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| TissGeneSummary for RTN1 |
 Gene summary |
| Basic gene information | Gene symbol | RTN1 |
| Gene name | reticulon 1 | |
| Synonyms | NSP | |
| Cytomap | UCSC genome browser: 14q23.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_021136.2, NM_206852.2,NM_001243115.1,NM_206857.1, | |
| Description | neuroendocrine-specific proteinreticulon-1 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 600865 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000139970 | ||
| HPRD : 02921 | ||
| Vega : OTTHUMG00000028947 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_RTN1 | |
| BioGPS: 6252 | ||
| Pathway | NCI Pathway Interaction Database: RTN1 | |
| KEGG: RTN1 | ||
| REACTOME: RTN1 | ||
| Pathway Commons: RTN1 | ||
| Context | iHOP: RTN1 | |
| ligand binding site mutation search in PubMed: RTN1 | ||
| UCL Cancer Institute: RTN1 | ||
| Assigned class in TissGDB* | C | |
| Included tissue-specific gene expression resources | HPA,TiGER | |
| Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | Brain | |
| Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | GBM,LGG | |
| Reference showing the relevant tissue of RTN1 | ||
| Description by TissGene annotations | Protective TissGene in OS Protective TissGene in RFS | |
| * 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 RTN1 |
| 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 |
| BRCA | 0.434934687 | 1.635080301 | -1.200145614 | 2.20E-10 | 8.45E-10 |
| LUSC | -1.178679606 | 1.257326276 | -2.436005882 | 2.92E-15 | 1.87E-14 |
| COAD | -1.752661129 | 0.089977332 | -1.842638462 | 2.50E-07 | 1.62E-06 |
| THCA | -1.26785272 | 0.272930331 | -1.540783051 | 9.24E-16 | 1.38E-14 |
| LUAD | -0.429553304 | 1.367453592 | -1.797006897 | 1.55E-13 | 1.33E-12 |
| PRAD | 2.401433101 | 1.279429255 | 1.122003846 | 1.85E-06 | 1.24E-05 |
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| TissGene-miRNA for RTN1 |
| 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 |
| ACC | hsa-miR-3666 | MIMAT0018088 | 0.02 | -0.27 | 78 |
| ACC | hsa-miR-520a-3p | MIMAT0002834 | 0.02 | -0.27 | 78 |
| ACC | hsa-miR-3666 | MIMAT0018088 | 0.02 | -0.27 | 78 |
| ACC | hsa-miR-520a-3p | MIMAT0002834 | 0.02 | -0.27 | 78 |
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| TissGeneMut for RTN1 |
| TissGeneSNV for RTN1 |
| 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.S103W | LUAD | 2 |
| p.R513W | SKCM | 2 |
| p.S367L | SKCM | 2 |
| p.P575S | SKCM | 2 |
| p.D221N | READ | 1 |
| p.A565E | LUSC | 1 |
| p.G347R | SKCM | 1 |
| p.F705S | LIHC | 1 |
| p.A577T | COAD | 1 |
| p.Q765X | SKCM | 1 |
| p.V205L | LIHC | 1 |
| p.G84D | LUSC | 1 |
| p.F605S | KIRP | 1 |
| p.A577T | HNSC | 1 |
| p.E385K | BLCA | 1 |
| p.V620M | COAD | 1 |
| p.Q765* | SKCM | 1 |
| p.E529K | LUAD | 1 |
| p.D226G | LIHC | 1 |
| p.R159L | CESC | 1 |
| p.T734I | STAD | 1 |
| p.S345F | SKCM | 1 |
| p.Q276H | BLCA | 1 |
| p.Q680H | LUSC | 1 |
| p.E302K | CESC | 1 |
| p.A494T | LUAD | 1 |
| p.P736S | PRAD | 1 |
| p.A5G | SKCM | 1 |
| p.G391R | LGG | 1 |
| p.E546* | ESCA | 1 |
| p.G391R | SKCM | 1 |
| p.K129R | STAD | 1 |
| p.R552Q | SARC | 1 |
| p.D698N | SKCM | 1 |
| p.D219N | LGG | 1 |
| p.P769T | STAD | 1 |
| p.A577T | OV | 1 |
| p.E546X | ESCA | 1 |
| p.P579A | BLCA | 1 |
| p.Q743_splice | LUSC | 1 |
| p.R596Q | LIHC | 1 |
| p.E214K | UCEC | 1 |
| p.A173E | LUAD | 1 |
| p.E216K | SKCM | 1 |
| p.T95A | UCEC | 1 |
| p.T296N | OV | 1 |
| p.S475L | ESCA | 1 |
| p.L161* | PAAD | 1 |
| p.Q531H | LUSC | 1 |
