TISIDB

Summary
Symbol	RFX3
Name	regulatory factor X, 3 (influences HLA class II expression)
Aliases	DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location	9p24.2
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 [ TOP ]
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 [ TOP ]
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 [ TOP ]
KEGG	-
Reactome	-

Summary
Symbol	RFX3
Name	regulatory factor X, 3 (influences HLA class II expression)
Aliases	DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location	9p24.2
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 [ TOP ]
There is no record.

Summary
Symbol	RFX3
Name	regulatory factor X, 3 (influences HLA class II expression)
Aliases	DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location	9p24.2
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

[ TOP ]

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
29301958	CRISPR-Cas9	melanoma	B16F10	Pmel-1 T cell	NA/NS	NA/NS
29301958	CRISPR-Cas9	melanoma	B16F10	OT-1 T cell	NA/NS	NA/NS
28783722	CRISPR-Cas9	melanoma	Mel624	2CT-CRISPR	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX+Anti-PD1	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX	NA/NS	NA/NS
25691366	RNAi	Breast cancer	MCF7	Luc-CTL assay	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Primary screen	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Secondary screen	NA/NS	NA/NS

Summary
Symbol	RFX3
Name	regulatory factor X, 3 (influences HLA class II expression)
Aliases	DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location	9p24.2
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

[ TOP ]

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
1	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	14	12	-0.037	0.874
2	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	6	5	0.094	0.862
3	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	7	-0.134	0.76
4	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	-0.047	0.906
5	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0.332	0.856
6	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	-0.525	0.822
7	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	26	23	-0.078	0.765
8	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	15	11	-0.241	0.727
9	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	11	12	0.107	0.886
10	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	4	8	-0.148	0.793
11	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	2	0	0	1
12	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	2	8	0.339	0.64
13	29443960	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	68	230	0.1	0.289

> Mutation difference between responders and non-responders

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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
1	25765070	Non-small cell lung cancer (NSCLC)	all	Anti-PD-1 (pembrolizumab)	14	17	7.1	0	7.1	0.452
2	25765070	Non-small cell lung cancer (NSCLC)	smoking	Anti-PD-1 (pembrolizumab)	10	3	10	0	10	1
3	25765070	Non-small cell lung cancer (NSCLC)	non-smoking	Anti-PD-1 (pembrolizumab)	4	14	0	0	0	1
4	26359337	Melanoma	all	Anti-CTLA-4 (ipilimumab)	27	73	18.5	4.1	14.4	0.0315
5	26359337	Melanoma	BRAFi	Anti-CTLA-4 (ipilimumab)	0	14	0	0	0	1
6	26359337	Melanoma	non-BRAFi	Anti-CTLA-4 (ipilimumab)	27	59	18.5	5.1	13.4	0.102
7	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	21	17	19	0	19	0.113
8	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	6	12.5	0	12.5	1
9	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	13	11	23.1	0	23.1	0.223
10	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	11.1	0	11.1	0.36
11	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0	0	0	1
12	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	25	0	25	0.364
13	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	38	27	7.9	0	7.9	0.26
14	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	22	13	9.1	0	9.1	0.519
15	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	16	14	6.2	0	6.2	1
16	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	11	13	0	0	0	1
17	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	6	1	0	0	0	1
18	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	5	12	0	0	0	1

Summary
Symbol	RFX3
Name	regulatory factor X, 3 (influences HLA class II expression)
Aliases	DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location	9p24.2
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 [ TOP ]

Summary
Symbol	RFX3
Name	regulatory factor X, 3 (influences HLA class II expression)
Aliases	DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location	9p24.2
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 [ TOP ]

> Immunostimulator [ TOP ]

> MHC molecule [ TOP ]

Summary
Symbol	RFX3
Name	regulatory factor X, 3 (influences HLA class II expression)
Aliases	DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location	9p24.2
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 [ TOP ]

> Receptor [ TOP ]

Summary
Symbol	RFX3
Name	regulatory factor X, 3 (influences HLA class II expression)
Aliases	DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location	9p24.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Distribution of RFX3 expression across immune and molecular subtypes. > Immune subtype > Molecular subtype

> Immune subtype [ TOP ]

> Molecular subtype [ TOP ]

Summary
Symbol	RFX3
Name	regulatory factor X, 3 (influences HLA class II expression)
Aliases	DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location	9p24.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Associations between RFX3 and clinical features. > Overall survival analysis > Cancer stage > Tumor grade

> Overall survival [ TOP ]

> Stage [ TOP ]

> Grade [ TOP ]

Summary
Symbol	RFX3
Name	regulatory factor X, 3 (influences HLA class II expression)
Aliases	DNA binding protein RFX3; Regulatory factor X 3; Transcription factor RFX3
Chromosomal Location	9p24.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Drugs targeting RFX3 collected from DrugBank database.

> Drugs from DrugBank database [ TOP ]
There is no record.

Browse RFX3