{"gene":"EFNA2","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":1994,"finding":"EFNA2 (ELF-1/Ephrin-A2) was identified as a membrane-bound ligand for the Eph family receptor tyrosine kinases Mek4 and Sek. The protein is GPI-anchored to the cell membrane, demonstrated by its sensitivity to phosphatidylinositol-specific phospholipase C. It was cloned using soluble receptor-alkaline phosphatase fusion proteins (RAP in situ) to identify regions of ligand expression, followed by cDNA library screening.","method":"Receptor-alkaline phosphatase fusion protein binding (RAP in situ), cDNA library screening, cell surface expression assays","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct biochemical identification of receptor-ligand interaction with GPI-anchor characterization, foundational cloning paper with multiple methods","pmids":["7522971"],"is_preprint":false},{"year":1995,"finding":"EFNA2 (ELF-1) is expressed in a complementary gradient in the tectum matching the gradient of its receptor Mek4 in the retina. Alkaline phosphatase fusion proteins of ELF-1 and Mek4 revealed direct molecular complementarity of reciprocal gradients, establishing a positional label system for retinotectal topographic map development.","method":"RNA in situ hybridization, alkaline phosphatase fusion protein binding assays on tissue sections","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — complementary gradient demonstrated by two orthogonal methods (ISH + AP-fusion binding), replicated context","pmids":["7634327"],"is_preprint":false},{"year":1996,"finding":"EFNA2 (ELF-1) acts as a repellent axon guidance factor in vitro, selectively repelling temporal but not nasal retinal axons. In vivo, retroviral overexpression of ELF-1 in the tectum caused temporal retinal axons to avoid ectopic ELF-1 patches and map to abnormally anterior positions, establishing a direct role in nasal-temporal retinotectal specificity.","method":"In vitro stripe/collapse assay, retroviral overexpression in vivo, retinal axon mapping","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vitro functional assay plus in vivo genetic manipulation with defined topographic phenotype, multiple orthogonal methods","pmids":["8797822"],"is_preprint":false},{"year":1995,"finding":"EFNA2 (ELF-1) was identified as a ligand for the Cek7 receptor tyrosine kinase (identical sequence to the Mek4/Sek ligand ELF-1). The expressed Cek7 ligand induces autophosphorylation of the Cek7 RTK, confirming its functional activity as a receptor activator.","method":"cDNA cloning, sequence analysis, receptor autophosphorylation assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — receptor autophosphorylation assay demonstrates functional activation, single lab with two methods (cloning + kinase assay)","pmids":["7876076"],"is_preprint":false},{"year":1997,"finding":"EFNA2 (ELF-1) shares repellent axon guidance function with RAGS for temporal retinal ganglion cell axons, but unlike RAGS is not repellent for nasal axons in two in vitro assays. The differential biological activity correlates with the strength of receptor interaction on RGC axons.","method":"In vitro stripe assay, growth cone collapse assay, receptor binding assays","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — two independent in vitro functional assays with receptor binding correlation, independent replication of EFNA2 repellent activity","pmids":["9135142"],"is_preprint":false},{"year":1996,"finding":"EFNA2 (ELF-1) is expressed in an increasing dorsal-to-ventral gradient in the septum and selectively allows growth of neurites from topographically appropriate lateral hippocampal neurons while inhibiting neurite outgrowth by medial hippocampal neurons. ELF-1 specifically binds the Eph receptor Bsk and elicits its tyrosine kinase activity, establishing the ELF-1/Bsk pair as a chemoaffinity system for hippocamposeptal topographic projections.","method":"In situ hybridization, neurite outgrowth assay, receptor binding assay, tyrosine kinase activation assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — functional neurite assay combined with receptor binding and kinase activation assays, multiple orthogonal methods in one study","pmids":["8855326"],"is_preprint":false},{"year":1997,"finding":"EFNA2 (ELF-1) and RAGS, when presented in membrane-bound or clustered Fc-chimeric forms (but not as unclustered soluble forms), activate the Eph receptor Cek8 and inhibit neurite growth of motoneurons expressing Cek8. This establishes a requirement for clustering/membrane presentation for functional receptor activation and demonstrates a role in regulating motoneuron axon growth.","method":"Receptor phosphorylation assay, neurite growth inhibition assay with clustered vs. soluble protein forms","journal":"Mechanisms of development","confidence":"High","confidence_rationale":"Tier 2 / Strong — mechanistic dissection of clustering requirement using biochemical and cell biological assays with defined receptor phosphorylation readout","pmids":["9232603"],"is_preprint":false},{"year":1997,"finding":"EFNA2 (ELF-1) was identified as a high-affinity ligand for the MDK1 (mouse developmental kinase 1) Eph-family receptor tyrosine kinase, with Kd of 1.7 × 10⁻¹⁰ M. Binding of ELF-1 or B61 to MDK1 leads to rapid autophosphorylation of MDK1 and tyrosine phosphorylation of an unknown 62 kDa phosphoprotein in Rat1 cells. MDK1-binding staining in embryos was abolished by PI-PLC treatment, consistent with GPI-anchored ligands.","method":"Scatchard binding analysis, receptor autophosphorylation assay, phosphotyrosine western blotting, PI-PLC treatment","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 1 / Moderate — quantitative binding kinetics plus downstream signaling assay, single lab with multiple orthogonal methods","pmids":["9010230"],"is_preprint":false},{"year":1998,"finding":"The genomic structure of human LERK-6/Ephrin-A2 (EPLG6/EFNA2) was determined, showing high conservation of intron/exon structure in the receptor-binding region with related ephrin-A family members (mouse LERK-3/Ephrin-A3 and LERK-4/Ephrin-A4).","method":"Genomic cloning, intron/exon structure analysis, sequence comparison","journal":"Genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — structural genomic characterization, single lab, single method","pmids":["9465306"],"is_preprint":false},{"year":2025,"finding":"A stiff extracellular matrix enhances EFNA2 expression in hypopharyngeal cancer cells. EFNA2 promotes proliferation, migration, epithelial-mesenchymal transition (EMT), and tumor growth in vivo. Gene editing of EFNA2 abrogated the pro-tumorigenic effects of high matrix stiffness, establishing EFNA2 as a mechanotransduction effector in