous SNV   11   2    1  31 1
synonymous SNV   1       1    2   
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
chr11:63342429p.R159R,PLA2G161
chr11:63357820p.R159Q,PLA2G161
chr11:63342430p.I134M,PLA2G161
chr11:63365622p.R126H,PLA2G161
chr11:63342504p.C113F,PLA2G161
chr11:63381479p.R95R,PLA2G161
chr11:63357582p.R95Q,PLA2G161
chr11:63357621p.I92I,PLA2G161
chr11:63357674p.S85L,PLA2G161
chr11:63357675p.A69V,PLA2G161

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 PLA2G16 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 PLA2G16

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

ADIRF,LBHD1___C11orf98,COX8A,ECI1,DEGS2,HRASLS5,HSD17B8,
MACROD1,MGMT,NINJ1,NME3,NSMCE1,NUPR1,OTUB1,
PLA2G16,POLR2G,RAB17,RARRES3,TMEM141,TMEM179B,TPRN
ABHD15,AGPAT2,ALDH2,AQP7,AVPI1,ADIRF,C14orf180,
CAMK1,CEBPA,CIDEA,CIDEC,FAH,FBXO27,GPR146,
LIPE,PJA1,PLA2G16,PNPLA2,ST6GALNAC6,TMEM132C,TYRO3

AHNAK2,ANXA2,ANXA2P2,BCL9L,C19orf66,CLCF1,FRMD8,
FSTL3,GJB4,HRASLS2,ITGA3,KPNA7,KRT19,LMNA,
LOC100131551,PLA2G16,PPL,RARRES3,S100A16,SERPINB5,TMEM51
APLN,APOL3,BLVRA,C1orf162,CBR3,CDC27,CFB,
CFI,DRAM1,FCN1,GABRP,GBP2,GIF,GMPR,
GRINA,IFITM3,PLA2G16,SAMHD1,SLFN12,STK3,STOM
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 PLA2G16


There's no related Drug.
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Cross referenced IDs for PLA2G16
* 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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