TissGeneSummary for RPGRIP1 |
Gene summary |
Basic gene information | Gene symbol | RPGRIP1 |
Gene name | retinitis pigmentosa GTPase regulator interacting protein 1 | |
Synonyms | CORD13|LCA6|RGI1|RGRIP|RPGRIP|RPGRIP1d | |
Cytomap | UCSC genome browser: 14q11 | |
Type of gene | protein-coding | |
RefGenes | NM_020366.3, | |
Description | RPGR-interacting protein 1X-linked retinitis pigmentosa GTPase regulator-interacting protein 1 | |
Modification date | 20141219 | |
dbXrefs | MIM : 605446 | |
HGNC : HGNC | ||
Ensembl : ENSG00000092200 | ||
HPRD : 05673 | ||
Vega : OTTHUMG00000170758 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RPGRIP1 | |
BioGPS: 57096 | ||
Pathway | NCI Pathway Interaction Database: RPGRIP1 | |
KEGG: RPGRIP1 | ||
REACTOME: RPGRIP1 | ||
Pathway Commons: RPGRIP1 | ||
Context | iHOP: RPGRIP1 | |
ligand binding site mutation search in PubMed: RPGRIP1 | ||
UCL Cancer Institute: RPGRIP1 | ||
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 RPGRIP1 | ||
Description by TissGene annotations | Cancer gene |
* 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 RPGRIP1 |
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 |
KIRC | -1.671971217 | -2.892855939 | 1.220884722 | 1.29E-13 | 5.92E-13 |
PRAD | -1.394525811 | -2.401089272 | 1.006563462 | 7.27E-07 | 5.34E-06 |
LUSC | -2.098745645 | -0.774565253 | -1.324180392 | 9.95E-13 | 4.57E-12 |
KIRP | -2.035198647 | -3.060873647 | 1.025675 | 0.000244 | 0.000767248 |
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TissGene-miRNA for RPGRIP1 |
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 RPGRIP1 |
TissGeneSNV for RPGRIP1 |
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.E800K | SKCM | 4 |
p.E710K | SKCM | 2 |
p.R768Q | SKCM | 2 |
p.W751* | SKCM | 2 |
p.Q967H | HNSC | 1 |
p.Q111K | LUAD | 1 |
p.G944W | LUAD | 1 |
p.S619Y | COAD | 1 |
p.R890* | UCEC | 1 |
p.R1010G | UCEC | 1 |
p.E576X | PRAD | 1 |
p.R52X | ESCA | 1 |
p.K615T | THCA | 1 |
p.S901Y | COAD | 1 |
p.L856F | COAD | 1 |
p.Q487* | CESC | 1 |
p.R103C | STAD | 1 |
p.S1065F | SKCM | 1 |
p.H1007L | BRCA | 1 |
p.D553E | CESC | 1 |
p.W1040R | TGCT | 1 |
p.M220V | HNSC | 1 |
p.R425I | UCEC | 1 |
p.L343F | BLCA | 1 |
p.W802X | SKCM | 1 |
p.T777N | GBM | 1 |
p.P18L | SKCM | 1 |
p.G944E | SKCM | 1 |
p.M1019I | SKCM | 1 |
p.I465M | PAAD | 1 |
p.F690Y | HNSC | 1 |
p.D614N | SKCM | 1 |
p.A547S | COAD | 1 |
p.P37L | LUAD | 1 |
p.E1020* | LUAD | 1 |
p.E629K | LGG | 1 |
p.E1170K | OV | 1 |
p.R755H | READ | 1 |
p.D877Y | LUAD | 1 |
p.W245R | THYM | 1 |
p.D349N | BLCA | 1 |
p.R890Q | SARC | 1 |
p.G104V | LUAD | 1 |
p.E497K | SKCM | 1 |
p.E1033Q | COAD | 1 |
p.A94E | STAD | 1 |
p.R560M | ESCA | 1 |
p.E996K | SKCM | 1 |
p.E933* | LUAD | 1 |
p.E348K | CESC | 1 |
p.E629Q | OV | 1 |
p.G990E | SKCM | 1 |
p.Y1002* | PRAD | 1 |
p.A641V | COAD | 1 |
p.S792L | STAD | 1 |
p.K28E | STAD | 1 |
p.T76S | LIHC | 1 |
p.P938Q | HNSC | 1 |
p.E1059K | HNSC | 1 |
p.E662Q | HNSC | 1 |
p.L620V | BLCA | 1 |
p.A403E | OV | 1 |
p.R73W | OV | 1 |
p.Q408R | LUAD | 1 |
p.R371Q | CESC | 1 |
p.E242K | SKCM | 1 |
p.A153P | ESCA | 1 |
p.P1202H | STAD | 1 |
p.E800K | STAD | 1 |
p.P931S | BLCA | 1 |
p.W815* | SKCM | 1 |
p.D366Y | UCEC | 1 |
p.D248Y | BLCA | 1 |
p.P971H | STAD | 1 |
p.E235K | CESC | 1 |
p.R54C | UCEC | 1 |
p.S39R | UCEC | 1 |
p.S1252N | COAD | 1 |
p.D18H | LUAD | 1 |
p.R168K | LIHC | 1 |
