TissGeneSummary for RGPD4 |
Gene summary |
Basic gene information | Gene symbol | RGPD4 |
Gene name | RANBP2-like and GRIP domain containing 4 | |
Synonyms | RGP4 | |
Cytomap | UCSC genome browser: 2q12.3 | |
Type of gene | protein-coding | |
RefGenes | NM_182588.2, | |
Description | ranBP2-like and GRIP domain-containing protein 4 | |
Modification date | 20141207 | |
dbXrefs | MIM : 612707 | |
HGNC : HGNC | ||
Ensembl : ENSG00000196862 | ||
Vega : OTTHUMG00000153208 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RGPD4 | |
BioGPS: 285190 | ||
Pathway | NCI Pathway Interaction Database: RGPD4 | |
KEGG: RGPD4 | ||
REACTOME: RGPD4 | ||
Pathway Commons: RGPD4 | ||
Context | iHOP: RGPD4 | |
ligand binding site mutation search in PubMed: RGPD4 | ||
UCL Cancer Institute: RGPD4 | ||
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 RGPD4 | ||
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 RGPD4 |
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 RGPD4 |
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 |
UCS | hsa-miR-205-5p | MIMAT0000266 | 0.045 | -0.27 | 56 |
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TissGeneMut for RGPD4 |
TissGeneSNV for RGPD4 |
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.R1394C | SKCM | 5 |
p.E1352K | SKCM | 4 |
p.E1320K | SKCM | 2 |
p.E1046K | SKCM | 2 |
p.L489I | UCEC | 2 |
p.D1400N | SKCM | 2 |
p.G931E | SKCM | 2 |
p.R1101Q | UCEC | 2 |
p.H1284Y | SKCM | 2 |
p.W1374* | SKCM | 2 |
p.G1571E | SKCM | 2 |
p.E1091K | SKCM | 2 |
p.K1355E | THCA | 2 |
p.E1598D | UCEC | 1 |
p.W1374X | SKCM | 1 |
p.Q933* | HNSC | 1 |
p.R23G | TGCT | 1 |
p.C3Y | LUAD | 1 |
p.S1322F | SKCM | 1 |
p.P1040T | LUAD | 1 |
p.W1077* | SKCM | 1 |
p.S86L | HNSC | 1 |
p.S1416N | SKCM | 1 |
p.P1240S | SKCM | 1 |
p.W1249* | SKCM | 1 |
p.R528G | TGCT | 1 |
p.S1348C | LUAD | 1 |
p.E1594Q | BLCA | 1 |
p.R1699K | SARC | 1 |
p.E1711K | SKCM | 1 |
p.R1425K | SKCM | 1 |
p.E745Q | CESC | 1 |
p.G1000* | CESC | 1 |
p.D1024N | SKCM | 1 |
p.S1661F | SKCM | 1 |
p.K1058N | ESCA | 1 |
p.Y1334* | LUAD | 1 |
p.E1544K | CESC | 1 |
p.D1370N | SKCM | 1 |
p.G1422R | LUAD | 1 |
p.I131M | UCEC | 1 |
p.I1687N | STAD | 1 |
p.F1722S | LIHC | 1 |
p.L1060R | PRAD | 1 |
p.L490F | SKCM | 1 |
p.R10Q | BLCA | 1 |
p.K721N | UCEC | 1 |
p.L590P | LUAD | 1 |
p.P1122T | LUAD | 1 |
p.K568E | SKCM | 1 |
p.H1668Y | SKCM | 1 |
p.F1160C | LUAD | 1 |
p.K1089Q | SKCM | 1 |
p.S18Y | CESC | 1 |
p.Q1326* | SKCM | 1 |
p.V1345L | SKCM | 1 |
p.R1447C | UCEC | 1 |
p.R120T | BRCA | 1 |
p.S928L | SKCM | 1 |
p.A19T | CESC | 1 |
p.L518F | ACC | 1 |
p.P1040R | LUAD | 1 |
p.R597L | LUAD | 1 |
p.D1025Y | HNSC | 1 |
p.K1375E | KIRP | 1 |
p.R1101G | LIHC | 1 |
p.E1022Q | LUAD | 1 |
p.K1688N | TGCT | 1 |
p.E1256K | HNSC | 1 |
p.G922E | SKCM | 1 |
p.S592F | SKCM | 1 |
p.V1597M | GBM | 1 |
p.L941F | SKCM | 1 |
p.E938K | SKCM | 1 |
p.E1091D | LUAD | 1 |
p.R1394C | UCEC | 1 |
p.E213G | UCEC | 1 |
p.S1568F | PRAD | 1 |
p.D1370H | BLCA | 1 |
p.G1019S | SKCM | 1 |
p.E1055K | SKCM | 1 |
p.E934* | LUAD | 1 |
p.S1315L | SKCM | 1 |
p.S1593C | LUAD | 1 |
p.G1671S | LUAD | 1 |
p.Q1043K | CESC | 1 |
p.E1256D | ESCA | 1 |
p.V1402L | UCEC | 1 |
p.W1646R | ACC | 1 |
p.D1136N | SKCM | 1 |
p.H507Y | LUAD | 1 |
p.Q1169R | SARC | 1 |
