TissGeneSummary for NSUN4 |
Gene summary |
Basic gene information | Gene symbol | NSUN4 |
Gene name | NOP2/Sun domain family, member 4 | |
Synonyms | SHTAP | |
Cytomap | UCSC genome browser: 1p34 | |
Type of gene | protein-coding | |
RefGenes | NM_001256127.1, NM_001256128.1,NM_199044.3,NR_045789.1,NR_045790.1, NR_045791.1, | |
Description | 5-methylcytosine rRNA methyltransferase NSUN4NOL1/NOP2/Sun domain family member 4putative methyltransferase NSUN4sperm head and tail associated protein | |
Modification date | 20141207 | |
dbXrefs | MIM : 615394 | |
HGNC : HGNC | ||
HPRD : 14842 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_NSUN4 | |
BioGPS: 387338 | ||
Pathway | NCI Pathway Interaction Database: NSUN4 | |
KEGG: NSUN4 | ||
REACTOME: NSUN4 | ||
Pathway Commons: NSUN4 | ||
Context | iHOP: NSUN4 | |
ligand binding site mutation search in PubMed: NSUN4 | ||
UCL Cancer Institute: NSUN4 | ||
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 NSUN4 | ||
Description by TissGene annotations | Have significant anti-correlated miRNA TissgsLTS |
* 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 | GO:0031167 | rRNA methylation | 23022348 | GO:0031167 | rRNA methylation | 23022348 |
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TissGeneExp for NSUN4 |
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 | -0.184991176 | 1.137268824 | -1.32226 | 4.25E-19 | 2.47E-17 |
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TissGene-miRNA for NSUN4 |
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 |
UCS | hsa-miR-222-3p | MIMAT0000279 | 0.0039 | -0.38 | 56 |
UCS | hsa-miR-221-3p | MIMAT0000278 | 0.002 | -0.41 | 56 |
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TissGeneMut for NSUN4 |
TissGeneSNV for NSUN4 |
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.R24I | UCEC | 2 |
p.E267K | CESC | 1 |
p.R130L | SKCM | 1 |
p.A294D | PAAD | 1 |
p.Y332H | COAD | 1 |
p.T351S | SKCM | 1 |
p.R10L | UCEC | 1 |
p.E362K | THYM | 1 |
p.R141C | HNSC | 1 |
p.S333I | PAAD | 1 |
p.P184S | LUSC | 1 |
p.D227Y | KIRP | 1 |
p.G186E | SKCM | 1 |
p.R141H | UCEC | 1 |
p.H85Y | SKCM | 1 |
p.V256A | UCEC | 1 |
p.A117T | COAD | 1 |
p.G185W | ESCA | 1 |
p.S122C | LUAD | 1 |
p.Q230E | BRCA | 1 |
p.T51A | COAD | 1 |
p.L297I | LUAD | 1 |
p.S308C | BLCA | 1 |
p.F372S | PAAD | 1 |
p.R262H | UCEC | 1 |
p.R262C | UCEC | 1 |
p.C197Y | STAD | 1 |
p.L315* | UCEC | 1 |
p.R381C | STAD | 1 |
p.S235* | PRAD | 1 |
p.N330S | LIHC | 1 |
p.P61S | GBM | 1 |
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TissGeneCNV for NSUN4 |
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 NSUN4 |
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 |
TCGAfusionPortal | PRADA | LUAD | TCGA-44-7670-01A | NSUN4-BMPR1B | Out-of-frame | Chr1:46810816 | Chr4:96044961 |
TCGAfusionPortal | PRADA | LUAD | TCGA-78-7153-01A | EIF4G3-NSUN4 | Out-of-frame | Chr1:21415631 | Chr1:46818540 |
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TissGeneNet for NSUN4 |
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 NSUN4 |
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 NSUN4 |
TissGeneDrug for NSUN4 |
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 NSUN4 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |