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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PNPLA4 |
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Phenotypic Information for PNPLA4(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PNPLA4 |
Familial Cancer Database: PNPLA4 |
* 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/ |
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KEGG_RETINOL_METABOLISM |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: PNPLA4 |
MedGen: PNPLA4 (Human Medical Genetics with Condition) | |
ClinVar: PNPLA4 | |
Phenotype | MGI: PNPLA4 (International Mouse Phenotyping Consortium) |
PhenomicDB: PNPLA4 |
Mutations for PNPLA4 |
* 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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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PNPLA4 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=19) | (# total SNVs=2) |
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(# total SNVs=0) | (# total SNVs=3) |
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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 |
chr23:7870101-7870101 | p.R187* | 2 |
chr23:7890084-7890084 | p.G79A | 1 |
chr23:7894159-7894159 | p.M1T | 1 |
chr23:7880069-7880069 | p.Q159H | 1 |
chr23:7890117-7890117 | p.K68M | 1 |
chr23:7868791-7868791 | p.S233F | 1 |
chr23:7880131-7880131 | p.L139I | 1 |
chr23:7890132-7890132 | p.N63S | 1 |
chr23:7868821-7868821 | p.L223P | 1 |
chr23:7889752-7889752 | p.? | 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 |   |   |   | 2 |   |   | 2 |   | 1 |   |   | 3 | 2 | 1 |   |   | 2 | 2 |   | 4 |
# mutation |   |   |   | 2 |   |   | 2 |   | 1 |   |   | 3 | 2 | 1 |   |   | 2 | 2 |   | 4 |
nonsynonymous SNV |   |   |   | 2 |   |   | 2 |   | 1 |   |   | 1 | 1 | 1 |   |   |   | 1 |   | 4 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   | 2 | 1 |   |   |   | 2 | 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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* 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 |
chrX:7889875 | p.S10L,PNPLA4 | 2 |
chrX:7889834 | p.L52L,PNPLA4 | 1 |
chrX:7868777 | p.A49A,PNPLA4 | 1 |
chrX:7889850 | p.G151S,PNPLA4 | 1 |
chrX:7868791 | p.A38T,PNPLA4 | 1 |
chrX:7868839 | p.S146F,PNPLA4 | 1 |
chrX:7890117 | p.V36V,PNPLA4 | 1 |
chrX:7868853 | p.V130E,PNPLA4 | 1 |
chrX:7894005 | p.G15G,PNPLA4 | 1 |
chrX:7868854 | p.S125S,PNPLA4 | 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 PNPLA4 |
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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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ABLIM3,CYB5D2,DYNLRB2,FOXA1,IFT46,MOAP1,NDFIP1, NPRL2,NUDT12,OSCP1,PIGV,PNPLA4,PTGR2,RBKS, SKP1,TCTA,TCTN1,TMC4,TMEM25,TTC8,XBP1 | APOO,ATP5A1,COA1,CDKN2AIPNL,CLYBL,CMBL,FGGY, HSPA9,KCNJ11,MRPL44,MRPS16,NDUFA10,NDUFA7,NDUFB4, NDUFC1,NDUFV2,PFN2,PNPLA4,PTGR2,TSPYL1,VPS52 |
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ARSD,ARSE,ASB9,EIF1AX,FAM104B,FUNDC1,GEMIN8, HCCS,HDHD1,JPX,NDUFB11,PDZD11,PNPLA4,PRDX4, RAB9A,RBBP7,RPS4X,SYAP1,TIMM17B,TRAPPC2,UXT | ABCC6P2,ARSD,ARSE,BCL2L14,C11orf52,RBBP8NL,EFNA4, HDHD1,IGBP1,ILVBL,LOC389332,NHEJ1,PIGV,PNPLA4, POF1B,PRKX,RPS4X,SMPDL3B,TMEM98,TRAPPC2,UBAC2 |
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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 PNPLA4 |
There's no related Drug. |
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Cross referenced IDs for PNPLA4 |
* 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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