HPC progression.","method":"Hydrogel matrix stiffness model, gene editing (EFNA2 knockout/knockdown), colony formation, EDU incorporation, Transwell migration/invasion assays, EMT marker western blotting, subcutaneous xenograft","journal":"Clinical and experimental otorhinolaryngology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — multiple functional assays plus in vivo tumorigenesis, single lab, mechanistic link between stiffness and EFNA2 established but upstream pathway not fully resolved","pmids":["40091591"],"is_preprint":false},{"year":2023,"finding":"EFNA2 is a direct target of miR-642b-5p in bone marrow mesenchymal stem cells. The circRNA hsa_circ_0006859 acts as a sponge for miR-642b-5p, thereby upregulating EFNA2 expression. Elevated EFNA2 inhibits osteogenic differentiation of BMSCs by inactivating Wnt signaling.","method":"RIP assay (RNA immunoprecipitation), luciferase reporter assay (implied by miRNA-target validation), overexpression/knockdown functional assays, OVX mouse model","journal":"International immunopharmacology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — non-protein locus (circRNA) study; EFNA2 protein role established only indirectly as downstream target, single lab, limited mechanistic detail for EFNA2 itself in abstract","pmids":["36764273"],"is_preprint":false}],"current_model":"EFNA2 (Ephrin-A2) is a GPI-anchored membrane-bound ligand for multiple Eph-family receptor tyrosine kinases (including EphA3/Mek4, EphA4/Sek, Cek7, Cek8, and MDK1) that, upon membrane-bound or clustered presentation, activates receptor autophosphorylation and downstream signaling; it functions as a repellent axon guidance cue with topographically selective effects (repelling temporal but not nasal retinal axons) and plays a role in establishing retinotectal and hippocamposeptal topographic projection maps, and in controlling motoneuron axon growth, while more recently being implicated in promoting cancer cell proliferation, migration, and EMT in response to increased extracellular matrix stiffness."},"narrative":{"mechanistic_narrative":"EFNA2 (Ephrin-A2/ELF-1) is a GPI-anchored, membrane-bound ligand for multiple Eph-family receptor tyrosine kinases that functions as a topographically graded guidance cue in the developing nervous system [PMID:7522971, PMID:7634327]. It binds and activates the receptors Mek4, Sek, Cek7, Bsk, Cek8, and MDK1, triggering receptor autophosphorylation and downstream tyrosine phosphorylation, with high-affinity binding to MDK1 (Kd ~1.7 × 10⁻¹⁰ M) [PMID:7522971, PMID:7876076, PMID:8855326, PMID:9010230]. Productive receptor activation requires membrane-bound or clustered presentation; unclustered soluble ligand is inactive [PMID:9232603]. Functionally, EFNA2 acts as a repellent axon guidance factor with selective topographic activity—repelling temporal but not nasal retinal axons—and its expression in complementary gradients in the tectum and septum establishes positional labels that pattern retinotectal and hippocamposeptal projection maps; clustered EFNA2 also inhibits motoneuron neurite growth [PMID:7634327, PMID:8797822, PMID:9135142, PMID:8855326, PMID:9232603]. Beyond neural development, EFNA2 is induced by stiff extracellular matrix and acts as a mechanotransduction effector promoting proliferation, migration, EMT, and tumor growth in hypopharyngeal cancer [PMID:40091591]. Its downstream signaling effectors beyond receptor activation remain largely uncharacterized in the available corpus.","teleology":[{"year":1994,"claim":"Established the molecular identity of EFNA2 as a GPI-anchored membrane ligand for Eph-family receptors, answering what class of molecule it is and how it is displayed.","evidence":"Receptor-AP fusion binding (RAP in situ), cDNA cloning, and PI-PLC sensitivity in cell surface assays","pmids":["7522971"],"confidence":"High","gaps":["Downstream signaling consequences of receptor binding not addressed","Physiological context of expression not yet defined"]},{"year":1995,"claim":"Demonstrated that EFNA2 and its receptor Mek4 are expressed in reciprocal complementary gradients, providing the molecular basis for a positional-label system in topographic map formation.","evidence":"RNA in situ hybridization plus AP-fusion binding on retinotectal tissue sections","pmids":["7634327"],"confidence":"High","gaps":["Correlational gradient mapping does not prove functional guidance","Mechanism of how graded binding translates to axon positioning unresolved"]},{"year":1995,"claim":"Confirmed EFNA2 functionally activates a receptor (Cek7) by inducing autophosphorylation, establishing it as a bona fide receptor activator beyond mere binding.","evidence":"cDNA cloning, sequence analysis, and receptor autophosphorylation assay","pmids":["7876076"],"confidence":"Medium","gaps":["Downstream effectors of Cek7 activation not identified","Single lab, limited orthogonal validation"]},{"year":1996,"claim":"Provided direct in vitro and in vivo evidence that EFNA2 is a repellent guidance cue with nasal-temporal selectivity, settling whether the gradient is functionally instructive for retinotectal specificity.","evidence":"In vitro stripe/collapse assay and retroviral overexpression in vivo with axon mapping","pmids":["8797822"],"confidence":"High","gaps":["Signaling pathway mediating repulsion not defined","Basis of nasal vs temporal differential response unexplained at this stage"]},{"year":1996,"claim":"Extended EFNA2's guidance role beyond the retinotectal system, showing it patterns hippocamposeptal projections via the Bsk receptor through graded, topographically selective neurite control.","evidence":"In situ hybridization, neurite outgrowth assay, receptor binding, and tyrosine kinase activation assay","pmids":["8855326"],"confidence":"High","gaps":["Intracellular signaling downstream of Bsk activation unresolved","How selectivity between medial and lateral neurons is encoded not determined"]},{"year":1997,"claim":"Clarified the functional distinction between EFNA2 and related ephrins, linking its selective repellent activity to the strength of receptor interaction on RGC axons.","evidence":"Two independent in vitro assays (stripe and collapse) with receptor binding correlation","pmids":["9135142"],"confidence":"High","gaps":["Molecular basis of differential receptor affinity not structurally defined"]},{"year":1997,"claim":"Identified clustering/membrane presentation as a strict requirement for EFNA2 receptor activation, defining a key mechanistic constraint on its signaling, and extended its function to motoneuron axon growth.","evidence":"Receptor phosphorylation and neurite growth inhibition assays comparing clustered Fc-chimeric vs soluble