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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PNPLA8 |
Basic gene info. | Gene symbol | PNPLA8 |
Gene name | patatin-like phospholipase domain containing 8 | |
Synonyms | IPLA2(GAMMA)|IPLA2-2|IPLA2G|iPLA2gamma | |
Cytomap | UCSC genome browser: 7q31 | |
Genomic location | chr7 :108110865-108166762 | |
Type of gene | protein-coding | |
RefGenes | NM_001256007.1, NM_001256008.1,NM_001256009.1,NM_001256010.1,NM_001256011.1, NM_015723.3, | |
Ensembl id | ENSG00000135241 | |
Description | PNPLA-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 date | 20141207 | |
dbXrefs | MIM : 612123 | |
HGNC : HGNC | ||
Ensembl : ENSG00000135241 | ||
HPRD : 13741 | ||
Vega : OTTHUMG00000154870 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PNPLA8 | |
BioGPS: 50640 | ||
Gene Expression Atlas: ENSG00000135241 | ||
The Human Protein Atlas: ENSG00000135241 | ||
Pathway | NCI Pathway Interaction Database: PNPLA8 | |
KEGG: PNPLA8 | ||
REACTOME: PNPLA8 | ||
ConsensusPathDB | ||
Pathway Commons: PNPLA8 | ||
Metabolism | MetaCyc: PNPLA8 | |
HUMANCyc: PNPLA8 | ||
Regulation | Ensembl's Regulation: ENSG00000135241 | |
miRBase: chr7 :108,110,865-108,166,762 | ||
TargetScan: NM_001256007 | ||
cisRED: ENSG00000135241 | ||
Context | iHOP: PNPLA8 | |
cancer metabolism search in PubMed: PNPLA8 | ||
UCL Cancer Institute: PNPLA8 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PNPLA8(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PNPLA8 |
Familial Cancer Database: PNPLA8 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PNPLA8 |
MedGen: PNPLA8 (Human Medical Genetics with Condition) | |
ClinVar: PNPLA8 | |
Phenotype | MGI: 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
breast | PNPLA8 | chr7 | 108137152 | 108137152 | chr7 | 108582879 | 108582879 | |
pancreas | PNPLA8 | chr7 | 108121280 | 108121300 | chr7 | 110259440 | 110259460 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PNPLA8 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 |
DB477711 | NRCAM | 1 | 302 | 7 | 108039879 | 108096829 | PNPLA8 | 300 | 477 | 7 | 108137998 | 108143088 | |
DB472533 | NRCAM | 1 | 302 | 7 | 108039879 | 108096829 | PNPLA8 | 300 | 490 | 7 | 108137985 | 108143088 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 2 |   |   |   |   |   |   |   | 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=71) | (# total SNVs=11) |
(# total SNVs=1) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr7:108143035-108143035 | p.L420V | 3 |
chr7:108155217-108155217 | p.K240M | 3 |
chr7:108128230-108128230 | p.E617E | 2 |
chr7:108137192-108137192 | p.I487M | 2 |
chr7:108155376-108155376 | p.R187H | 2 |
chr7:108119718-108119718 | p.R662C | 2 |
chr7:108155570-108155570 | p.M122I | 2 |
chr7:108112860-108112860 | p.F778L | 2 |
chr7:108142960-108142960 | p.L445I | 2 |
chr7:108155058-108155058 | p.R293H | 2 |
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SNV Counts per Each Loci in TCGA data |
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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 |   | 19 |   |   | 2 |   | 3 | 1 |   | 10 | 5 | 1 |   |   | 6 | 4 |   | 8 |
# mutation |   | 3 |   | 18 |   |   | 2 |   | 3 | 1 |   | 11 | 5 | 1 |   |   | 7 | 4 |   | 9 |
nonsynonymous SNV |   | 3 |   | 18 |   |   | 2 |   | 3 | 1 |   | 7 | 4 | 1 |   |   | 4 | 3 |   | 9 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   | 4 | 1 |   |   |   | 3 | 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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr7:108155217 | p.K240R,PNPLA8 | 2 |
chr7:108119718 | p.F778L,PNPLA8 | 2 |
chr7:108155376 | p.R187H,PNPLA8 | 2 |
chr7:108112860 | p.R662C,PNPLA8 | 2 |
chr7:108119758 | p.W602C,PNPLA8 | 1 |
chr7:108155179 | p.E384K,PNPLA8 | 1 |
chr7:108155557 | p.M1V,PNPLA8 | 1 |
chr7:108142951 | p.R555G,PNPLA8 | 1 |
chr7:108112970 | p.V383D,PNPLA8 | 1 |
chr7:108154727 | p.K240E,PNPLA8 | 1 |
Other DBs for Point Mutations |
Copy 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 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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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 |
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