p.S1003L | SKCM | 1 |
p.G671R | SKCM | 1 |
p.S688L | SKCM | 1 |
p.A513T | BRCA | 1 |
p.H554R | LGG | 1 |
p.D860E | LGG | 1 |
p.P174A | LGG | 1 |
p.E348X | ESCA | 1 |
p.N506S | HNSC | 1 |
p.E430K | SKCM | 1 |
p.S1161P | LUAD | 1 |
p.W802* | SKCM | 1 |
p.P760S | SKCM | 1 |
p.D949N | SKCM | 1 |
p.E900X | THYM | 1 |
p.H704N | SKCM | 1 |
p.P136T | LUAD | 1 |
p.D877N | SKCM | 1 |
p.E900D | LUSC | 1 |
p.W13* | SKCM | 1 |
p.E1222* | UCEC | 1 |
p.I226M | CESC | 1 |
p.Q920H | UCS | 1 |
p.P667L | SKCM | 1 |
p.P820L | SKCM | 1 |
p.H1172R | BLCA | 1 |
p.E559D | ESCA | 1 |
p.E320K | BLCA | 1 |
p.G1261* | UCEC | 1 |
p.Q998R | SKCM | 1 |
p.D550N | SKCM | 1 |
p.E576* | PRAD | 1 |
p.D548Y | THYM | 1 |
p.M544I | LIHC | 1 |
p.R52* | SKCM | 1 |
p.A635T | STAD | 1 |
p.P963S | SKCM | 1 |
p.S601L | STAD | 1 |
p.E249K | SKCM | 1 |
p.R371L | UCEC | 1 |
p.K1220N | COAD | 1 |
p.K521N | CESC | 1 |
p.T713S | LUSC | 1 |
p.M41V | OV | 1 |
p.Q920H | LUAD | 1 |
p.T545S | LIHC | 1 |
p.A1068T | READ | 1 |
p.T516P | UCEC | 1 |
p.N377K | UCEC | 1 |
p.G990E | STAD | 1 |
p.S970F | SKCM | 1 |
p.Q487E | HNSC | 1 |
p.M220L | HNSC | 1 |
p.E55K | COAD | 1 |
p.P469L | SKCM | 1 |
p.E913D | UCEC | 1 |
p.E958K | SKCM | 1 |
p.E957G | SKCM | 1 |
p.P493L | SARC | 1 |
p.Y1021X | READ | 1 |
p.R43W | HNSC | 1 |
p.F853C | SKCM | 1 |
p.R52Q | UCEC | 1 |
p.S200F | UCEC | 1 |
p.I1276V | OV | 1 |
p.D946N | SKCM | 1 |
p.L38F | BLCA | 1 |
p.Y1146C | STAD | 1 |
p.E605K | SKCM | 1 |
p.E804A | UCEC | 1 |
p.G746E | SKCM | 1 |
p.R888L | LUAD | 1 |
p.N250H | UCEC | 1 |
p.Q1141H | ESCA | 1 |
p.V921M | HNSC | 1 |
p.I703T | UCEC | 1 |
p.Q1141H | COAD | 1 |
p.K380T | UCEC | 1 |
p.S871F | SKCM | 1 |
p.V874A | COAD | 1 |
p.Q1014X | KIRC | 1 |
p.L528V | SKCM | 1 |
p.E455K | SKCM | 1 |
p.R138H | STAD | 1 |
p.M1118I | UCEC | 1 |
p.S27* | CESC | 1 |
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TissGeneCNV for RPGRIP1 |
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 RPGRIP1 |
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 RPGRIP1 |
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 RPGRIP1 |
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 RPGRIP1 |
TissGeneDrug for RPGRIP1 |
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 RPGRIP1 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0339527 | Leber Congenital Amaurosis | 18 | BeFree,CTD_human,ORPHANET |
umls:C0035334 | Retinitis Pigmentosa | 7 | BeFree,CTD_human,LHGDN |
umls:C0035304 | Retinal Degeneration | 4 | BeFree |
umls:C0854723 | Retinal Dystrophies | 4 | BeFree,CTD_human |
umls:C0035309 | Retinal Diseases | 3 | BeFree,GAD |
umls:C0376288 | Amaurosis | 2 | BeFree |
umls:C1854260 | LEBER CONGENITAL AMAUROSIS 6 (disorder) | 2 | CLINVAR,MGD,UNIPROT |
umls:C1998028 | Photoreceptor degeneration | 2 | BeFree |
umls:C2750720 | Cone-Rod Dystrophy 13 | 2 | CLINVAR,CTD_human,UNIPROT |
umls:C0005754 | Congenital blindness | 1 | BeFree |
umls:C0017601 | Glaucoma | 1 | BeFree |
umls:C0028738 | Nystagmus | 1 | BeFree,CTD_human |
umls:C0042798 | Low Vision | 1 | BeFree |
umls:C0339573 | Glaucoma, Primary Open Angle | 1 | BeFree |
umls:C0524851 | Neurodegenerative Disorders | 1 | BeFree |
umls:C0687120 | Nephronophthisis | 1 | BeFree |
umls:C0917796 | Optic Atrophy, Hereditary, Leber | 1 | BeFree |
umls:C3714506 | Meckel syndrome type 1 | 1 | BeFree |
umls:C0265215 | Meckel-Gruber syndrome | 0 | ORPHANET |