forms","pmids":["9232603"],"confidence":"High","gaps":["Stoichiometry and geometry of functional clusters not resolved","Downstream growth-inhibitory effectors unidentified"]},{"year":1997,"claim":"Quantified high-affinity binding to the MDK1 receptor and detected a downstream phosphorylation event, advancing understanding of the proximal signaling output.","evidence":"Scatchard analysis, receptor autophosphorylation, phosphotyrosine western blotting, and PI-PLC treatment in Rat1 cells","pmids":["9010230"],"confidence":"High","gaps":["Identity of the 62 kDa phosphoprotein never established","Functional consequence of MDK1 activation not characterized"]},{"year":1998,"claim":"Defined the human EFNA2 genomic structure, showing conservation of the receptor-binding exon architecture across ephrin-A family members.","evidence":"Genomic cloning, intron/exon analysis, and sequence comparison","pmids":["9465306"],"confidence":"Medium","gaps":["No functional inference beyond structural conservation","Single method, single lab"]},{"year":2025,"claim":"Implicated EFNA2 as a mechanotransduction effector in cancer, showing matrix stiffness induces its expression to drive proliferation, migration, and EMT, a role outside its developmental guidance functions.","evidence":"Hydrogel stiffness model, EFNA2 gene editing, colony/EDU/Transwell assays, EMT marker blotting, and xenografts in hypopharyngeal cancer cells","pmids":["40091591"],"confidence":"Medium","gaps":["Upstream pathway linking stiffness sensing to EFNA2 induction not resolved","Whether Eph-receptor signaling mediates the pro-tumorigenic effect not tested","Single lab"]},{"year":2023,"claim":"Positioned EFNA2 as a downstream node of a circRNA-miRNA axis regulating osteogenic differentiation, implicating it in Wnt-dependent BMSC biology.","evidence":"RIP assay, luciferase reporter, overexpression/knockdown, and OVX mouse model","pmids":["36764273"],"confidence":"Low","gaps":["EFNA2 role established only indirectly as a downstream target; not independently validated as a protein effector","Direct molecular link between EFNA2 and Wnt inactivation not demonstrated"]},{"year":null,"claim":"The intracellular signaling effectors transducing EFNA2-driven Eph receptor activation and how its developmental guidance role connects to its cancer mechanotransduction function remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No defined downstream signaling cascade beyond receptor autophosphorylation","62 kDa phosphoprotein and other effectors unidentified","No structural model of ligand-receptor selectivity"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0048018","term_label":"receptor ligand activity","supporting_discovery_ids":[0,3,5,7]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3,6,7]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,7]}],"pathway":[{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[1,2,5]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3,6,7]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[9]}],"complexes":[],"partners":["EPHA3","EPHA4"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O43921","full_name":"Ephrin-A2","aliases":["EPH-related receptor tyrosine kinase ligand 6","LERK-6","HEK7 ligand","HEK7-L"],"length_aa":213,"mass_kda":23.9,"function":"Cell surface GPI-bound ligand for Eph receptors, a family of receptor tyrosine kinases which are crucial for migration, repulsion and adhesion during neuronal, vascular and epithelial development. Binds promiscuously Eph receptors residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling. With the EPHA2 receptor may play a role in bone remodeling through regulation of osteoclastogenesis and osteoblastogenesis (By similarity)","subcellular_location":"Cell membrane","url":"https://www.uniprot.org/uniprotkb/O43921/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/EFNA2","classification":"Not Classified","n_dependent_lines":7,"n_total_lines":1208,"dependency_fraction":0.005794701986754967},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/EFNA2","total_profiled":1310},"omim":[{"mim_id":"602756","title":"EPHRIN A2; EFNA2","url":"https://www.omim.org/entry/602756"},{"mim_id":"601535","title":"EPHRIN A5; EFNA5","url":"https://www.omim.org/entry/601535"},{"mim_id":"601381","title":"EPHRIN A3; EFNA3","url":"https://www.omim.org/entry/601381"},{"mim_id":"601380","title":"EPHRIN A4; EFNA4","url":"https://www.omim.org/entry/601380"},{"mim_id":"162010","title":"NERVE GROWTH FACTOR RECEPTOR; NGFR","url":"https://www.omim.org/entry/162010"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Mitochondria","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"gallbladder","ntpm":3.3},{"tissue":"intestine","ntpm":11.6},{"tissue":"liver","ntpm":12.6}],"url":"https://www.proteinatlas.org/search/EFNA2"},"hgnc":{"alias_symbol":["ELF-1","LERK6"],"prev_symbol":["EPLG6"]},"alphafold":{"accession":"O43921","domains":[{"cath_id":"2.60.40.420","chopping":"33-171","consensus_level":"high","plddt":94.1645,"start":33,"end":171}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O43921","model_url":"https://alphafold.ebi.ac.uk/files/AF-O43921-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O43921-F1-predicted_aligned_error_v6.png","plddt_mean":79.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=EFNA2","jax_strain_url":"https://www.jax.org/strain/search?query=EFNA2"},"sequence":{"accession":"O43921","fasta_url":"https://rest.uniprot.org/uniprotkb/O43921.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O43921/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O43921"}},"corpus_meta":[{"pmid":"7634327","id":"PMC_7634327","title":"Complementary gradients in expression and binding of ELF-1 and Mek4 in development of the topographic retinotectal projection map.","date":"1995","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/7634327","citation_count":674,"is_preprint":false},{"pmid":"8797822","id":"PMC_8797822","title":"Topographically specific effects of ELF-1 on retinal axon guidance in vitro and retinal axon mapping in vivo.","date":"1996","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/8797822","citation_count":366,"is_preprint":false},{"pmid":"7522971","id":"PMC_7522971","title":"Identification and cloning of ELF-1, a developmentally expressed ligand for the Mek4 and Sek receptor tyrosine kinases.","date":"1994","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/7522971","citation_count":326,"is_preprint":false},{"pmid":"1545787","id":"PMC_1545787","title":"cis-acting sequences required for inducible interleukin-2 enhancer function bind a novel Ets-related protein, Elf-1.","date":"1992","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/1545787","citation_count":255,"is_preprint":false},{"pmid":"9135142","id":"PMC_9135142","title":"Shared