FOXA1 Gene

HGNC Family	Forkhead boxes (FOX)
Name	forkhead box A1
Description	This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. [provided by RefSeq, Jul 2008]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n FOXA1 functions as a master “pioneer” transcription factor that modulates chromatin accessibility to enable the binding of key nuclear receptors and other lineage‐specific transcription factors. In cancer and development, FOXA1 “opens” condensed chromatin at distal enhancers, thereby facilitating estrogen receptor (ER) and androgen receptor (AR) binding to their target sites, as demonstrated in studies of ER‐mediated chromatin association and enhancer organization in breast cancer ("}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "4"}]}, {"type": "t", "text": ").\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In ER‐positive breast cancers, FOXA1 is indispensable for establishing ER–chromatin interactions and works in concert with other factors such as GATA3 to maintain luminal differentiation and ensure the proper hormonal response ("}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": ").\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In prostate cancer, FOXA1 plays a critical role in shaping the AR cistrome. Altered FOXA1 expression or mutation reprograms AR binding, driving distinct transcriptional programs that correlate with clinical outcomes ("}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "6", "end_ref": "9"}]}, {"type": "t", "text": ").\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Beyond its role in hormone signaling, FOXA1 is critical for normal development. It cooperates with related family members (such as FOXA2) to regulate organ specification—for example, controlling the expression of key genes during pancreatic and hepatic lineage commitment—and influences the differentiation of midbrain dopaminergic neurons, underscoring its broad function in cell fate determination ("}, {"type": "fg", "children": [{"type": "fg_f", "ref": "10"}]}, {"type": "t", "text": ").\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Moreover, aberrant FOXA1 activity contributes to cancer progression. Enhancer reprogramming driven by FOXA1 has been implicated in promoting metastatic traits in pancreatic ductal adenocarcinoma, and deregulation of FOXA1—whether through recurrent mutations or via upstream regulatory mechanisms such as competing endogenous RNA networks—can influence tumor heterogeneity in hepatocellular and prostate cancers ("}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "12", "end_ref": "14"}]}, {"type": "t", "text": ").\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Finally, dynamic interactions between FOXA1 and other transcription factors—including steroid receptors like ER and the glucocorticoid receptor—further refine its pioneer function and modulate context‐dependent gene regulation ("}, {"type": "fg", "children": [{"type": "fg_f", "ref": "15"}]}, {"type": "t", "text": ").\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Jason S Carroll, X Shirley Liu, Alexander S Brodsky, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2005.05.008"}], "href": "https://doi.org/10.1016/j.cell.2005.05.008"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16009131"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16009131"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Mathieu Lupien, Jérôme Eeckhoute, Clifford A Meyer, et al. "}, {"type": "b", "children": [{"type": "t", "text": "FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2008.01.018"}], "href": "https://doi.org/10.1016/j.cell.2008.01.018"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18358809"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18358809"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Antoni Hurtado, Kelly A Holmes, Caryn S Ross-Innes, et al. "}, {"type": "b", "children": [{"type": "t", "text": "FOXA1 is a key determinant of estrogen receptor function and endocrine response."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Genet (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ng.730"}], "href": "https://doi.org/10.1038/ng.730"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21151129"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21151129"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Vasiliki Theodorou, Rory Stark, Suraj Menon, et al. "}, {"type": "b", "children": [{"type": "t", "text": "GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genome Res (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1101/gr.139469.112"}], "href": "https://doi.org/10.1101/gr.139469.112"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23172872"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23172872"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Hosein Kouros-Mehr, Euan M Slorach, Mark D Sternlicht, et al. "}, {"type": "b", "children": [{"type": "t", "text": "GATA-3 maintains the differentiation of the luminal cell fate in the mammary gland."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2006.09.048"}], "href": "https://doi.org/10.1016/j.cell.2006.09.048"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17129787"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17129787"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Dong Wang, Ivan Garcia-Bassets, Chris Benner, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature10006"}], "href": "https://doi.org/10.1038/nature10006"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21572438"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21572438"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Biswajyoti Sahu, Marko Laakso, Kristian Ovaska, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signalling and prostate cancer."