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| TissGeneSummary for LRCH4 |
 Gene summary |
| Basic gene information | Gene symbol | LRCH4 |
| Gene name | leucine-rich repeats and calponin homology (CH) domain containing 4 | |
| Synonyms | LRN|LRRN1|LRRN4|PP14183 | |
| Cytomap | UCSC genome browser: 7q22 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001289934.1, NM_002319.4, | |
| Description | leucine rich repeat neuronal 4leucine-rich neuronal proteinleucine-rich repeat and calponin homology domain-containing protein 4 | |
| Modification date | 20141207 | |
| dbXrefs | HGNC : HGNC | |
| Ensembl : ENSG00000077454 | ||
| HPRD : 10062 | ||
| Vega : OTTHUMG00000159544 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_LRCH4 | |
| BioGPS: 4034 | ||
| Pathway | NCI Pathway Interaction Database: LRCH4 | |
| KEGG: LRCH4 | ||
| REACTOME: LRCH4 | ||
| Pathway Commons: LRCH4 | ||
| Context | iHOP: LRCH4 | |
| ligand binding site mutation search in PubMed: LRCH4 | ||
| UCL Cancer Institute: LRCH4 | ||
| Assigned class in TissGDB* | C | |
| Included tissue-specific gene expression resources | TiGER,GTEx | |
| Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | TestisThymus | |
| Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | TGCTTHYM | |
| Reference showing the relevant tissue of LRCH4 | ||
| Description by TissGene annotations | Protective TissGene in OS 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 |
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| TissGeneExp for LRCH4 |
| 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) |
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| 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) |
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| 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. |
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| 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) |
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| - 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 |
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| TissGene-miRNA for LRCH4 |
| 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 LRCH4 |
| TissGeneSNV for LRCH4 |
| 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. |
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| 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) |
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| - nsSNVs sorted by frequency. |
| AAchange | Cancer type | # samples |
| p.S183F | SKCM | 2 |
| p.P485H | ESCA | 1 |
| p.D74_splice | LUSC | 1 |
| p.Q245* | SKCM | 1 |
| p.P397L | COAD | 1 |
| p.R104T | LUSC | 1 |
| p.R333Q | COAD | 1 |
| p.R394Q | DLBC | 1 |
| p.P381L | KIRC | 1 |
| p.R162Q | UCEC | 1 |
| p.S461C | SKCM | 1 |
| p.E199K | SARC | 1 |
| p.F80V | SKCM | 1 |
| p.V663I | STAD | 1 |
| p.E316K | HNSC | 1 |
| p.S212F | SKCM | 1 |
| p.R336W | STAD | 1 |
| p.G634E | SKCM | 1 |
| p.D350H | BLCA | 1 |
| p.L438F | PAAD | 1 |
| p.S515G | LUAD | 1 |
| p.A452V | SKCM | 1 |
| p.R545H | STAD | 1 |
| p.G314A | HNSC | 1 |
| p.V448M | STAD | 1 |
| p.D536N | LGG | 1 |
| p.P205S | SKCM | 1 |
| p.P362L | SKCM | 1 |
| p.P535T | OV | 1 |
| p.R644W | STAD | 1 |
| p.P555L | SKCM | 1 |
| p.R293W | UCEC | 1 |
| p.R190W | SKCM | 1 |
| p.R190Q | SKCM | 1 |
| p.A41V | COAD | 1 |
| p.E316V | ACC | 1 |
| p.A649V | PRAD | 1 |
| p.E177K | SKCM | 1 |
| p.P351L | SKCM | 1 |
| p.E199K | SKCM | 1 |
| p.G456S | OV | 1 |
| p.A447T | UCEC | 1 |
| p.R215H | UCEC | 1 |
| p.E609K | HNSC | 1 |
| p.F223I | SKCM | 1 |
| p.A446T | THYM | 1 |
| p.S346L | SKCM | 1 |
| p.E85K | BLCA | 1 |
| p.R327Q | STAD | 1 |
| p.E562K | ESCA | 1 |
| p.E605K | HNSC | 1 |
| p.P278L | THYM | 1 |
| p.R679P | BLCA | 1 |
| p.A268S | KIRP | 1 |
| p.E199K | UCEC | 1 |
| p.P362S | SKCM | 1 |
| p.S359G | LIHC | 1 |
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| TissGeneCNV for LRCH4 |
| 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 LRCH4 |
| 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 |
| Chimerdb3.0 | ChiTaRs | NA | BI052970 | SEC31A-LRCH4 | chr4:83770072 | chr7:100174335 | |
| Chimerdb3.0 | ChiTaRs | NA | AV704306 | TNKS1BP1-LRCH4 | chr11:57075591 | chr7:100172283 | |
| Chimerdb3.0 | ChiTaRs | NA | BE709716 | LRCH4-TBC1D1 | chr7:100178707 | chr4:38091674 | |
| Chimerdb3.0 | ChiTaRs | NA | AW182813 | OXR1-LRCH4 | chr8:107285002 | chr7:100179483 |
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| TissGeneNet for LRCH4 |
| 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) |
| BRCA (tumor) | BRCA (normal) |
| LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (tumor) | LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (normal) |
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| COAD (tumor) | COAD (normal) |
| LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (tumor) | LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (normal) |
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| HNSC (tumor) | HNSC (normal) |
| LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (tumor) | LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (normal) |
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| KICH (tumor) | KICH (normal) |
| LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (tumor) | LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (normal) |
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| KIRC (tumor) | KIRC (normal) |
| LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (tumor) | LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (normal) |
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| KIRP (tumor) | KIRP (normal) |
| LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (tumor) | LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (normal) |
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| LIHC (tumor) | LIHC (normal) |
| LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (tumor) | LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (normal) |
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| LUAD (tumor) | LUAD (normal) |
| LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (tumor) | LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (normal) |
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| LUSC (tumor) | LUSC (normal) |
| LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (tumor) | LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (normal) |
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| PRAD (tumor) | PRAD (normal) |
| LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (tumor) | LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (normal) |
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| STAD (tumor) | STAD (normal) |
| LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (tumor) | LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (normal) |
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| THCA (tumor) | THCA (normal) |
| LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (tumor) | LRCH4, RTN4, MDFI, RBBP6, TADA2A, SIN3A, CA8 (normal) |
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| TissGeneProg for LRCH4 |
| 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. |
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| 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. |
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| 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. |
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| 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 LRCH4 |
| TissGeneDrug for LRCH4 |
| 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 LRCH4 |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0025500 | Mesothelioma | 1 | BeFree |
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