and distinct functions of RAGS and ELF-1 in guiding retinal axons.","date":"1997","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/9135142","citation_count":218,"is_preprint":false},{"pmid":"8493578","id":"PMC_8493578","title":"Regulation of the Ets-related transcription factor Elf-1 by binding to the retinoblastoma protein.","date":"1993","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/8493578","citation_count":212,"is_preprint":false},{"pmid":"1909284","id":"PMC_1909284","title":"Developmental function of Elf-1: an essential transcription factor during embryogenesis in Drosophila.","date":"1991","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/1909284","citation_count":171,"is_preprint":false},{"pmid":"8289796","id":"PMC_8289796","title":"Activation of the granulocyte-macrophage colony-stimulating factor promoter in T cells requires cooperative binding of Elf-1 and AP-1 transcription factors.","date":"1994","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/8289796","citation_count":140,"is_preprint":false},{"pmid":"8855326","id":"PMC_8855326","title":"Regulation of topographic projection in the brain: Elf-1 in the hippocamposeptal system.","date":"1996","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/8855326","citation_count":132,"is_preprint":false},{"pmid":"8896456","id":"PMC_8896456","title":"An IL-2 response element in the human IL-2 receptor alpha chain promoter is a composite element that binds Stat5, Elf-1, HMG-I(Y) and a GATA family protein.","date":"1996","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/8896456","citation_count":128,"is_preprint":false},{"pmid":"1527846","id":"PMC_1527846","title":"A novel Ets-related transcription factor, Elf-1, binds to human immunodeficiency virus type 2 regulatory elements that are required for inducible trans activation in T cells.","date":"1992","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/1527846","citation_count":109,"is_preprint":false},{"pmid":"8543159","id":"PMC_8543159","title":"The torso response element binds GAGA and NTF-1/Elf-1, and regulates tailless by relief of repression.","date":"1995","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/8543159","citation_count":101,"is_preprint":false},{"pmid":"10212281","id":"PMC_10212281","title":"Regulation of the human interleukin-5 promoter by Ets transcription factors. Ets1 and Ets2, but not Elf-1, cooperate with GATA3 and HTLV-I Tax1.","date":"1999","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10212281","citation_count":90,"is_preprint":false},{"pmid":"8943338","id":"PMC_8943338","title":"Elf-1 and Stat5 bind to a critical element in a new enhancer of the human interleukin-2 receptor alpha gene.","date":"1996","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/8943338","citation_count":90,"is_preprint":false},{"pmid":"7935370","id":"PMC_7935370","title":"Elf-1 binds to a critical element in a second CD4 enhancer.","date":"1994","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/7935370","citation_count":89,"is_preprint":false},{"pmid":"8228815","id":"PMC_8228815","title":"Molecular regulation of the human IL-3 gene: inducible T cell-restricted expression requires intact AP-1 and Elf-1 nuclear protein binding sites.","date":"1993","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/8228815","citation_count":77,"is_preprint":false},{"pmid":"14966269","id":"PMC_14966269","title":"The scl +18/19 stem cell enhancer is not required for hematopoiesis: identification of a 5' bifunctional hematopoietic-endothelial enhancer bound by Fli-1 and Elf-1.","date":"2004","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/14966269","citation_count":76,"is_preprint":false},{"pmid":"8756667","id":"PMC_8756667","title":"Characterization of NERF, a novel transcription factor related to the Ets factor ELF-1.","date":"1996","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/8756667","citation_count":76,"is_preprint":false},{"pmid":"8543160","id":"PMC_8543160","title":"Binding sites for transcription factor NTF-1/Elf-1 contribute to the ventral repression of decapentaplegic.","date":"1995","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/8543160","citation_count":75,"is_preprint":false},{"pmid":"8895518","id":"PMC_8895518","title":"MEF, a novel transcription factor with an Elf-1 like DNA binding domain but distinct transcriptional activating properties.","date":"1996","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/8895518","citation_count":71,"is_preprint":false},{"pmid":"7556093","id":"PMC_7556093","title":"IgM receptor-mediated transactivation of the IgH 3' enhancer couples a novel Elf-1-AP-1 protein complex to the developmental control of enhancer function.","date":"1995","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/7556093","citation_count":68,"is_preprint":false},{"pmid":"10395650","id":"PMC_10395650","title":"The transcription factors Elf-1 and GATA-1 bind to cell-specific enhancer elements of human high-affinity IgE receptor alpha-chain gene.","date":"1999","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/10395650","citation_count":64,"is_preprint":false},{"pmid":"11884456","id":"PMC_11884456","title":"Phosphorylation and O-linked glycosylation of Elf-1 leads to its translocation to the nucleus and binding to the promoter of the TCR zeta-chain.","date":"2002","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/11884456","citation_count":59,"is_preprint":false},{"pmid":"16484587","id":"PMC_16484587","title":"Endoglin expression in the endothelium is regulated by Fli-1, Erg, and Elf-1 acting on the promoter and a -8-kb enhancer.","date":"2006","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/16484587","citation_count":58,"is_preprint":false},{"pmid":"8887642","id":"PMC_8887642","title":"A potential role for Elf-1 in terminal transferase gene regulation.","date":"1996","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/8887642","citation_count":54,"is_preprint":false},{"pmid":"21148815","id":"PMC_21148815","title":"Differential requirements for the Ets transcription factor Elf-1 in the development of NKT cells and NK cells.","date":"2010","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/21148815","citation_count":51,"is_preprint":false},{"pmid":"12421992","id":"PMC_12421992","title":"Defective production of functional 98-kDa form of Elf-1 is responsible for the decreased expression of TCR zeta-chain in patients with systemic lupus erythematosus.","date":"2002","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/12421992","citation_count":50,"is_preprint":false},{"pmid":"11157678","id":"PMC_11157678","title":"Elf-1 is a transcriptional regulator of the Tie2 gene during vascular