RFX1 Gene

Name	regulatory factor X, 1 (influences HLA class II expression)
Description	This gene encodes a member of the regulatory factor X (RFX) family of transcription factors, which are characterized by a winged-helix DNA-binding domain. The encoded transcription factor contains an N-terminal activation domain and a C-terminal repression domain, and may activate or repress target gene expression depending on cellular context. This transcription factor has been shown to regulate a wide variety of genes involved in immunity and cancer, including the MHC class II genes and genes that may be involved in cancer progression. This gene exhibits altered expression in glioblastoma and the autoimmune disease systemic lupus erythematosis (SLE). [provided by RefSeq, Jul 2016]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nRegulatory Factor X1 (RFX1) is a versatile transcription factor that plays a key role in maintaining genomic integrity and orchestrating epigenetic regulation. In non‐neuronal cells, RFX1 functions analogously to its yeast homologue Crt1 by binding to its own promoter and to promoters of genes involved in DNA replication (e.g. RNR‐R2), thereby mediating the DNA damage and replication checkpoint response. Moreover, RFX1 participates in the repression of gene transcription through recruiting histone deacetylases and other co‐repressors; for example, in the regulation of collagen α2(I) gene expression, RFX1 preferentially interacts with HDAC1 and mSin3A, while binding more avidly to methylated DNA sequences, and it also contributes to the immediate early serum response by binding to an Id2 promoter element, thereby influencing cell cycle control."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn neural and tumor contexts, RFX1 functions as a negative regulator of cell proliferation and influences differentiation. In human neuroblastoma cells, for instance, RFX1 overexpression suppresses proliferation by down‐regulating growth factors such as transforming growth factor β2 (TGFβ2) and the downstream ERK signaling cascade. In glioblastoma cells, RFX1 regulates genes such as CD44 and fibroblast growth factor 1 (FGF1), where its overexpression diminishes neurosphere formation and stem cell maintenance, suggesting a tumor‐suppressive role. Consistently, in CD4⁺ T cells from systemic lupus erythematosus (SLE) patients, reduced RFX1 levels lead to epigenetic dysregulation at promoters of immune regulatory genes (e.g. CD11a and CD70), contributing to autoimmune hyperactivity, while similar anti‐proliferative effects mediated by RFX1 are demonstrated in breast cancer models where RFX1 induces the expression of the tyrosine phosphatase SHP1."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "4", "end_ref": "10"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nAdditional roles of RFX1 extend to modulating gene expression in diverse physiological and pathological contexts. In hepatocellular carcinoma, RFX1 deletion correlates with a poor prognosis, underscoring its potential tumor‐suppressor function. In activated monocytes, decreased RFX1 activity appears to contribute to the overexpression of proinflammatory receptors like TLR4, which are implicated in coronary artery disease. Moreover, in microglia, reduced miR‐124 results in elevated RFX1 levels that subsequently suppress apolipoprotein E (ApoE) expression, thereby impairing amyloid‐β uptake. RFX1’s binding to specific viral sequences has also been implicated in modulating adeno‐associated virus (AAV) transgene expression, highlighting its broader role in transcriptional regulation across different cell types."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "11", "end_ref": "15"}]}, {"type": "t", "text": ""}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Yoav Lubelsky, Nina Reuven, Yosef Shaul "}, {"type": "b", "children": [{"type": "t", "text": "Autorepression of rfx1 gene expression: functional conservation from yeast to humans in response to DNA replication arrest."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.25.23.10665-10673.2005"}], "href": "https://doi.org/10.1128/MCB.25.23.10665-10673.2005"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16287876"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16287876"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Yong Xu, Pritam K Sengupta, Edward Seto, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Regulatory factor for X-box family proteins differentially interact with histone deacetylases to repress collagen alpha2(I) gene (COL1A2) expression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M511724200"}], "href": "https://doi.org/10.1074/jbc.M511724200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16464847"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16464847"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Kui-Rong Wang, Tomoyuki Nemoto, Yoshifumi Yokota "}, {"type": "b", "children": [{"type": "t", "text": "RFX1 mediates the serum-induced immediate early response of Id2 gene expression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M703448200"}], "href": "https://doi.org/10.1074/jbc.M703448200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17630394"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17630394"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Jinhong Huang, Asako Furuya, Teiichi Furuichi "}, {"type": "b", "children": [{"type": "t", "text": "Very-KIND, a KIND domain containing RasGEF, controls dendrite growth by linking Ras small GTPases and MAP2."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Biol (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1083/jcb.200702036"}], "href": "https://doi.org/10.1083/jcb.200702036"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17984326"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17984326"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Yi-Chao Hsu, Wei-Chih Liao, Chien-Yu Kao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Regulation of FGF1 gene promoter through transcription factor RFX1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M109.081463"}], "href": "https://doi.org/10.1074/jbc.M109.081463"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20189986"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20189986"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Ming Zhao, Yimin Sun, Fei Gao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Epigenetics and SLE: RFX1 downregulation causes CD11a and CD70 overexpression by altering epigenetic modifications in lupus CD4+ T cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Autoimmun (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jaut.2010.02.002"}], "href": "https://doi.org/10.1016/j.jaut.2010.02.002"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20223637"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20223637"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Ming Zhao, Xiaoyan Wu, Qing Zhang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "RFX1 regulates CD70 and CD11a expression in lupus T cells by recruiting the histone methyltransferase SUV39H1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Arthritis Res Ther (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/ar3214"}], "href": "https://doi.org/10.1186/ar3214"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21192791"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21192791"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Shahreen Amin, Ashok Kumar, Ladan Nilchi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Breast cancer cells proliferation is regulated by tyrosine phosphatase SHP1 through c-jun N-terminal kinase and cooperative induction of RFX-1 and AP-4 transcription factors."