PKNOX1 Gene

HGNC Family	Homeoboxes
Name	PBX/knotted 1 homeobox 1
Description	Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in angiogenesis and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within camera-type eye development; hemopoiesis; and positive regulation of transcription by RNA polymerase II. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Mar 2025]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nPKNOX1, also known as PREP1, is a TALE homeodomain transcription factor that plays a pivotal role in cellular homeostasis by modulating key gene‐expression programs. In the context of immune regulation, PKNOX1 contributes to the transcriptional activation of interleukin‑10 in response to apoptotic cells, thereby supporting the anti‐inflammatory feedback needed for tissue homeostasis."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": " In addition, as part of heterodimeric complexes with PBX proteins, PKNOX1 helps regulate the expression of genes such as PF4, influencing differentiation processes that are essential for proper organ development"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": ";."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn cancer and genomic stability contexts, PKNOX1 exhibits complex functions. On one hand, studies in non‐small cell lung cancer have shown that overexpression of PKNOX1 can drive epithelial–mesenchymal transition and promote metastasis by modulating TGF‑β/SMAD signaling and facilitating the stabilization and accumulation of PBX1."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": " On the other hand, loss or reduction of PKNOX1 levels has been linked to impaired genomic integrity—leading to increased DNA damage, altered replication timing, and facilitation of oncogene‑induced transformation"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": ";"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": ";."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": " Structural analyses have further illuminated the specific interfaces within the PKNOX1–PBX1 complexes that underpin its transcriptional activity."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "8"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nMoreover, dysregulation of PKNOX1 has been implicated in oncogenesis in various tissues. For example, recent evidence suggests that aberrant expression of PKNOX1 may exacerbate stomach adenocarcinoma, highlighting its potential role as a modulator of tumor progression in a tissue‐specific context."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "9"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Elaine Y Chung, Jianguo Liu, Yoichiro Homma, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Interleukin-10 expression in macrophages during phagocytosis of apoptotic cells is mediated by homeodomain proteins Pbx1 and Prep-1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Immunity (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.immuni.2007.11.014"}], "href": "https://doi.org/10.1016/j.immuni.2007.11.014"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18093541"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18093541"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Ma Francisca Sánchez-Font, Anna Bosch-Comas, Roser Gonzàlez-Duarte, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Overexpression of FABP7 in Down syndrome fetal brains is associated with PKNOX1 gene-dosage imbalance."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nucleic Acids Res (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/nar/gkg396"}], "href": "https://doi.org/10.1093/nar/gkg396"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12771203"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12771203"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Elisa Bernardi, Gianluca Deflorian, Federica Pezzimenti, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Characterization of the regulatory region of the zebrafish Prep1.1 gene: analogies to the promoter of the human PREP1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "PLoS One (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1371/journal.pone.0015047"}], "href": "https://doi.org/10.1371/journal.pone.0015047"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21203543"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21203543"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Maurizio Risolino, Nadia Mandia, Francescopaolo Iavarone, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Transcription factor PREP1 induces EMT and metastasis by controlling the TGF-β-SMAD3 pathway in non-small cell lung adenocarcinoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.1407074111"}], "href": "https://doi.org/10.1073/pnas.1407074111"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25157139"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25157139"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "E Longobardi, G Iotti, P Di Rosa, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Prep1 (pKnox1)-deficiency leads to spontaneous tumor development in mice and accelerates EmuMyc lymphomagenesis: a tumor suppressor role for Prep1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Oncol (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.molonc.2010.01.001"}], "href": "https://doi.org/10.1016/j.molonc.2010.01.001"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20106730"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20106730"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Giorgio Iotti, Elena Longobardi, Silvia Masella, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Homeodomain transcription factor and tumor suppressor Prep1 is required to maintain genomic stability."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.1105216108"}], "href": "https://doi.org/10.1073/pnas.1105216108"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21715654"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21715654"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Angela Palmigiano, Francesco Santaniello, Aurora Cerutti, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PREP1 tumor suppressor protects the late-replicating DNA by controlling its replication timing and symmetry."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Sci Rep (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41598-018-21363-4"}], "href": "https://doi.org/10.1038/s41598-018-21363-4"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29453404"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29453404"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Dan Ye, Guohua Lou, Tianbao Zhang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "MiR-17 family-mediated regulation of Pknox1 influences hepatic steatosis and insulin signaling."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Mol Med (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1111/jcmm.13902"}], "href": "https://doi.org/10.1111/jcmm.13902"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30338914"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30338914"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Roland Immler, Katrin Nussbaumer, Axel Doerner, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CCR3-dependent eosinophil recruitment is regulated by sialyltransferase ST3Gal-IV."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2024)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.2319057121"}], "href": "https://doi.org/10.1073/pnas.2319057121"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "38687790"}], "href": "https://pubmed.ncbi.nlm.nih.gov/38687790"}]}]}]}
Synonyms	PREP1, PKONX1C
Proteins	PKNX1_HUMAN
NCBI Gene ID	5316
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

PKNOX1 has 5,861 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 112 datasets.

Click the + buttons to view associations for PKNOX1 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

PKNOX1 Gene

Functional Associations

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

	Dataset	Summary
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of PKNOX1 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 PKNOX1 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of PKNOX1 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 PKNOX1 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 PKNOX1 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 PKNOX1 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 PKNOX1 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 PKNOX1 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 PKNOX1 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 PKNOX1 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with PKNOX1 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with PKNOX1 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 PKNOX1 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of PKNOX1 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 PKNOX1 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 PKNOX1 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing PKNOX1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing PKNOX1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores	cellular components containing PKNOX1 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing PKNOX1 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 PKNOX1 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 PKNOX1 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 PKNOX1 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with PKNOX1 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Disease Associations	diseases associated with PKNOX1 gene/protein from the curated CTD Gene-Disease Associations dataset.
	dbGAP Gene-Trait Associations	traits associated with PKNOX1 gene in GWAS and other genetic association datasets from the dbGAP Gene-Trait Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of PKNOX1 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 PKNOX1 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with PKNOX1 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 PKNOX1 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 PKNOX1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with PKNOX1 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 PKNOX1 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 PKNOX1 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of PKNOX1 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 PKNOX1 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with PKNOX1 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with PKNOX1 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 PKNOX1 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with PKNOX1 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.