Browse RGPD3

Summary
SymbolRGPD3
NameRANBP2-like and GRIP domain containing 3
Aliases RanBP2-like and GRIP domain-containing protein 3
Chromosomal Location2q12.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Basic function annotation.
> Subcellular Location, Domain and Function
> Gene Ontology
> KEGG and Reactome Pathway
> Subcellular Location, Domain and Function
 
Subcellular Location -
Domain PF01465 GRIP domain
PF16704 Rab binding domain
PF00638 RanBP1 domain
Function

-

> Gene Ontology
 
Biological Process GO:0000042 protein targeting to Golgi
GO:0000301 retrograde transport, vesicle recycling within Golgi
GO:0006891 intra-Golgi vesicle-mediated transport
GO:0034067 protein localization to Golgi apparatus
GO:0048193 Golgi vesicle transport
GO:0072600 establishment of protein localization to Golgi
Molecular Function -
Cellular Component -
> KEGG and Reactome Pathway
 
KEGG hsa03013 RNA transport
Reactome -
Summary
SymbolRGPD3
NameRANBP2-like and GRIP domain containing 3
Aliases RanBP2-like and GRIP domain-containing protein 3
Chromosomal Location2q12.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between RGPD3 and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.
> Text Mining
 

There is no record.

Summary
SymbolRGPD3
NameRANBP2-like and GRIP domain containing 3
Aliases RanBP2-like and GRIP domain-containing protein 3
Chromosomal Location2q12.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.
> High-throughput Screening
  Statistical results of RGPD3 in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell NA/NSNA/NS
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell NA/NSNA/NS
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NSNA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NSNA/NS
24476824shRNAmelanomaB16Primary screen NA/NSNA/NS
24476824shRNAmelanomaB16Secondary screen NA/NSNA/NS
Summary
SymbolRGPD3
NameRANBP2-like and GRIP domain containing 3
Aliases RanBP2-like and GRIP domain-containing protein 3
Chromosomal Location2q12.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets.
> Expression difference between responders and non-responders
> Mutation difference between responders and non-responders
> Expression difference between responders and non-responders
 
Points in the above scatter plot represent the expression difference of RGPD3 in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.1310.54
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)650.0060.989
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-0.230.512
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 916-1.5130.0087
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59-1.5380.464
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 47-1.4910.527
729033130MelanomaallAnti-PD-1 (nivolumab) 26230.2720.424
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 15110.260.852
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 11120.3140.837
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 48-0.0320.939
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 280.2720.66
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 68230-0.2770.0972
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of RGPD3 in various data sets.
No PMID Cancer type Group Drug # Res # NRes % Mut/Res % Mut/NRes % Diff (R vs NR) Pval Anno
125765070Non-small cell lung cancer (NSCLC)allAnti-PD-1 (pembrolizumab) 14170001
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 1030001
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 27737.49.6-2.21
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 01407.1-7.11
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 27597.410.2-2.81
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)211723.811.8120.427
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)8612.5012.51
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)131130.818.212.60.649
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 91622.231.2-91
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 592033.3-13.31
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 472528.6-3.61
1329033130MelanomaallAnti-PD-1 (nivolumab) 38275.33.71.61
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 221307.7-7.70.371
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 161412.5012.50.485
1629301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 11130001
1729301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 610001
1829301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 5120001
Summary
SymbolRGPD3
NameRANBP2-like and GRIP domain containing 3
Aliases RanBP2-like and GRIP domain-containing protein 3
Chromosomal Location2q12.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of RGPD3. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.
> Lymphocyte
 
Summary
SymbolRGPD3
NameRANBP2-like and GRIP domain containing 3
Aliases RanBP2-like and GRIP domain-containing protein 3
Chromosomal Location2q12.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of RGPD3. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by RGPD3.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolRGPD3
NameRANBP2-like and GRIP domain containing 3
Aliases RanBP2-like and GRIP domain-containing protein 3
Chromosomal Location2q12.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of RGPD3. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolRGPD3
NameRANBP2-like and GRIP domain containing 3
Aliases RanBP2-like and GRIP domain-containing protein 3
Chromosomal Location2q12.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of RGPD3 expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolRGPD3
NameRANBP2-like and GRIP domain containing 3
Aliases RanBP2-like and GRIP domain-containing protein 3
Chromosomal Location2q12.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between RGPD3 and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolRGPD3
NameRANBP2-like and GRIP domain containing 3
Aliases RanBP2-like and GRIP domain-containing protein 3
Chromosomal Location2q12.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting RGPD3 collected from DrugBank database.
> Drugs from DrugBank database
 

There is no record.