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cancer Res (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1158/1541-7786.MCR-11-0097"}], "href": "https://doi.org/10.1158/1541-7786.MCR-11-0097"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21719561"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21719561"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Chenzhuo Feng, Zhiyi Zuo "}, {"type": "b", "children": [{"type": "t", "text": "Regulatory factor X1-induced down-regulation of transforming growth factor β2 transcription in human neuroblastoma cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M111.338590"}], "href": "https://doi.org/10.1074/jbc.M111.338590"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22582395"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22582395"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Chenzhuo Feng, Ying Zhang, Jinbo Yin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Regulatory factor X1 is a new tumor suppressive transcription factor that acts via direct downregulation of CD44 in glioblastoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Neuro Oncol (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/neuonc/nou010"}], "href": "https://doi.org/10.1093/neuonc/nou010"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24526308"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24526308"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Yu Guo, Ming Zhao, Qianjin Lu "}, {"type": "b", "children": [{"type": "t", "text": "Transcription factor RFX1 is ubiquitinated by E3 ligase STUB1 in systemic lupus erythematosus."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Clin Immunol (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.clim.2016.06.003"}], "href": "https://doi.org/10.1016/j.clim.2016.06.003"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27283392"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27283392"}]}, {"type": "r", "ref": 12, "children": [{"type": "t", "text": "Chen-Zhuo Feng, Jin-Bo Yin, Jian-Jun Yang, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "Downregulation of RFX1 predicts poor prognosis of patients with small hepatocellular carcinoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Eur J Surg Oncol (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.ejso.2018.04.017"}], "href": "https://doi.org/10.1016/j.ejso.2018.04.017"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29764705"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29764705"}]}, {"type": "r", "ref": 15, "children": [{"type": "t", "text": "Pei Du, Keqin Gao, Yu Cao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "RFX1 downregulation contributes to TLR4 overexpression in CD14"}, {"type": "a", "children": [{"type": "t", "text": "sup"}], "href": "sup"}, {"type": "t", "text": "+"}, {"type": "a", "children": [{"type": "t", "text": "/sup"}], "href": "/sup"}, {"type": "t", "text": " monocytes via epigenetic mechanisms in coronary artery disease."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Clin Epigenetics (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s13148-019-0646-9"}], "href": "https://doi.org/10.1186/s13148-019-0646-9"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30857550"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30857550"}]}]}]}
Synonyms	RFX, EFC
Proteins	RFX1_HUMAN
NCBI Gene ID	5989
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

RFX1 has 6,455 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 114 datasets.

Click the + buttons to view associations for RFX1 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

RFX1 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by RFX1 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of RFX1 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of RFX1 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of RFX1 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of RFX1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of RFX1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of RFX1 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of RFX1 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of RFX1 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of RFX1 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of RFX1 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of RFX1 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of RFX1 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with RFX1 protein from the CCLE Cell Line Proteomics dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of RFX1 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of RFX1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of RFX1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CM4AI U2OS Cell Map Protein Localization Assemblies	assemblies containing RFX1 protein from integrated AP-MS and IF data from the CM4AI U2OS Cell Map Protein Localization Assemblies dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing RFX1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing RFX1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing RFX1 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with RFX1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with RFX1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of RFX1 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with RFX1 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with RFX1 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with RFX1 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by RFX1 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with RFX1 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with RFX1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with RFX1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with RFX1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with RFX1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at RFX1 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of RFX1 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of RFX1 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing RFX1 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of RFX1 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with RFX1 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
	GeneSigDB Published Gene Signatures	PubMedIDs of publications reporting gene signatures containing RFX1 from the GeneSigDB Published Gene Signatures dataset.