RFX2 Gene

Name	regulatory factor X, 2 (influences HLA class II expression)
Description	This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X3, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with other RFX family members. This protein can bind to cis elements in the promoter of the IL-5 receptor alpha gene. Two transcript variants encoding different isoforms have been described for this gene, and both variants utilize alternative polyadenylation sites. [provided by RefSeq, Jul 2008]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nRecent studies have revealed that RFX2, a member of the Regulatory Factor X transcription factor family, plays a crucial role in orchestrating gene expression programs that underlie the formation and function of cilia. In multiciliated epithelial cells, RFX2 regulates genes essential for ciliogenesis, cilia function, and cell movement – a process vital for apical surface expansion and overall tissue morphogenesis. Moreover, RFX transcription factors, including RFX2, bind to conserved X-box elements in promoters such as that of the ALMS1 gene during growth arrest, thereby contributing to the control of ciliary gene expression."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nBeyond its established role in traditional ciliogenesis, RFX2 also modulates the expression of genes associated with motile cilia in various tissues. For example, overexpression studies have shown that RFX2 directly enhances the ADGB promoter activity, highlighting its participation in regulating genes involved in the formation of motile cilia in the reproductive tract, lungs, and brain. In parallel, RFX2, in concert with other family members, directly binds to a critical cis-element in the FGF1B promoter to support neural stem/progenitor cell maintenance and promote neurosphere formation. Such findings underscore RFX2 as a key factor in integrating ciliary function with specialized cell type behavior."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn addition to its roles in ciliogenesis and neural stem cell regulation, RFX2 has been implicated in modulating signal transduction pathways within epithelial cells. It contributes to transcriptional control in response to Ras signaling by binding to specific cis-regulatory elements, thereby influencing cell proliferation and differentiation. Genetic studies further link alterations in RFX2 with disruptions in spermatogenesis, suggesting an association with male infertility. Collectively, these insights reveal the multifaceted functions of RFX2 in coordinating both ciliary and non-ciliary gene regulatory networks critical for development, homeostasis, and disease."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Mei-I Chung, Taejoon Kwon, Fan Tu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Coordinated genomic control of ciliogenesis and cell movement by RFX2."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Elife (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.7554/eLife.01439"}], "href": "https://doi.org/10.7554/eLife.01439"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24424412"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24424412"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Tracey L Purvis, Tom Hearn, Cosma Spalluto, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Transcriptional regulation of the Alström syndrome gene ALMS1 by members of the RFX family and Sp1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Gene (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.gene.2010.03.015"}], "href": "https://doi.org/10.1016/j.gene.2010.03.015"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20381594"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20381594"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Teng Wei Koay, Carina Osterhof, Ilaria M C Orlando, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Androglobin gene expression patterns and FOXJ1-dependent regulation indicate its functional association with ciliogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jbc.2021.100291"}], "href": "https://doi.org/10.1016/j.jbc.2021.100291"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33453283"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33453283"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Yi-Chao Hsu, Chien-Yu Kao, Yu-Fen Chung, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Ciliogenic RFX transcription factors regulate FGF1 gene promoter."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Biochem (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/jcb.24127"}], "href": "https://doi.org/10.1002/jcb.24127"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22415835"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22415835"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Susann Maijgren, Inderpreet Sur, Mats Nilsson, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Involvement of RFX proteins in transcriptional activation from a Ras-responsive enhancer element."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Arch Dermatol Res (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s00403-004-0456-5"}], "href": "https://doi.org/10.1007/s00403-004-0456-5"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15024578"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15024578"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Samudra Pal, Pranab Paladhi, Saurav Dutta, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Novel variations in spermatogenic transcription regulators RFX2 and TAF7 increase risk of azoospermia."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Assist Reprod Genet (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s10815-021-02352-5"}], "href": "https://doi.org/10.1007/s10815-021-02352-5"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "34762273"}], "href": "https://pubmed.ncbi.nlm.nih.gov/34762273"}]}]}]}
Proteins	RFX2_HUMAN
NCBI Gene ID	5990
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

RFX2 has 6,313 functional associations with biological entities spanning 8 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) extracted from 117 datasets.

Click the + buttons to view associations for RFX2 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

RFX2 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 RFX2 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 RFX2 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 RFX2 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 RFX2 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 RFX2 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 RFX2 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 RFX2 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 RFX2 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 RFX2 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 RFX2 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 RFX2 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of RFX2 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 RFX2 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with RFX2 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with RFX2 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of RFX2 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of RFX2 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 RFX2 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	gene perturbations changing expression of RFX2 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of RFX2 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing RFX2 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing RFX2 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with RFX2 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 RFX2 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with RFX2 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with RFX2 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with RFX2 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of RFX2 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by RFX2 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores	diseases associated with RFX2 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with RFX2 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 RFX2 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 RFX2 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with RFX2 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 RFX2 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 RFX2 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of RFX2 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 RFX2 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with RFX2 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with RFX2 gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.