TissGeneSummary for PNLDC1 |
Gene summary |
Basic gene information | Gene symbol | PNLDC1 |
Gene name | poly(A)-specific ribonuclease (PARN)-like domain containing 1 | |
Synonyms | - | |
Cytomap | UCSC genome browser: 6q25.3 | |
Type of gene | protein-coding | |
RefGenes | NM_001271862.1, NM_173516.2, | |
Description | poly(A)-specific ribonuclease PARN-like domain-containing protein 1 | |
Modification date | 20141207 | |
dbXrefs | HGNC : HGNC | |
Ensembl : ENSG00000146453 | ||
HPRD : 17868 | ||
Vega : OTTHUMG00000015941 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PNLDC1 | |
BioGPS: 154197 | ||
Pathway | NCI Pathway Interaction Database: PNLDC1 | |
KEGG: PNLDC1 | ||
REACTOME: PNLDC1 | ||
Pathway Commons: PNLDC1 | ||
Context | iHOP: PNLDC1 | |
ligand binding site mutation search in PubMed: PNLDC1 | ||
UCL Cancer Institute: PNLDC1 | ||
Assigned class in TissGDB* | C | |
Included tissue-specific gene expression resources | HPA,GTEx | |
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | Testis | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | TGCT | |
Reference showing the relevant tissue of PNLDC1 | ||
Description by TissGene annotations |
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO term | PubMed ID |
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TissGeneExp for PNLDC1 |
Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01) |
Gene expressions across normal tissues of GTEx data (GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct) - Here, we shows the matched tissue types only among our 28 cancer types. |
Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
KICH | -2.420440005 | -1.207524005 | -1.212916 | 1.17E-05 | 3.67E-05 |
KIRP | -2.24332413 | -1.03933038 | -1.20399375 | 0.000969 | 0.00267549 |
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TissGene-miRNA for PNLDC1 |
Significantly anti-correlated miRNAs of TissGene across 28 cancer types (Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016) (TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21) (TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16) (Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25)) |
Cancer type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
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TissGeneMut for PNLDC1 |
TissGeneSNV for PNLDC1 |
nsSNV counts per each loci. Different colors of circles represent different cancer types. Circle size denotes number of samples. (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) * Click on the image to enlarge it in a new window. |
Somatic nucleotide variants of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of mutated samples) The numbers in parentheses are numbers of samples with mutation (nsSNVs). (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) |
- nsSNVs sorted by frequency. |
AAchange | Cancer type | # samples |
p.R213H | UCEC | 2 |
p.R213C | READ | 2 |
p.H335D | BLCA | 1 |
p.Y81* | SKCM | 1 |
p.A363V | LUSC | 1 |
p.R236S | UCEC | 1 |
p.V101F | ESCA | 1 |
p.F2Y | STAD | 1 |
p.K45N | HNSC | 1 |
p.K45N | CESC | 1 |
p.N399T | LUAD | 1 |
p.S417C | OV | 1 |
p.I74R | STAD | 1 |
p.H367R | LUAD | 1 |
p.R159W | STAD | 1 |
p.F356C | BLCA | 1 |
p.P84R | BLCA | 1 |
p.H263Q | READ | 1 |
p.L82F | READ | 1 |
p.E435K | BLCA | 1 |
p.W160L | UCEC | 1 |
p.D133N | HNSC | 1 |
p.P431L | COAD | 1 |
p.V506I | GBM | 1 |
p.Q457H | UCEC | 1 |
p.P307L | SKCM | 1 |
p.R429M | CHOL | 1 |
p.F94L | UCEC | 1 |
p.Q102* | BLCA | 1 |
p.A352E | LUAD | 1 |
p.G404R | SKCM | 1 |
p.Y415N | SKCM | 1 |
p.R24H | STAD | 1 |
p.E435K | COAD | 1 |
p.A366V | PAAD | 1 |
p.R213C | UCEC | 1 |
p.Q278L | HNSC | 1 |
p.A468V | LIHC | 1 |
p.E93Q | THCA | 1 |
p.K228T | SKCM | 1 |
p.Q278K | HNSC | 1 |
p.F242S | STAD | 1 |
p.L35V | HNSC | 1 |
p.R402* | BLCA | 1 |
p.W160R | COAD | 1 |
p.A352V | LGG | 1 |
p.S77F | PRAD | 1 |
p.P307S | SKCM | 1 |
p.K473T | UCEC | 1 |
p.S382L | SKCM | 1 |
p.L216V | READ | 1 |
p.V390M | UCEC | 1 |
p.R452* | STAD | 1 |
p.P421S | SKCM | 1 |
p.S239Y | BLCA | 1 |
p.T86M | STAD | 1 |
p.G237S | SKCM | 1 |
p.R452X | STAD | 1 |
p.A336S | LIHC | 1 |
p.L445F | UCS | 1 |
p.Q43* | UCEC | 1 |
p.E340K | BLCA | 1 |
p.R142C | READ | 1 |
p.G137E | SKCM | 1 |
p.D354N | SKCM | 1 |
p.L445I | READ | 1 |
p.F10V | BLCA | 1 |
p.W441* | GBM | 1 |
p.Q443H | BRCA | 1 |
p.D200N | SKCM | 1 |
p.D292N | BLCA | 1 |
p.Q32* | UCEC | 1 |
p.R452Q | CESC | 1 |
p.P416S | SKCM | 1 |
p.C497F | CESC | 1 |
p.Q48H | BLCA | 1 |
p.E446D | LUSC | 1 |
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TissGeneCNV for PNLDC1 |
Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples) (TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16) |
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TissGeneFusions for PNLDC1 |
Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
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TissGeneNet for PNLDC1 |
Co-expressed gene networks based on protein-protein interaction data (CePIN) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (PINA2 ppi data) |
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TissGeneProg for PNLDC1 |
Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image to enlarge it in a new window. |
Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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TissGeneClin for PNLDC1 |
TissGeneDrug for PNLDC1 |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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TissGeneDisease for PNLDC1 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0022658 | Kidney Diseases | 1 | GAD |
umls:C0038454 | Cerebrovascular accident | 1 | GAD |
umls:C0038525 | Subarachnoid Hemorrhage | 1 | GAD |
umls:C0151699 | Intracranial Hemorrhages | 1 | GAD |
umls:C2937358 | Cerebral Hemorrhage | 1 | GAD |