development.","date":"2001","source":"Circulation research","url":"https://pubmed.ncbi.nlm.nih.gov/11157678","citation_count":49,"is_preprint":false},{"pmid":"9786909","id":"PMC_9786909","title":"Transcriptional regulation of the stem cell leukemia gene by PU.1 and Elf-1.","date":"1998","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9786909","citation_count":49,"is_preprint":false},{"pmid":"18714041","id":"PMC_18714041","title":"PP2A dephosphorylates Elf-1 and determines the expression of CD3zeta and FcRgamma in human systemic lupus erythematosus T cells.","date":"2008","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/18714041","citation_count":49,"is_preprint":false},{"pmid":"11313289","id":"PMC_11313289","title":"PU.1 exhibits partial functional redundancy with Spi-B, but not with Ets-1 or Elf-1.","date":"2001","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/11313289","citation_count":46,"is_preprint":false},{"pmid":"16352813","id":"PMC_16352813","title":"Critical role for the Ets transcription factor ELF-1 in the development of tumor angiogenesis.","date":"2005","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/16352813","citation_count":45,"is_preprint":false},{"pmid":"26355672","id":"PMC_26355672","title":"In HIV-positive patients, myeloid-derived suppressor cells induce T-cell anergy by suppressing CD3ζ expression through ELF-1 inhibition.","date":"2015","source":"AIDS (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/26355672","citation_count":44,"is_preprint":false},{"pmid":"9232603","id":"PMC_9232603","title":"The inhibitory effect on neurite outgrowth of motoneurons exerted by the ligands ELF-1 and RAGS.","date":"1997","source":"Mechanisms of development","url":"https://pubmed.ncbi.nlm.nih.gov/9232603","citation_count":38,"is_preprint":false},{"pmid":"8350410","id":"PMC_8350410","title":"Activation of the human T-cell leukemia virus type I enhancer is mediated by binding sites for Elf-1 and the pets factor.","date":"1993","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/8350410","citation_count":38,"is_preprint":false},{"pmid":"11145839","id":"PMC_11145839","title":"BLyS BINDS TO B CELLS WITH HIGH AFFINITY AND INDUCES ACTIVATION OF THE TRANSCRIPTION FACTORS NF-kappaB AND ELF-1.","date":"2001","source":"Cytokine","url":"https://pubmed.ncbi.nlm.nih.gov/11145839","citation_count":38,"is_preprint":false},{"pmid":"7876076","id":"PMC_7876076","title":"cDNA cloning and characterization of a Cek7 receptor protein-tyrosine kinase ligand that is identical to the ligand (ELF-1) for the Mek-4 and Sek receptor protein-tyrosine kinases.","date":"1995","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/7876076","citation_count":38,"is_preprint":false},{"pmid":"9510181","id":"PMC_9510181","title":"Elf-1 regulates basal expression from the T cell antigen receptor zeta-chain gene promoter.","date":"1998","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/9510181","citation_count":35,"is_preprint":false},{"pmid":"9104808","id":"PMC_9104808","title":"Elf-1 contributes to the function of the complex interleukin (IL)-2-responsive enhancer in the mouse IL-2 receptor alpha gene.","date":"1997","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/9104808","citation_count":34,"is_preprint":false},{"pmid":"10233904","id":"PMC_10233904","title":"Elf-1 and PU.1 induce expression of gp91(phox) via a promoter element mutated in a subset of chronic granulomatous disease patients.","date":"1999","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/10233904","citation_count":32,"is_preprint":false},{"pmid":"10400620","id":"PMC_10400620","title":"Myeloid ELF-1-like factor up-regulates lysozyme transcription in epithelial cells.","date":"1999","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10400620","citation_count":32,"is_preprint":false},{"pmid":"14636650","id":"PMC_14636650","title":"The emerging role of the myeloid Elf-1 like transcription factor in hematopoiesis.","date":"2003","source":"Blood cells, molecules & diseases","url":"https://pubmed.ncbi.nlm.nih.gov/14636650","citation_count":31,"is_preprint":false},{"pmid":"10780882","id":"PMC_10780882","title":"Expression pattern of the Ets-related transcription factor Elf-1.","date":"1998","source":"Molecular medicine (Cambridge, Mass.)","url":"https://pubmed.ncbi.nlm.nih.gov/10780882","citation_count":31,"is_preprint":false},{"pmid":"28954885","id":"PMC_28954885","title":"Green Tea Polyphenol EGCG Upregulates Tollip Expression by Suppressing Elf-1 Expression.","date":"2017","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/28954885","citation_count":30,"is_preprint":false},{"pmid":"23284001","id":"PMC_23284001","title":"Human papilloma virus (HPV) E7-mediated attenuation of retinoblastoma (Rb) induces hPygopus2 expression via Elf-1 in cervical cancer.","date":"2013","source":"Molecular cancer research : MCR","url":"https://pubmed.ncbi.nlm.nih.gov/23284001","citation_count":29,"is_preprint":false},{"pmid":"17167770","id":"PMC_17167770","title":"The suppressive effect of myeloid Elf-1-like factor (MEF) in osteogenic differentiation.","date":"2007","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/17167770","citation_count":29,"is_preprint":false},{"pmid":"8666284","id":"PMC_8666284","title":"Cloning and expression of the murine Elf-1 cDNA.","date":"1996","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/8666284","citation_count":28,"is_preprint":false},{"pmid":"9180266","id":"PMC_9180266","title":"Transcriptional activity and constitutive nuclear localization of the ETS protein Elf-1.","date":"1997","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/9180266","citation_count":28,"is_preprint":false},{"pmid":"14976184","id":"PMC_14976184","title":"Myeloid Elf-1-like factor, an ETS transcription factor, up-regulates lysozyme transcription in epithelial cells through interaction with promyelocytic leukemia protein.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/14976184","citation_count":26,"is_preprint":false},{"pmid":"15907486","id":"PMC_15907486","title":"Sp1-dependent regulation of Myeloid Elf-1 like factor in human epithelial cells.","date":"2005","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/15907486","citation_count":26,"is_preprint":false},{"pmid":"10347164","id":"PMC_10347164","title":"A potential role for Elf-1 in CD4 promoter function.","date":"1999","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10347164","citation_count":26,"is_preprint":false},{"pmid":"19285002","id":"PMC_19285002","title":"O-GlcNAc inhibits interaction between Sp1 and Elf-1 transcription factors.","date":"2009","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/19285002","citation_count":24,"is_preprint":false},{"pmid":"20346215","id":"PMC_20346215","title":"Expression of Elf-1 and survivin in non-small cell lung cancer and their relationship to intratumoral microvessel density.","date":"2010","source":"Chinese journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/20346215","citation_count":22,"is_preprint":false},{"pmid":"8824239","id":"PMC_8824239","title":"ELF-1 interacts with and transactivates the IgH enhancer pi site.","date":"1996","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8824239","citation_count":20,"is_preprint":false},{"pmid":"21867680","id":"PMC_21867680","title":"Transcription of the Tollip gene is elevated in intestinal epithelial cells through impaired O-GlcNAcylation-dependent nuclear translocation of the negative regulator Elf-1.","date":"2011","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/21867680","citation_count":20,"is_preprint":false},{"pmid":"31289447","id":"PMC_31289447","title":"ELF-1 expression in nasopharyngeal carcinoma facilitates proliferation and metastasis of cancer cells via modulation of CCL2/CCR2 signaling.","date":"2019","source":"Cancer management and research","url":"https://pubmed.ncbi.nlm.nih.gov/31289447","citation_count":19,"is_preprint":false},{"pmid":"12883651","id":"PMC_12883651","title":"The significance of Elf-1 expression in epithelial ovarian carcinoma.","date":"2003","source":"International journal of molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/12883651","citation_count":18,"is_preprint":false},{"pmid":"12798703","id":"PMC_12798703","title":"Clinical relevance of Elf-1 overexpression in endometrial carcinoma.","date":"2003","source":"Gynecologic oncology","url":"https://pubmed.ncbi.nlm.nih.gov/12798703","citation_count":18,"is_preprint":false},{"pmid":"20525788","id":"PMC_20525788","title":"Transcriptional regulation of Elf-1: locus-wide analysis reveals four distinct promoters, a tissue-specific enhancer, control by PU.1 and the importance of Elf-1 downregulation for erythroid maturation.","date":"2010","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/20525788","citation_count":18,"is_preprint":false},{"pmid":"16464244","id":"PMC_16464244","title":"Regulation of the human LAT gene by the Elf-1 transcription factor.","date":"2006","source":"BMC molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/16464244","citation_count":16,"is_preprint":false},{"pmid":"36764273","id":"PMC_36764273","title":"CircRNA hsa_circ_0006859 inhibits the osteogenic differentiation of BMSCs and aggravates osteoporosis by targeting miR-642b-5p/miR-483-3p and upregulating EFNA2/DOCK3.","date":"2023","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/36764273","citation_count":14,"is_preprint":false},{"pmid":"26643049","id":"PMC_26643049","title":"The hematopoietic regulator, ELF-1, enhances the transcriptional response to Interferon-β of the OAS1 anti-viral gene.","date":"2015","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/26643049","citation_count":14,"is_preprint":false},{"pmid":"17878388","id":"PMC_17878388","title":"Elf-1 binds to GGAA elements on the FcRgamma promoter and represses its expression.","date":"2007","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/17878388","citation_count":14,"is_preprint":false},{"pmid":"18629488","id":"PMC_18629488","title":"Suppressive effect of Elf-1 on FcepsilonRI alpha-chain expression in primary mast cells.","date":"2008","source":"Immunogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/18629488","citation_count":13,"is_preprint":false},{"pmid":"9524226","id":"PMC_9524226","title":"Cloning of a novel human ELF-1-related ETS transcription factor, ELFR, its characterization and chromosomal assignment relative to ELF-1.","date":"1998","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/9524226","citation_count":13,"is_preprint":false},{"pmid":"12117724","id":"PMC_12117724","title":"Opposing functions of the Ets factors NERF and ELF-1 during chicken blood vessel development.","date":"2002","source":"Arteriosclerosis, thrombosis, and vascular biology","url":"https://pubmed.ncbi.nlm.nih.gov/12117724","citation_count":12,"is_preprint":false},{"pmid":"12884363","id":"PMC_12884363","title":"Ets protein Elf-1 bidirectionally suppresses transcriptional activities of the tumor suppressor Tsc2 gene and the repair-related Nth1 gene.","date":"2003","source":"Molecular carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/12884363","citation_count":12,"is_preprint":false},{"pmid":"23700553","id":"PMC_23700553","title":"The transcription factors myeloid elf-1-like factor (MEF) and distal-less homeobox 5 (Dlx5) inversely regulate the differentiation of osteoblasts and adipocytes in bone marrow.","date":"2013","source":"Adipocyte","url":"https://pubmed.ncbi.nlm.nih.gov/23700553","citation_count":12,"is_preprint":false},{"pmid":"29915163","id":"PMC_29915163","title":"Five ETS family members, ELF-1, ETV-4, ETV-3L, ETS-1, and ETS-2 upregulate human leukocyte-associated immunoglobulin-like receptor-1 gene basic promoter activity.","date":"2018","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/29915163","citation_count":11,"is_preprint":false},{"pmid":"22307523","id":"PMC_22307523","title":"Myeloid Elf-1-like factor stimulates adipogenic differentiation through the induction of peroxisome proliferator-activated receptor γ expression in bone marrow.","date":"2012","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/22307523","citation_count":11,"is_preprint":false},{"pmid":"15286431","id":"PMC_15286431","title":"The regulation of human beta-defensin 2 by the ETS transcription factor MEF (myeloid Elf-1-like factor) is enhanced by promyelocytic leukemia protein.","date":"2004","source":"Journal of pharmacological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/15286431","citation_count":11,"is_preprint":false},{"pmid":"16904644","id":"PMC_16904644","title":"SUMO down-regulates the activity of Elf4/myeloid Elf-1-like factor.","date":"2006","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/16904644","citation_count":10,"is_preprint":false},{"pmid":"9465306","id":"PMC_9465306","title":"Characterization of the genes for mouse LERK-3/Ephrin-A3 (Epl3), mouse LERK-4/Ephrin-A4 (Epl4), and human LERK-6/Ephrin-A2 (EPLG6): conservation of intron/exon structure.","date":"1998","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/9465306","citation_count":9,"is_preprint":false},{"pmid":"27040637","id":"PMC_27040637","title":"The ETS Factor Myeloid Elf-1-Like Factor (MEF)/Elf4 Is Transcriptionally and Functionally Activated by Hypoxia.","date":"2016","source":"Biological & pharmaceutical bulletin","url":"https://pubmed.ncbi.nlm.nih.gov/27040637","citation_count":8,"is_preprint":false},{"pmid":"21465527","id":"PMC_21465527","title":"PTH regulates myleoid ELF-1-like factor (MEF)-induced MAB-21-like-1 (MAB21L1) expression through the JNK1 pathway.","date":"2011","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21465527","citation_count":7,"is_preprint":false},{"pmid":"9010230","id":"PMC_9010230","title":"Identification of Elf-1 and B61 as high affinity ligands for the receptor tyrosine kinase MDK1.","date":"1997","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/9010230","citation_count":7,"is_preprint":false},{"pmid":"11210123","id":"PMC_11210123","title":"Splice isoforms of transcription factor Elf-1 affecting its regulatory function in transcription-molecular cloning of rat Elf-1.","date":"2000","source":"Bioscience, biotechnology, and biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11210123","citation_count":7,"is_preprint":false},{"pmid":"37586179","id":"PMC_37586179","title":"Transcription activation of SPINK4 by ELF-1 augments progression of colon cancer by regulating biological behaviors.","date":"2023","source":"Tissue & cell","url":"https://pubmed.ncbi.nlm.nih.gov/37586179","citation_count":4,"is_preprint":false},{"pmid":"19624906","id":"PMC_19624906","title":"[Expression and significance of Elf-1 and vascular endothelial growth factor in non-small cell lung cancer].","date":"2009","source":"Ai zheng = Aizheng = Chinese journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/19624906","citation_count":3,"is_preprint":false},{"pmid":"40091591","id":"PMC_40091591","title":"EFNA2 Mediates Stiffness-Regulated Hypopharyngeal Cancer Progression.","date":"2025","source":"Clinical and experimental otorhinolaryngology","url":"https://pubmed.ncbi.nlm.nih.gov/40091591","citation_count":1,"is_preprint":false},{"pmid":"40057592","id":"PMC_40057592","title":"Transcription factor ELF-1 protects against colitis by maintaining intestinal epithelium homeostasis.","date":"2025","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/40057592","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":38716,"output_tokens":3344,"usd":0.083154,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10211,"output_tokens":3358,"usd":0.067502,"stage2_stop_reason":"end_turn"},"total_usd":0.150656,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"I need to carefully classify these papers. The gene EFNA2 has aliases ELF-1, LERK6, EPLG6. However, there is a critical disambiguation issue here:\n\n1. **EFNA2/ELF-1 (Ephrin-A2)**: A GPI-anchored membrane ligand for Eph receptor tyrosine kinases (papers 1, 2, 3, 5, 9, 34, 37, 61, 73, 76, 80)\n2. **ELF-1 (E74-like factor 1)**: An Ets-family transcription factor (papers 4, 6, 7, 8, 10-32, 35-36, 38-40, 43-48, 51-52, 54-55, 59-60, 62-63, 65, 67, 69, 77-78, 81) — this is a DIFFERENT gene (ELF1, gene ID 1997, chr13), NOT EFNA2\n\nThe symbol collision: The HGNC aliases provided say ELF-1 refers to EFNA2. But papers 4, 6, 8, etc. clearly describe an Ets transcription factor ELF-1 that is a completely different protein from Ephrin-A2. This is an alias collision where \"ELF-1\" was used for two completely different proteins historically.\n\nEFNA2 (Ephrin-A2) = membrane ligand for Eph RTKs, GPI-anchored\nELF-1 (E74-like factor 1) = Ets transcription factor\n\nI will only extract discoveries about EFNA2/Ephrin-A2 (the GPI-anchored Eph ligand).\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1994,\n      \"finding\": \"EFNA2 (ELF-1/Ephrin-A2) was identified as a membrane-bound ligand for the Eph family receptor tyrosine kinases Mek4 and Sek. The protein is GPI-anchored to the cell membrane, demonstrated by its sensitivity to phosphatidylinositol-specific phospholipase C. It was cloned using soluble receptor-alkaline phosphatase fusion proteins (RAP in situ) to identify regions of ligand expression, followed by cDNA library screening.\",\n      \"method\": \"Receptor-alkaline phosphatase fusion protein binding (RAP in situ), cDNA library screening, cell surface expression assays\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct biochemical identification of receptor-ligand interaction with GPI-anchor characterization, foundational cloning paper with multiple methods\",\n      \"pmids\": [\"7522971\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"EFNA2 (ELF-1) is expressed in a complementary gradient in the tectum matching the gradient of its receptor Mek4 in the retina. Alkaline phosphatase fusion proteins of ELF-1 and Mek4 revealed direct molecular complementarity of reciprocal gradients, establishing a positional label system for retinotectal topographic map development.\",\n      \"method\": \"RNA in situ hybridization, alkaline phosphatase fusion protein binding assays on tissue sections\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — complementary gradient demonstrated by two orthogonal methods (ISH + AP-fusion binding), replicated context\",\n      \"pmids\": [\"7634327\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"EFNA2 (ELF-1) acts as a repellent axon guidance factor in vitro, selectively repelling temporal but not nasal retinal axons. In vivo, retroviral overexpression of ELF-1 in the tectum caused temporal retinal axons to avoid ectopic ELF-1 patches and map to abnormally anterior positions, establishing a direct role in nasal-temporal retinotectal specificity.\",\n      \"method\": \"In vitro stripe/collapse assay, retroviral overexpression in vivo, retinal axon mapping\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vitro functional assay plus in vivo genetic manipulation with defined topographic phenotype, multiple orthogonal methods\",\n      \"pmids\": [\"8797822\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"EFNA2 (ELF-1) was identified as a ligand for the Cek7 receptor tyrosine kinase (identical sequence to the Mek4/Sek ligand ELF-1). The expressed Cek7 ligand induces autophosphorylation of the Cek7 RTK, confirming its functional activity as a receptor activator.\",\n      \"method\": \"cDNA cloning, sequence analysis, receptor autophosphorylation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — receptor autophosphorylation assay demonstrates functional activation, single lab with two methods (cloning + kinase assay)\",\n      \"pmids\": [\"7876076\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"EFNA2 (ELF-1) shares repellent axon guidance function with RAGS for temporal retinal ganglion cell axons, but unlike RAGS is not repellent for nasal axons in two in vitro assays. The differential biological activity correlates with the strength of receptor interaction on RGC axons.