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 PNPLA2
Basic gene info.Gene symbolPNPLA2
Gene namepatatin-like phospholipase domain containing 2
Synonyms1110001C14Rik|ATGL|PEDF-R|TTS-2.2|TTS2|iPLA2zeta
CytomapUCSC genome browser: 11p15.5
Genomic locationchr11 :818900-825571
Type of geneprotein-coding
RefGenesNM_020376.3,
Ensembl idENSG00000177666
DescriptionIPLA2-zetaTTS2.2adipose triglyceride lipasecalcium-independent phospholipase A2desnutrinpatatin-like phospholipase domain containing protein 2patatin-like phospholipase domain-containing protein 2pigment epithelium-derived factortransport-secretio
Modification date20141207
dbXrefs MIM : 609059
HGNC : HGNC
Ensembl : ENSG00000177666
HPRD : 11443
Vega : OTTHUMG00000133309
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PNPLA2
BioGPS: 57104
Gene Expression Atlas: ENSG00000177666
The Human Protein Atlas: ENSG00000177666
PathwayNCI Pathway Interaction Database: PNPLA2
KEGG: PNPLA2
REACTOME: PNPLA2
ConsensusPathDB
Pathway Commons: PNPLA2
MetabolismMetaCyc: PNPLA2
HUMANCyc: PNPLA2
RegulationEnsembl's Regulation: ENSG00000177666
miRBase: chr11 :818,900-825,571
TargetScan: NM_020376
cisRED: ENSG00000177666
ContextiHOP: PNPLA2
cancer metabolism search in PubMed: PNPLA2
UCL Cancer Institute: PNPLA2
Assigned class in ccmGDBC

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Phenotypic Information for PNPLA2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PNPLA2
Familial Cancer Database: PNPLA2
* 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
Orphanet
DiseaseKEGG Disease: PNPLA2
MedGen: PNPLA2 (Human Medical Genetics with Condition)
ClinVar: PNPLA2
PhenotypeMGI: PNPLA2 (International Mouse Phenotyping Consortium)
PhenomicDB: PNPLA2

Mutations for PNPLA2
* 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 PNPLA2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG960633PNPLA21424311820586820922PNPLA222634811820923821042
AV703000UNC1191350172687471526875703PNPLA234543511825127825217
BQ446930PNPLA21911311825124825218CCDC162P1003286109669115109669342
BI017246PNPLA21226211821832822552GHITM255361108591219385912300
BU960554HM133230203015404430157173PNPLA221840711825028825217

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=19)
Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr11:823809-823809p.P291P3
chr11:821806-821806p.S122S3
chr11:822398-822398p.R163H2
chr11:824789-824789p.L481P2
chr11:821985-821985p.V150M1
chr11:822557-822557p.L216P1
chr11:824014-824014p.C312C1
chr11:822001-822004p.L159fs*961
chr11:822601-822601p.P231S1
chr11:824015-824015p.V313M1

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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   21      12 1 13 8
# mutation   21      12 1 13 8
nonsynonymous SNV   21      1    13 5
synonymous SNV            2 1    3
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
chr11:822398p.R163H2
chr11:822471p.A267V1
chr11:822494p.S281S1
chr11:821634p.A65V1
chr11:822507p.V313M1
chr11:821651p.R383R1
chr11:823570p.E71Q1
chr11:821676p.R79Q1
chr11:823707p.A141T1
chr11:821958p.N142S1

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 PNPLA2 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 PNPLA2

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

LMNTD2,TMEM259,CD151,CIRBP,D2HGDH,CRACR2B,FAM160A2,
JMJD7-PLA2G4B,KANK3,PIDD1,MZF1,NOXA1,PCSK4,PLEKHH3,
PNPLA2,RAPGEF3,RASSF7,RNH1,SPSB3,TENC1,ZNF219
ABHD15,ACAA2,ACACB,AGPAT2,ALDH2,AQP7,ADIRF,
FAM213A,CAMK1,CEBPA,CIDEC,CSPG4,FAH,HEPN1,
LIPE,MLXIPL,PLA2G16,PNPLA2,RDH5,TMEM132C,TYRO3

ABTB1,AQP7,ARRDC2,B3GALT4,BET1L,C14orf180,CD151,
CIDEC,GSN,INSR,MADD,MEGF6,MGLL,MOB2,
PLCD1,PNPLA2,POLD4,SPSB3,TRADD,YPEL3,ZER1
AGPAT3,ATG9A,C1orf106,CTSD,EPN1,EPS8L2,ESPN,
FTH1,FTH1P3,HECTD3,KIAA2013,LOC151534,PIGS,PNPLA2,
SLC9A3R1,SPINT1,STARD3,TICAM1,TMEM175,TNIP1,TOM1
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 PNPLA2


There's no related Drug.
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Cross referenced IDs for PNPLA2
* 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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