| p.E353K | ESCA | 1 |
| p.F681L | UCEC | 1 |
| p.S702F | SKCM | 1 |
| p.R273K | PAAD | 1 |
| p.G337E | SKCM | 1 |
| p.K650N | CESC | 1 |
| p.G144C | LUAD | 1 |
| p.S268F | LUSC | 1 |
| p.E664Q | LUAD | 1 |
| p.M170I | GBM | 1 |
| p.S560F | UCEC | 1 |
| p.V620M | STAD | 1 |
| p.E322K | SKCM | 1 |
| p.R596W | HNSC | 1 |
| p.T676M | STAD | 1 |
| p.E653K | SKCM | 1 |
| p.P290H | ESCA | 1 |
| p.E203K | BLCA | 1 |
| p.A517V | SKCM | 1 |
| p.E256K | SKCM | 1 |
| p.S110C | BLCA | 1 |
| p.S731L | ESCA | 1 |
| p.P340T | LUAD | 1 |
| p.P488T | THYM | 1 |
| p.Q669* | HNSC | 1 |
| p.P290H | UCEC | 1 |
| p.E535K | SKCM | 1 |
| p.L523P | HNSC | 1 |
| p.L592P | SKCM | 1 |
| p.K568N | LUAD | 1 |
| p.V245M | UCEC | 1 |
| p.S137L | SKCM | 1 |
| p.R639C | COAD | 1 |
| p.T200P | ESCA | 1 |
| p.R552Q | UCEC | 1 |
| p.D198G | KIRC | 1 |
| p.E424K | SKCM | 1 |
| p.P148S | LUAD | 1 |
| p.G409R | SKCM | 1 |
| p.R514Q | LUAD | 1 |
| p.Y594N | CESC | 1 |
| p.P392Q | ESCA | 1 |
| p.P488H | HNSC | 1 |
| p.A775T | STAD | 1 |
| p.S86F | SKCM | 1 |
| p.K482M | SKCM | 1 |
| p.D266N | LUSC | 1 |
| p.H91R | GBM | 1 |
| p.D152Y | BLCA | 1 |
| p.G247* | HNSC | 1 |
| p.V623F | LUAD | 1 |
| p.S139R | THYM | 1 |
| p.P146H | LUAD | 1 |
| p.S258F | STAD | 1 |
| p.P519T | LUSC | 1 |
| p.P736S | LUSC | 1 |
| p.E507K | SKCM | 1 |
| p.S558L | BLCA | 1 |
| p.V245E | COAD | 1 |
| p.P280L | SKCM | 1 |
| p.L582M | LUSC | 1 |
| p.T96A | STAD | 1 |
| p.V624M | COAD | 1 |
| p.T286M | COAD | 1 |
| p.L543M | LUAD | 1 |
| p.G515D | LUAD | 1 |
| p.S560F | SKCM | 1 |
| p.M189I | SKCM | 1 |
| p.S464N | COAD | 1 |
| p.Q673* | LUAD | 1 |
| p.E214K | READ | 1 |
| p.A359T | STAD | 1 |
| p.G329V | LUAD | 1 |
| p.K232E | LUAD | 1 |
| p.E385* | BLCA | 1 |
| p.T651N | THYM | 1 |
| p.E289Q | CESC | 1 |
| p.T286M | GBM | 1 |
| p.A406T | BLCA | 1 |
| p.G347E | SKCM | 1 |
| p.E508* | LUAD | 1 |
| p.L584I | COAD | 1 |
| p.A59V | STAD | 1 |
| p.Q208R | COAD | 1 |
| p.L127P | LUSC | 1 |
| p.S367L | READ | 1 |
| p.V623I | OV | 1 |
| p.C113* | UCEC | 1 |
| p.V604M | COAD | 1 |
| p.A343P | ACC | 1 |
| p.P392L | HNSC | 1 |
| p.D198V | LIHC | 1 |
| p.G160C | LUAD | 1 |
| p.A565V | ESCA | 1 |
| p.T171A | HNSC | 1 |
| p.P340R | LUAD | 1 |
| p.T286K | ESCA | 1 |
| p.P392L | COAD | 1 |
| p.A744_splice | LUSC | 1 |
| p.E142K | SKCM | 1 |
| p.R237L | LUAD | 1 |
| p.R499W | SKCM | 1 |
| p.E130K | SKCM | 1 |
| p.G125E | SKCM | 1 |
| p.L127P | ESCA | 1 |
| p.R691M | LUSC | 1 |
| p.G147V | LUAD | 1 |
| p.A717T | STAD | 1 |
| p.D99Y | UCEC | 1 |
| p.S164Y | HNSC | 1 |
| p.R272P | ESCA | 1 |
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| TissGeneCNV for RTN1 |
| 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 RTN1 |
| 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 | BM510146 | YME1L1-RTN1 | chr10:27443300 | chr14:60062898 | |
| Chimerdb3.0 | ChiTaRs | NA | AK054747 | RTN1-DPYSL2 | chr14:60067808 | chr8:26514351 | |
| Chimerdb3.0 | ChiTaRs | NA | AF003522 | RTN1-DLL1 | chr14:60063163 | chr6:170591301 | |
| Chimerdb3.0 | TopHat-Fusion | LUSC | TCGA-22-4594-01A | SAMD12-AS1-RTN1 | Out-of-Frame | chr8:119634042 | chr14:60074209 |
| TCGAfusionPortal | PRADA | BRCA | TCGA-A7-A6VV-01A | SYNE2-RTN1 | Out-of-frame | Chr14:64434564 | Chr14:60213199 |
| TCGAfusionPortal | PRADA | LUSC | TCGA-22-4594-01A | SAMD12-RTN1 | In-frame | Chr8:119634043 | Chr14:60074210 |
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| TissGeneNet for RTN1 |
| 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) |
| RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (tumor) | RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (normal) |
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| COAD (tumor) | COAD (normal) |
| RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (tumor) | RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (normal) |
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| HNSC (tumor) | HNSC (normal) |
| RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (tumor) | RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (normal) |
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| KICH (tumor) | KICH (normal) |
| RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (tumor) | RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (normal) |
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| KIRC (tumor) | KIRC (normal) |
| RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (tumor) | RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (normal) |
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| KIRP (tumor) | KIRP (normal) |
| RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (tumor) | RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (normal) |
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| LIHC (tumor) | LIHC (normal) |
| RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (tumor) | RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (normal) |
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| LUAD (tumor) | LUAD (normal) |
| RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (tumor) | RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (normal) |
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| LUSC (tumor) | LUSC (normal) |
| RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (tumor) | RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (normal) |
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| PRAD (tumor) | PRAD (normal) |
| RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (tumor) | RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (normal) |
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| STAD (tumor) | STAD (normal) |
| RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (tumor) | RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (normal) |
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| THCA (tumor) | THCA (normal) |
| RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (tumor) | RTN1, BCL2L1, SPAST, HDAC8, PLEKHF2, FAM160A2, UGCG (normal) |
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| TissGeneProg for RTN1 |
| 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 RTN1 |
| TissGeneDrug for RTN1 |
| 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 RTN1 |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0006142 | Malignant neoplasm of breast | 1 | BeFree |
| umls:C0009402 | Colorectal Carcinoma | 1 | BeFree |
| umls:C0021400 | Influenza | 1 | BeFree |
| umls:C0024031 | Low Back Pain | 1 | BeFree |
| umls:C0024115 | Lung diseases | 1 | BeFree |
| umls:C0037773 | Spastic Paraplegia, Hereditary | 1 | BeFree |
| umls:C0040336 | Tobacco Use Disorder | 1 | GAD |
| umls:C0151744 | Myocardial Ischemia | 1 | CTD_human |
| umls:C0238198 | Gastrointestinal Stromal Tumors | 1 | BeFree |
| umls:C0346629 | Malignant neoplasm of large intestine | 1 | BeFree |
| umls:C0596263 | Carcinogenesis | 1 | BeFree |
| umls:C0678222 | Breast Carcinoma | 1 | BeFree |
| umls:C3809250 | ESTROGEN RESISTANCE | 1 | BeFree |
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