TissGeneSummary for LRRN4 |
Gene summary |
Basic gene information | Gene symbol | LRRN4 |
Gene name | leucine rich repeat neuronal 4 | |
Synonyms | C20orf75|NLRR-4|NLRR4|dJ1056H1.1 | |
Cytomap | UCSC genome browser: 20p12.3 | |
Type of gene | protein-coding | |
RefGenes | NM_152611.4, | |
Description | leucine-rich repeat neuronal protein 4neuronal leucine-rich repeat protein 4 | |
Modification date | 20141207 | |
dbXrefs | HGNC : HGNC | |
Ensembl : ENSG00000125872 | ||
HPRD : 12784 | ||
Vega : OTTHUMG00000031825 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LRRN4 | |
BioGPS: 164312 | ||
Pathway | NCI Pathway Interaction Database: LRRN4 | |
KEGG: LRRN4 | ||
REACTOME: LRRN4 | ||
Pathway Commons: LRRN4 | ||
Context | iHOP: LRRN4 | |
ligand binding site mutation search in PubMed: LRRN4 | ||
UCL Cancer Institute: LRRN4 | ||
Assigned class in TissGDB* | B | |
Included tissue-specific gene expression resources | HPA,TiGER,GTEx | |
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | KidneyLung | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | KIRC,KIRP,KICHLUAD,LUSC | |
Reference showing the relevant tissue of LRRN4 | ||
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 LRRN4 |
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 |
LUSC | 0.16825664 | 5.502038993 | -5.333782353 | 3.24E-23 | 5.70E-22 |
LUAD | 3.619658871 | 5.668350251 | -2.048691379 | 9.08E-10 | 4.84E-09 |
HNSC | -0.834645138 | -2.603231185 | 1.768586047 | 3.94E-07 | 3.36E-06 |
KIRP | 5.567594324 | 3.390566199 | 2.177028125 | 7.44E-06 | 3.20E-05 |
COAD | -1.363334763 | -3.021384763 | 1.65805 | 3.30E-08 | 2.59E-07 |
KIRC | 2.01500231 | 3.489080088 | -1.474077778 | 5.49E-06 | 1.31E-05 |
KICH | -2.014924301 | 3.411359699 | -5.426284 | 4.32E-16 | 1.13E-14 |
STAD | -0.344361926 | -1.469924426 | 1.1255625 | 0.00698 | 0.025561805 |
BLCA | -1.476185775 | -3.24894367 | 1.772757895 | 0.000299 | 0.002692211 |
LIHC | -2.038084301 | -0.748770301 | -1.289314 | 0.000355 | 0.001074189 |
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TissGene-miRNA for LRRN4 |
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 LRRN4 |
TissGeneSNV for LRRN4 |
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.V445I | STAD | 1 |
p.R492C | LUAD | 1 |
p.L148F | COAD | 1 |
p.L573F | STAD | 1 |
p.A393T | UCEC | 1 |
p.S489L | UCEC | 1 |
p.P138L | READ | 1 |
p.S407F | SKCM | 1 |
p.E590D | LUSC | 1 |
p.Q498E | LUAD | 1 |
p.T368P | SKCM | 1 |
p.C671Y | STAD | 1 |
p.E617K | SKCM | 1 |
p.A689T | UVM | 1 |
p.R328I | UCEC | 1 |
p.Q100R | KIRP | 1 |
p.G609W | UCEC | 1 |
p.D336H | LUAD | 1 |
p.P294S | SKCM | 1 |
p.A703T | STAD | 1 |
p.D730N | DLBC | 1 |
p.S496L | UCS | 1 |
p.R328K | SKCM | 1 |
p.Q302* | BRCA | 1 |
p.Q611H | UCEC | 1 |
p.C377* | LGG | 1 |
p.S489L | BLCA | 1 |
p.P375T | COAD | 1 |
p.C260Y | ESCA | 1 |
p.Q261E | BLCA | 1 |
p.G459V | LIHC | 1 |
p.G484D | THCA | 1 |
p.L233F | COAD | 1 |
p.P551L | UCS | 1 |
p.D731N | SKCM | 1 |
p.R14C | STAD | 1 |
p.Q281R | PRAD | 1 |
p.R328I | CESC | 1 |
p.S702F | HNSC | 1 |
p.R613H | PAAD | 1 |
p.G371W | SKCM | 1 |
p.R426W | THYM | 1 |
p.S436C | SKCM | 1 |
p.E518K | SKCM | 1 |
p.D718N | UCEC | 1 |
p.P138L | PCPG | 1 |
p.H504Q | LUSC | 1 |
p.H608Y | BLCA | 1 |
p.C568W | STAD | 1 |
p.D199H | HNSC | 1 |
p.R88P | MESO | 1 |
p.S664F | SKCM | 1 |
p.K327N | READ | 1 |
p.Q498H | UCEC | 1 |
p.Q286* | CESC | 1 |
p.I471M | BLCA | 1 |
p.S414F | LGG | 1 |
p.P499L | SARC | 1 |
p.N254K | KIRP | 1 |
p.E94K | LUAD | 1 |
p.W420X | STAD | 1 |
p.W667* | SKCM | 1 |
p.R648C | STAD | 1 |
p.T141A | COAD | 1 |
p.R240Q | PAAD | 1 |
p.E94K | LGG | 1 |
p.L177I | THYM | 1 |
p.R240W | LUSC | 1 |
p.T141A | PCPG | 1 |
p.E49K | CESC | 1 |
p.W420* | STAD | 1 |
p.Q286K | UCEC | 1 |
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TissGeneCNV for LRRN4 |
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 LRRN4 |
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-75-6205-01A | LRRN4-MCM8 | In-frame | Chr20:6031425 | Chr20:5974152 |
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TissGeneNet for LRRN4 |
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 LRRN4 |
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 LRRN4 |
TissGeneDrug for LRRN4 |
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 LRRN4 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0025500 | Mesothelioma | 1 | BeFree |
umls:C0567312 | Menopause present (finding) | 1 | GAD |