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "EMBO J (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/emboj.2011.328"}], "href": "https://doi.org/10.1038/emboj.2011.328"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21915096"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21915096"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Mark M Pomerantz, Fugen Li, David Y Takeda, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Genet (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ng.3419"}], "href": "https://doi.org/10.1038/ng.3419"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26457646"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26457646"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Jessica L L Robinson, Stewart Macarthur, Caryn S Ross-Innes, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Androgen receptor driven transcription in molecular apocrine breast cancer is mediated by FoxA1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "EMBO J (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/emboj.2011.216"}], "href": "https://doi.org/10.1038/emboj.2011.216"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21701558"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21701558"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Nan Gao, John LeLay, Marko Z Vatamaniuk, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Dynamic regulation of Pdx1 enhancers by Foxa1 and Foxa2 is essential for pancreas development."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Dev (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1101/gad.1752608"}], "href": "https://doi.org/10.1101/gad.1752608"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19141476"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19141476"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Anna L M Ferri, Wei Lin, Yannis E Mavromatakis, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Foxa1 and Foxa2 regulate multiple phases of midbrain dopaminergic neuron development in a dosage-dependent manner."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Development (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/dev.000141"}], "href": "https://doi.org/10.1242/dev.000141"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17596284"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17596284"}]}, {"type": "r", "ref": 12, "children": [{"type": "t", "text": "Jae-Seok Roe, Chang-Il Hwang, Tim D D Somerville, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Enhancer Reprogramming Promotes Pancreatic Cancer Metastasis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2017.07.007"}], "href": "https://doi.org/10.1016/j.cell.2017.07.007"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28757253"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28757253"}]}, {"type": "r", "ref": 13, "children": [{"type": "t", "text": "Yufeng Wang, Liu Yang, Tianxiang Chen, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A novel lncRNA MCM3AP-AS1 promotes the growth of hepatocellular carcinoma by targeting miR-194-5p/FOXA1 axis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cancer (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s12943-019-0957-7"}], "href": "https://doi.org/10.1186/s12943-019-0957-7"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30782188"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30782188"}]}, {"type": "r", "ref": 14, "children": [{"type": "t", "text": "Zhaoyu Li, Geetu Tuteja, Jonathan Schug, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Foxa1 and Foxa2 are essential for sexual dimorphism in liver cancer."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2011.11.026"}], "href": "https://doi.org/10.1016/j.cell.2011.11.026"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22265403"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22265403"}]}, {"type": "r", "ref": 15, "children": [{"type": "t", "text": "Erin E Swinstead, Tina B Miranda, Ville Paakinaho, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Steroid Receptors Reprogram FoxA1 Occupancy through Dynamic Chromatin Transitions."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2016.02.067"}], "href": "https://doi.org/10.1016/j.cell.2016.02.067"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27062924"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27062924"}]}]}]}
Synonyms	HNF3A, TCF3A
Proteins	FOXA1_HUMAN
NCBI Gene ID	3169
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

FOXA1 has 7,963 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 112 datasets.

Click the + buttons to view associations for FOXA1 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

FOXA1 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 FOXA1 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of FOXA1 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 FOXA1 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 FOXA1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of FOXA1 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 FOXA1 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 FOXA1 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 FOXA1 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of FOXA1 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 FOXA1 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with FOXA1 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with FOXA1 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 FOXA1 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of FOXA1 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 FOXA1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of FOXA1 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing FOXA1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing FOXA1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing FOXA1 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 FOXA1 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 FOXA1 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 FOXA1 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with FOXA1 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with FOXA1 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with FOXA1 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by FOXA1 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 FOXA1 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 FOXA1 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 FOXA1 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 FOXA1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with FOXA1 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 FOXA1 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 FOXA1 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of FOXA1 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 FOXA1 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with FOXA1 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with FOXA1 gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of FOXA1 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with FOXA1 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 FOXA1 from the GeneSigDB Published Gene Signatures dataset.