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 PNPLA8
Basic gene info.Gene symbolPNPLA8
Gene namepatatin-like phospholipase domain containing 8
SynonymsIPLA2(GAMMA)|IPLA2-2|IPLA2G|iPLA2gamma
CytomapUCSC genome browser: 7q31
Genomic locationchr7 :108110865-108166762
Type of geneprotein-coding
RefGenesNM_001256007.1,
NM_001256008.1,NM_001256009.1,NM_001256010.1,NM_001256011.1,
NM_015723.3,
Ensembl idENSG00000135241
DescriptionPNPLA-gammacalcium-independent phospholipase A2-gammaiPLA2 gammaiPLA2-gammaintracellular membrane-associated calcium-independent phospholipase A2 gammamembrane-associated calcium-independent phospholipase A2 gammapatatin-like phospholipase domain-co
Modification date20141207
dbXrefs MIM : 612123
HGNC : HGNC
Ensembl : ENSG00000135241
HPRD : 13741
Vega : OTTHUMG00000154870
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PNPLA8
BioGPS: 50640
Gene Expression Atlas: ENSG00000135241
The Human Protein Atlas: ENSG00000135241
PathwayNCI Pathway Interaction Database: PNPLA8
KEGG: PNPLA8
REACTOME: PNPLA8
ConsensusPathDB
Pathway Commons: PNPLA8
MetabolismMetaCyc: PNPLA8
HUMANCyc: PNPLA8
RegulationEnsembl's Regulation: ENSG00000135241
miRBase: chr7 :108,110,865-108,166,762
TargetScan: NM_001256007
cisRED: ENSG00000135241
ContextiHOP: PNPLA8
cancer metabolism search in PubMed: PNPLA8
UCL Cancer Institute: PNPLA8
Assigned class in ccmGDBC

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Phenotypic Information for PNPLA8(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PNPLA8
Familial Cancer Database: PNPLA8
* 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: PNPLA8
MedGen: PNPLA8 (Human Medical Genetics with Condition)
ClinVar: PNPLA8
PhenotypeMGI: PNPLA8 (International Mouse Phenotyping Consortium)
PhenomicDB: PNPLA8

Mutations for PNPLA8
* 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
breastPNPLA8chr7108137152108137152chr7108582879108582879
pancreasPNPLA8chr7108121280108121300chr7110259440110259460
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 PNPLA8 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB477711NRCAM13027108039879108096829PNPLA83004777108137998108143088
DB472533NRCAM13027108039879108096829PNPLA83004907108137985108143088

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 # sample2       1 2  1   
GAIN (# sample)1       1 2  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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=71)
Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr7:108143035-108143035p.L420V3
chr7:108155217-108155217p.K240M3
chr7:108137192-108137192p.I487M2
chr7:108155376-108155376p.R187H2
chr7:108119718-108119718p.R662C2
chr7:108155570-108155570p.M122I2
chr7:108112860-108112860p.F778L2
chr7:108142960-108142960p.L445I2
chr7:108155058-108155058p.R293H2
chr7:108128230-108128230p.E617E2

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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 3 19  2 31 1051  64 8
# mutation 3 18  2 31 1151  74 9
nonsynonymous SNV 3 18  2 31 741  43 9
synonymous SNV           41   31  
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
chr7:108155217p.R187H,PNPLA82
chr7:108119718p.R662C,PNPLA82
chr7:108155376p.K240R,PNPLA82
chr7:108112860p.F778L,PNPLA82
chr7:108155179p.F215F,PNPLA81
chr7:108119758p.Y737C,PNPLA81
chr7:108155557p.K470T,PNPLA81
chr7:108142951p.I353S,PNPLA81
chr7:108112970p.D704N,PNPLA81
chr7:108154727p.T460T,PNPLA81

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 PNPLA8 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 PNPLA8

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

ANKIB1,CBLL1,COG5,DDX3X,DLD,DNAJB9,HBP1,
KRIT1,LUZP6,MKLN1,KMT2C,KMT2E,NAPEPLD,PNPLA8,
RINT1,SLC25A40,THAP5,WASL,ZBTB11,ZNF800,ZYG11B
ANKRD13C,ARL5A,BNIP2,C2orf69,CHUK,DDX3X,HAUS2,
HECA,NCKAP1,BLOC1S6,PNPLA8,PRKAR1A,SHOC2,STYX,
TBC1D23,TMED5,TOR1AIP1,UBL3,UBQLN1,USP16,VPS37A

ANKIB1,BCAP29,C7orf60,RBM48,CAPZA2,CBLL1,CCDC132,
COG5,DNAJB9,HBP1,LUZP6,PNPLA8,POT1,RABGEF1,
RHEB,RINT1,SRPK2,SYPL1,TES,THAP5,YPEL5
C12orf29,C12orf4,TRAPPC13,CLDND1,COMMD2,CREM,DIMT1,
FGFR1OP2,MOB4,MRPL50,MRPS10,MTMR6,PACRGL,PNPLA8,
POLR2K,RWDD1,STRAP,TSNAX,UBA3,USP15,YAF2
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 PNPLA8


There's no related Drug.
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Cross referenced IDs for PNPLA8
* 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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