p.N591K | THCA | 1 |
p.F1160L | LUAD | 1 |
p.A19T | THYM | 1 |
p.A1752V | UCEC | 1 |
p.L1672P | LUAD | 1 |
p.N1670I | LGG | 1 |
p.D1370Y | BLCA | 1 |
p.S1583R | BLCA | 1 |
p.A772V | SARC | 1 |
p.E1046Q | CESC | 1 |
p.V12I | UCEC | 1 |
p.P624S | UCEC | 1 |
p.Q1392H | HNSC | 1 |
p.L712M | CESC | 1 |
p.S531Y | UCEC | 1 |
p.D1667E | BLCA | 1 |
p.Q529P | LUAD | 1 |
p.A1681E | BRCA | 1 |
p.G547R | LUAD | 1 |
p.E775Q | CESC | 1 |
p.G1571A | KIRC | 1 |
p.G760E | LUAD | 1 |
p.R597Q | SKCM | 1 |
p.L1405R | UCEC | 1 |
p.E1320D | STAD | 1 |
p.E1046A | SKCM | 1 |
p.P573L | GBM | 1 |
p.F1296V | UCEC | 1 |
p.S1264N | BLCA | 1 |
p.E1031K | BLCA | 1 |
p.K522N | LUAD | 1 |
p.P1245T | LUAD | 1 |
p.C1109S | LUAD | 1 |
p.L1733I | LIHC | 1 |
p.S1593T | LIHC | 1 |
p.F369L | UCEC | 1 |
p.Q1169R | LUAD | 1 |
p.L124H | GBM | 1 |
p.F1004L | UCEC | 1 |
p.L500* | SKCM | 1 |
p.N107I | GBM | 1 |
p.K1190T | ESCA | 1 |
p.S1264I | LUAD | 1 |
p.W1646R | SARC | 1 |
p.L1733I | UCEC | 1 |
p.A1015E | LIHC | 1 |
p.S1295I | LUAD | 1 |
p.E9K | SKCM | 1 |
p.T1528I | UCEC | 1 |
p.Q1657H | LUAD | 1 |
p.N1607K | CESC | 1 |
p.E1049K | SKCM | 1 |
p.Y606N | SKCM | 1 |
p.L1144V | BRCA | 1 |
p.E1354K | SKCM | 1 |
p.K1688R | SKCM | 1 |
p.K25Q | LIHC | 1 |
p.E1677K | SKCM | 1 |
p.G127R | SKCM | 1 |
p.R770* | BRCA | 1 |
p.E1346K | HNSC | 1 |
p.P1040L | SKCM | 1 |
p.H689Y | SKCM | 1 |
p.N957S | SARC | 1 |
p.V1356F | LUAD | 1 |
p.K1375I | SKCM | 1 |
p.E1653K | SKCM | 1 |
p.D921H | BRCA | 1 |
p.L1156V | LUAD | 1 |
p.L44P | LIHC | 1 |
p.L941F | BLCA | 1 |
p.E1354V | STAD | 1 |
p.E1758K | SKCM | 1 |
p.R1187K | LUAD | 1 |
p.D694N | OV | 1 |
p.E1327K | SKCM | 1 |
p.E559K | SKCM | 1 |
p.P1413L | SKCM | 1 |
p.P1337L | SKCM | 1 |
p.S1660R | HNSC | 1 |
p.V1710M | LUAD | 1 |
p.D944N | SKCM | 1 |
p.F1021S | PRAD | 1 |
p.F30L | UCEC | 1 |
p.R1377M | UCEC | 1 |
p.Q1657H | BLCA | 1 |
p.D951N | SKCM | 1 |
p.E1376K | SKCM | 1 |
p.I1411T | LUAD | 1 |
p.A1228V | KIRP | 1 |
p.K1086* | SKCM | 1 |
p.V1074I | HNSC | 1 |
p.T1423R | LUAD | 1 |
p.K1391R | SKCM | 1 |
p.Q1701K | LUAD | 1 |
p.W607* | SKCM | 1 |
p.E119K | SKCM | 1 |
p.S1580R | UCEC | 1 |
p.G1422W | STAD | 1 |
p.R1279K | SKCM | 1 |
p.A1027G | LGG | 1 |
p.E1584K | SKCM | 1 |
p.G1422R | SKCM | 1 |
p.E1165K | SKCM | 1 |
p.Q1043R | UCEC | 1 |
p.P1240L | SKCM | 1 |
p.I962M | UCEC | 1 |
p.P20L | SKCM | 1 |
p.R1101* | ESCA | 1 |
p.G1019S | UCEC | 1 |
p.R1674W | SKCM | 1 |
p.K1691E | SKCM | 1 |
p.E1584K | BLCA | 1 |
p.R770Q | SKCM | 1 |
p.K721Q | UCEC | 1 |
p.G1053* | PRAD | 1 |
p.V1710L | LUAD | 1 |
p.R1399K | STAD | 1 |
p.G1291R | SKCM | 1 |
p.P91L | HNSC | 1 |
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TissGeneCNV for RGPD4 |
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 RGPD4 |
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 | FusionScan | BRCA | TCGA-AC-A2QH-01A | RANBP2-RGPD4 | Out-of-Frame | chr2:109352705 | chr2:108459464 |
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TissGeneNet for RGPD4 |
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 RGPD4 |
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 RGPD4 |
TissGeneDrug for RGPD4 |
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 RGPD4 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |