TissGeneSummary for RGPD3 |
Gene summary |
Basic gene information | Gene symbol | RGPD3 |
Gene name | RANBP2-like and GRIP domain containing 3 | |
Synonyms | RGP3 | |
Cytomap | UCSC genome browser: 2q13 | |
Type of gene | protein-coding | |
RefGenes | NM_001144013.1, | |
Description | ranBP2-like and GRIP domain-containing protein 3 | |
Modification date | 20141207 | |
dbXrefs | MIM : 612706 | |
HGNC : HGNC | ||
Ensembl : ENSG00000153165 | ||
Vega : OTTHUMG00000153182 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RGPD3 | |
BioGPS: 653489 | ||
Pathway | NCI Pathway Interaction Database: RGPD3 | |
KEGG: RGPD3 | ||
REACTOME: RGPD3 | ||
Pathway Commons: RGPD3 | ||
Context | iHOP: RGPD3 | |
ligand binding site mutation search in PubMed: RGPD3 | ||
UCL Cancer Institute: RGPD3 | ||
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 RGPD3 | ||
Description by TissGene annotations | 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 RGPD3 |
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 |
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TissGene-miRNA for RGPD3 |
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 RGPD3 |
TissGeneSNV for RGPD3 |
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.R816C | UCEC | 23 |
p.L812R | UCEC | 18 |
p.E755K | SKCM | 6 |
p.N756D | PRAD | 5 |
p.N756D | UCEC | 3 |
p.S1472Y | UCEC | 2 |
p.N756D | HNSC | 2 |
p.E559K | SKCM | 2 |
p.R1394C | SKCM | 2 |
p.S1138F | SKCM | 2 |
p.E1675K | SKCM | 2 |
p.H1284R | BRCA | 2 |
p.G1125E | SKCM | 2 |
p.E753K | SKCM | 2 |
p.R1394C | UCEC | 2 |
p.E1698D | SKCM | 1 |
p.E1287K | LGG | 1 |
p.D1261A | OV | 1 |
p.L812R | BRCA | 1 |
p.L1209F | BLCA | 1 |
p.E1256K | SKCM | 1 |
p.G547V | UCEC | 1 |
p.D1286V | GBM | 1 |
p.E1363* | UCEC | 1 |
p.K823T | PCPG | 1 |
p.E1320K | SKCM | 1 |
p.G960S | SKCM | 1 |
p.P882S | BRCA | 1 |
p.R1410K | SKCM | 1 |
p.H778Q | LUAD | 1 |
p.D807Y | UCEC | 1 |
p.E1022K | CESC | 1 |
p.E1159K | SKCM | 1 |
p.V1735G | COAD | 1 |
p.R816C | UVM | 1 |
p.L1106P | LUAD | 1 |
p.K1150T | COAD | 1 |
p.A1258D | UCEC | 1 |
p.P1342H | STAD | 1 |
p.S881* | HNSC | 1 |
p.T1243N | UCEC | 1 |
p.W1077* | SKCM | 1 |
p.S1126L | SKCM | 1 |
p.E1091K | HNSC | 1 |
p.A13T | MESO | 1 |
p.E1091D | SKCM | 1 |
p.R1674Q | SKCM | 1 |
p.N1670K | UCEC | 1 |
p.A1148T | READ | 1 |
p.D698N | BRCA | 1 |
p.V12I | UCEC | 1 |
p.Y1334* | UCEC | 1 |
p.H569R | CESC | 1 |
p.P898S | SKCM | 1 |
p.E41D | UCEC | 1 |
p.G1140D | SKCM | 1 |
p.I776M | SKCM | 1 |
p.R23* | SKCM | 1 |
p.L1088F | SKCM | 1 |
p.D1389G | LUAD | 1 |
p.D944N | SKCM | 1 |
p.G112* | LUAD | 1 |
p.M1684K | BRCA | 1 |
p.E1220Q | BLCA | 1 |
p.N1737S | LGG | 1 |
p.K721N | UCEC | 1 |
p.E1352K | SKCM | 1 |
p.S1126T | LUAD | 1 |
p.D1261N | BLCA | 1 |
p.S1303C | LUAD | 1 |
p.T1246K | LUAD | 1 |
p.E938K | SKCM | 1 |
p.L730I | UCEC | 1 |
p.L124H | ESCA | 1 |
p.M1118I | SARC | 1 |
p.V1074A | UCEC | 1 |
p.S1660R | UCEC | 1 |
p.R955Q | HNSC | 1 |
p.K1440N | ESCA | 1 |
p.G112E | LGG | 1 |
p.E1336Q | BRCA | 1 |
p.R1102G | STAD | 1 |
p.G1244E | SKCM | 1 |
p.T1679I | UCEC | 1 |
p.R1146* | LUAD | 1 |
p.G1201E | SKCM | 1 |
p.G1227S | SKCM | 1 |
p.R770Q | UCEC | 1 |
p.F1720L | LUAD | 1 |
p.K957* | SKCM | 1 |
p.N756D | KIRP | 1 |
p.S749* | SKCM | 1 |
p.Q1386H | UCEC | 1 |
p.K957M | SKCM | 1 |
p.M1118I | SKCM | 1 |
p.M751V | UCEC | 1 |
p.K989E | SKCM | 1 |
p.G987D | SKCM | 1 |
p.E1758K | SKCM | 1 |
p.T1115M | CESC | 1 |
p.P1734S | SKCM | 1 |
p.A1148E | BLCA | 1 |
p.G995R | SKCM | 1 |
p.N1239I | BLCA | 1 |
p.E1256V | SKCM | 1 |
p.R690S | KIRC | 1 |
p.M1I | ESCA | 1 |
p.W1374X | SKCM | 1 |
p.A772V | KIRP | 1 |
p.G1056D | SKCM | 1 |
p.K1107* | STAD | 1 |
p.D1212N | SKCM | 1 |
p.R85_splice | UCEC | 1 |
p.N756D | GBM | 1 |
p.S768Y | UCEC | 1 |
p.P762R | LUAD | 1 |
p.D1136N | SKCM | 1 |
p.K734N | UCEC | 1 |
p.R770* | UCEC | 1 |
p.S1665R | LUAD | 1 |
p.R10Q | DLBC | 1 |
p.S997L | SKCM | 1 |
p.W1374* | SKCM | 1 |
p.L890F | SKCM | 1 |
p.A186T | UCEC | 1 |
p.E1287K | BLCA | 1 |
p.E775Q | CESC | 1 |
p.L812R | ESCA | 1 |
p.Y1008C | UCEC | 1 |
p.R1097G | SKCM | 1 |
p.H689Y | SKCM | 1 |
p.E1321K | SKCM | 1 |
p.T784S | GBM | 1 |
p.E942K | SKCM | 1 |
p.L769F | PAAD | 1 |
p.L1282I | UCEC | 1 |
p.K1163N | ESCA | 1 |
p.Q950K | LUAD | 1 |
p.V1716G | SKCM | 1 |
p.G112R | BLCA | 1 |
p.S1665R | CESC | 1 |
p.K1107X | STAD | 1 |
p.D1253N | SKCM | 1 |
p.A894V | UCEC | 1 |
p.S1200N | ESCA | 1 |
p.L134Q | LUAD | 1 |
p.V1371I | UCEC | 1 |
p.G767C | SKCM | 1 |
p.E1730Q | BLCA | 1 |
p.K1304M | LUAD | 1 |
p.S758R | BLCA | 1 |
p.E1241K | BLCA | 1 |
p.S937R | BRCA | 1 |
p.D1400N | SKCM | 1 |
p.H1284R | LIHC | 1 |
p.S205L | UCEC | 1 |
p.G1350S | LUAD | 1 |
p.K1058N | STAD | 1 |
p.R770Q | SKCM | 1 |
p.P898L | SKCM | 1 |
p.S14L | UCEC | 1 |
p.L812R | PCPG | 1 |
p.E1653D | PAAD | 1 |
p.V1441X | COAD | 1 |
p.R23* | UCEC | 1 |
p.E119K | SKCM | 1 |
p.S14* | BLCA | 1 |
p.I962M | UCEC | 1 |
p.T979A | UCEC | 1 |
p.K106E | SKCM | 1 |
p.E753K | ESCA | 1 |
p.E1728K | SKCM | 1 |
p.Y1061* | SKCM | 1 |
p.A1129T | SKCM | 1 |
p.Y1365* | LUAD | 1 |
p.Y764H | SKCM | 1 |
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TissGeneCNV for RGPD3 |
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 RGPD3 |
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 RGPD3 |
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 RGPD3 |
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 RGPD3 |
TissGeneDrug for RGPD3 |
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 RGPD3 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |