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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PNPLA3 |
Basic gene info. | Gene symbol | PNPLA3 |
Gene name | patatin-like phospholipase domain containing 3 | |
Synonyms | ADPN|C22orf20|iPLA(2)epsilon | |
Cytomap | UCSC genome browser: 22q13.31 | |
Genomic location | chr22 :44319618-44343448 | |
Type of gene | protein-coding | |
RefGenes | NM_025225.2, | |
Ensembl id | ENSG00000100344 | |
Description | acylglycerol O-acyltransferaseadiponutrincalcium-independent phospholipase A2-epsiloniPLA2-epsiloniPLA2epsilonpatatin-like phospholipase domain-containing protein 3 | |
Modification date | 20141222 | |
dbXrefs | MIM : 609567 | |
HGNC : HGNC | ||
Ensembl : ENSG00000100344 | ||
HPRD : 12430 | ||
Vega : OTTHUMG00000150555 | ||
Protein | UniProt: Q9NST1 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PNPLA3 | |
BioGPS: 80339 | ||
Gene Expression Atlas: ENSG00000100344 | ||
The Human Protein Atlas: ENSG00000100344 | ||
Pathway | NCI Pathway Interaction Database: PNPLA3 | |
KEGG: PNPLA3 | ||
REACTOME: PNPLA3 | ||
ConsensusPathDB | ||
Pathway Commons: PNPLA3 | ||
Metabolism | MetaCyc: PNPLA3 | |
HUMANCyc: PNPLA3 | ||
Regulation | Ensembl's Regulation: ENSG00000100344 | |
miRBase: chr22 :44,319,618-44,343,448 | ||
TargetScan: NM_025225 | ||
cisRED: ENSG00000100344 | ||
Context | iHOP: PNPLA3 | |
cancer metabolism search in PubMed: PNPLA3 | ||
UCL Cancer Institute: PNPLA3 | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
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Phenotypic Information for PNPLA3(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PNPLA3 |
Familial Cancer Database: PNPLA3 |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in BRCA 6, |
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, 6 http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html, 7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
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KEGG_GLYCEROLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
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OMIM | 609567; gene. 613282; phenotype. |
Orphanet | 33271; Non-alcoholic fatty liver disease. |
Disease | KEGG Disease: PNPLA3 |
MedGen: PNPLA3 (Human Medical Genetics with Condition) | |
ClinVar: PNPLA3 | |
Phenotype | MGI: PNPLA3 (International Mouse Phenotyping Consortium) |
PhenomicDB: PNPLA3 |
Mutations for PNPLA3 |
* 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. |
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- Statistics for Tissue and Mutation type | Top |
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- For Inter-chromosomal Variations |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
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- 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'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | PNPLA3 | chr22 | 44336871 | 44336891 | PNPLA3 | chr22 | 44329431 | 44329451 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PNPLA3 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=38) | (# total SNVs=20) |
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(# total SNVs=3) | (# total SNVs=2) |
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* 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 position | Mutation(aa) | Unique sampleID count |
chr22:44324727-44324727 | p.I148M | 3 |
chr22:44324730-44324730 | p.P149P | 2 |
chr22:44333032-44333032 | p.P287S | 2 |
chr22:44333050-44333050 | p.A293P | 2 |
chr22:44328871-44328871 | p.T200T | 2 |
chr22:44342182-44342182 | p.F456I | 2 |
chr22:44342183-44342183 | p.F456Y | 2 |
chr22:44324726-44324726 | p.I148T | 2 |
chr22:44322960-44322960 | p.S111S | 1 |
chr22:44332968-44332968 | p.S265S | 1 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 3 | 1 | 1 | 11 |   |   | 2 |   | 3 |   |   | 5 | 2 |   |   |   | 2 | 2 |   | 9 |
# mutation | 3 | 1 | 1 | 11 |   |   | 2 |   | 3 |   |   | 5 | 2 |   |   |   | 3 | 2 |   | 12 |
nonsynonymous SNV | 2 | 1 |   | 6 |   |   |   |   | 2 |   |   | 3 | 1 |   |   |   | 1 | 2 |   | 7 |
synonymous SNV | 1 |   | 1 | 5 |   |   | 2 |   | 1 |   |   | 2 | 1 |   |   |   | 2 |   |   | 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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* 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 Position | Mutation(aa) | Unique sampleID count |
chr22:44335929 | p.L346L | 2 |
chr22:44322980 | p.T119T | 1 |
chr22:44340602 | p.E251D | 1 |
chr22:44328953 | p.L398L | 1 |
chr22:44333018 | p.R133R | 1 |
chr22:44322984 | p.G253D | 1 |
chr22:44340650 | p.L398L | 1 |
chr22:44328958 | p.D136N | 1 |
chr22:44333039 | p.S264L | 1 |
chr22:44323026 | p.L402L | 1 |
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* 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. |
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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 PNPLA3 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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 |
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ASPM,ATP10A,C1orf105,ADTRP,CARD18,CYP2F1,DHCR7, DIAPH2,ELOVL4,EYA3,FADS2,FAM83D,KRT79,NHSL1, PNPLA1,PNPLA3,PNPLA5,PSAPL1,SOAT1,SULF1,UCHL5 | ACACA,ACLY,ACSL1,CDKN2C,CYB5A,ELOVL5,EYS, FADS1,FASN,HIBCH,LSS,MCCC1,ME1,OLFM2, PNPLA3,SEL1L2,SUOX,TF,THRSP,TMEM132B,TSKU |
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ATP5A1,CA9,CLSPN,ELOVL6,GALNT1,HMGCS1,LPIN1, MAP2K1,ME2,PCSK9,PFKP,PGAM1,PIAS2,PKM, PLA2G3,PNPLA3,POLR2A,RBBP8,SREBF1,STARD4,THRAP3 | AKAP14,MFSD12,CCNO,CYP24A1,DDX4,ESX1,BRINP2, FMO9P,GAGE2D,GOLGA8DP,HAR1B,INSL6,IRX2,ITGA2B, LIMS3-LOC440895,PAGE1,PNPLA3,SNORA2B,SPRR2E,TBX18,TDRD12 |
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* 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 |
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Pharmacological Information for PNPLA3 |
There's no related Drug. |
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Cross referenced IDs for PNPLA3 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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