Browse RFX3

Summary
SymbolRFX3
Nameregulatory factor X, 3 (influences HLA class II expression)
Aliases DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location9p24.2
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 Nucleus
Domain PF04589 RFX1 transcription activation region
PF02257 RFX DNA-binding domain
Function

Transcription factor required for ciliogenesis and islet cell differentiation during endocrine pancreas development. Essential for the differentiation of nodal monocilia and left-right asymmetry specification during embryogenesis. Required for the biogenesis of motile cilia by governing growth and beating efficiency of motile cells. Also required for ciliated ependymal cell differentiation. Regulates the expression of genes involved in ciliary assembly (DYNC2LI1, FOXJ1 and BBS4) and genes involved in ciliary motility (DNAH11, DNAH9 and DNAH5) (By similarity). Together with RFX6, participates in the differentiation of 4 of the 5 islet cell types during endocrine pancreas development, with the exception of pancreatic PP (polypeptide-producing) cells. Regulates transcription by forming a heterodimer with another RFX protein and binding to the X-box in the promoter of target genes (PubMed:20148032). Represses transcription of MAP1A in non-neuronal cells but not in neuronal cells (PubMed:12411430).

> Gene Ontology
 
Biological Process GO:0001539 cilium or flagellum-dependent cell motility
GO:0002064 epithelial cell development
GO:0002065 columnar/cuboidal epithelial cell differentiation
GO:0002066 columnar/cuboidal epithelial cell development
GO:0002067 glandular epithelial cell differentiation
GO:0002068 glandular epithelial cell development
GO:0002069 columnar/cuboidal epithelial cell maturation
GO:0002070 epithelial cell maturation
GO:0002071 glandular epithelial cell maturation
GO:0002790 peptide secretion
GO:0002791 regulation of peptide secretion
GO:0003309 type B pancreatic cell differentiation
GO:0003323 type B pancreatic cell development
GO:0003341 cilium movement
GO:0003351 epithelial cilium movement
GO:0007018 microtubule-based movement
GO:0007368 determination of left/right symmetry
GO:0007389 pattern specification process
GO:0009306 protein secretion
GO:0009799 specification of symmetry
GO:0009855 determination of bilateral symmetry
GO:0009914 hormone transport
GO:0010720 positive regulation of cell development
GO:0010817 regulation of hormone levels
GO:0010927 cellular component assembly involved in morphogenesis
GO:0015833 peptide transport
GO:0021700 developmental maturation
GO:0023061 signal release
GO:0030031 cell projection assembly
GO:0030072 peptide hormone secretion
GO:0030073 insulin secretion
GO:0030856 regulation of epithelial cell differentiation
GO:0030858 positive regulation of epithelial cell differentiation
GO:0031016 pancreas development
GO:0031018 endocrine pancreas development
GO:0035270 endocrine system development
GO:0035883 enteroendocrine cell differentiation
GO:0042384 cilium assembly
GO:0042886 amide transport
GO:0044782 cilium organization
GO:0046879 hormone secretion
GO:0046883 regulation of hormone secretion
GO:0048469 cell maturation
GO:0050708 regulation of protein secretion
GO:0050796 regulation of insulin secretion
GO:0060271 cilium morphogenesis
GO:0060285 cilium-dependent cell motility
GO:0060287 epithelial cilium movement involved in determination of left/right asymmetry
GO:0072560 type B pancreatic cell maturation
GO:0090087 regulation of peptide transport
GO:0090276 regulation of peptide hormone secretion
GO:2000074 regulation of type B pancreatic cell development
GO:2000078 positive regulation of type B pancreatic cell development
Molecular Function GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000987 core promoter proximal region sequence-specific DNA binding
GO:0001159 core promoter proximal region DNA binding
GO:0003705 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding
Cellular Component GO:0000785 chromatin
GO:0000790 nuclear chromatin
GO:0005667 transcription factor complex
GO:0044454 nuclear chromosome part
> KEGG and Reactome Pathway
 
KEGG -
Reactome -
Summary
SymbolRFX3
Nameregulatory factor X, 3 (influences HLA class II expression)
Aliases DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location9p24.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between RFX3 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
SymbolRFX3
Nameregulatory factor X, 3 (influences HLA class II expression)
Aliases DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location9p24.2
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 RFX3 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
SymbolRFX3
Nameregulatory factor X, 3 (influences HLA class II expression)
Aliases DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location9p24.2
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 RFX3 in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.0370.874
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)650.0940.862
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-0.1340.76
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 916-0.0470.906
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590.3320.856
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 47-0.5250.822
729033130MelanomaallAnti-PD-1 (nivolumab) 2623-0.0780.765
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 1511-0.2410.727
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 11120.1070.886
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 48-0.1480.793
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 280.3390.64
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 682300.10.289
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of RFX3 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) 14177.107.10.452
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 103100101
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 277318.54.114.40.0315
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 275918.55.113.40.102
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)2117190190.113
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)8612.5012.51
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)131123.1023.10.223
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 91611.1011.10.36
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590001
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 47250250.364
1329033130MelanomaallAnti-PD-1 (nivolumab) 38277.907.90.26
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22139.109.10.519
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16146.206.21
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
SymbolRFX3
Nameregulatory factor X, 3 (influences HLA class II expression)
Aliases DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location9p24.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of RFX3. 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
SymbolRFX3
Nameregulatory factor X, 3 (influences HLA class II expression)
Aliases DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location9p24.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of RFX3. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by RFX3.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolRFX3
Nameregulatory factor X, 3 (influences HLA class II expression)
Aliases DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location9p24.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of RFX3. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolRFX3
Nameregulatory factor X, 3 (influences HLA class II expression)
Aliases DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location9p24.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of RFX3 expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolRFX3
Nameregulatory factor X, 3 (influences HLA class II expression)
Aliases DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location9p24.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between RFX3 and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolRFX3
Nameregulatory factor X, 3 (influences HLA class II expression)
Aliases DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location9p24.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting RFX3 collected from DrugBank database.
> Drugs from DrugBank database
 

There is no record.