\",\n      \"method\": \"In vitro stripe assay, growth cone collapse assay, receptor binding assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — two independent in vitro functional assays with receptor binding correlation, independent replication of EFNA2 repellent activity\",\n      \"pmids\": [\"9135142\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"EFNA2 (ELF-1) is expressed in an increasing dorsal-to-ventral gradient in the septum and selectively allows growth of neurites from topographically appropriate lateral hippocampal neurons while inhibiting neurite outgrowth by medial hippocampal neurons. ELF-1 specifically binds the Eph receptor Bsk and elicits its tyrosine kinase activity, establishing the ELF-1/Bsk pair as a chemoaffinity system for hippocamposeptal topographic projections.\",\n      \"method\": \"In situ hybridization, neurite outgrowth assay, receptor binding assay, tyrosine kinase activation assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — functional neurite assay combined with receptor binding and kinase activation assays, multiple orthogonal methods in one study\",\n      \"pmids\": [\"8855326\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"EFNA2 (ELF-1) and RAGS, when presented in membrane-bound or clustered Fc-chimeric forms (but not as unclustered soluble forms), activate the Eph receptor Cek8 and inhibit neurite growth of motoneurons expressing Cek8. This establishes a requirement for clustering/membrane presentation for functional receptor activation and demonstrates a role in regulating motoneuron axon growth.\",\n      \"method\": \"Receptor phosphorylation assay, neurite growth inhibition assay with clustered vs. soluble protein forms\",\n      \"journal\": \"Mechanisms of development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — mechanistic dissection of clustering requirement using biochemical and cell biological assays with defined receptor phosphorylation readout\",\n      \"pmids\": [\"9232603\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"EFNA2 (ELF-1) was identified as a high-affinity ligand for the MDK1 (mouse developmental kinase 1) Eph-family receptor tyrosine kinase, with Kd of 1.7 × 10⁻¹⁰ M. Binding of ELF-1 or B61 to MDK1 leads to rapid autophosphorylation of MDK1 and tyrosine phosphorylation of an unknown 62 kDa phosphoprotein in Rat1 cells. MDK1-binding staining in embryos was abolished by PI-PLC treatment, consistent with GPI-anchored ligands.\",\n      \"method\": \"Scatchard binding analysis, receptor autophosphorylation assay, phosphotyrosine western blotting, PI-PLC treatment\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — quantitative binding kinetics plus downstream signaling assay, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"9010230\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"The genomic structure of human LERK-6/Ephrin-A2 (EPLG6/EFNA2) was determined, showing high conservation of intron/exon structure in the receptor-binding region with related ephrin-A family members (mouse LERK-3/Ephrin-A3 and LERK-4/Ephrin-A4).\",\n      \"method\": \"Genomic cloning, intron/exon structure analysis, sequence comparison\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — structural genomic characterization, single lab, single method\",\n      \"pmids\": [\"9465306\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A stiff extracellular matrix enhances EFNA2 expression in hypopharyngeal cancer cells. EFNA2 promotes proliferation, migration, epithelial-mesenchymal transition (EMT), and tumor growth in vivo. Gene editing of EFNA2 abrogated the pro-tumorigenic effects of high matrix stiffness, establishing EFNA2 as a mechanotransduction effector in HPC progression.\",\n      \"method\": \"Hydrogel matrix stiffness model, gene editing (EFNA2 knockout/knockdown), colony formation, EDU incorporation, Transwell migration/invasion assays, EMT marker western blotting, subcutaneous xenograft\",\n      \"journal\": \"Clinical and experimental otorhinolaryngology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — multiple functional assays plus in vivo tumorigenesis, single lab, mechanistic link between stiffness and EFNA2 established but upstream pathway not fully resolved\",\n      \"pmids\": [\"40091591\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"EFNA2 is a direct target of miR-642b-5p in bone marrow mesenchymal stem cells. The circRNA hsa_circ_0006859 acts as a sponge for miR-642b-5p, thereby upregulating EFNA2 expression. Elevated EFNA2 inhibits osteogenic differentiation of BMSCs by inactivating Wnt signaling.\",\n      \"method\": \"RIP assay (RNA immunoprecipitation), luciferase reporter assay (implied by miRNA-target validation), overexpression/knockdown functional assays, OVX mouse model\",\n      \"journal\": \"International immunopharmacology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — non-protein locus (circRNA) study; EFNA2 protein role established only indirectly as downstream target, single lab, limited mechanistic detail for EFNA2 itself in abstract\",\n      \"pmids\": [\"36764273\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"EFNA2 (Ephrin-A2) is a GPI-anchored membrane-bound ligand for multiple Eph-family receptor tyrosine kinases (including EphA3/Mek4, EphA4/Sek, Cek7, Cek8, and MDK1) that, upon membrane-bound or clustered presentation, activates receptor autophosphorylation and downstream signaling; it functions as a repellent axon guidance cue with topographically selective effects (repelling temporal but not nasal retinal axons) and plays a role in establishing retinotectal and hippocamposeptal topographic projection maps, and in controlling motoneuron axon growth, while more recently being implicated in promoting cancer cell proliferation, migration, and EMT in response to increased extracellular matrix stiffness.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"EFNA2 (Ephrin-A2/ELF-1) is a GPI-anchored, membrane-bound ligand for multiple Eph-family receptor tyrosine kinases that functions as a topographically graded guidance cue in the developing nervous system [#0, #1]. It binds and activates the receptors Mek4, Sek, Cek7, Bsk, Cek8, and MDK1, triggering receptor autophosphorylation and downstream tyrosine phosphorylation, with high-affinity binding to MDK1 (Kd ~1.7 \\u00d7 10\\u207b\\u00b9\\u2070 M) [#0, #3, #5, #7]. Productive receptor activation requires membrane-bound or clustered presentation; unclustered soluble ligand is inactive [#6]. Functionally, EFNA2 acts as a repellent axon guidance factor with selective topographic activity\\u2014repelling temporal but not nasal retinal axons\\u2014and its expression in complementary gradients in the tectum and septum establishes positional labels that pattern retinotectal and hippocamposeptal projection maps; clustered EFNA2 also inhibits motoneuron neurite growth [#1, #2, #4, #5, #6]. Beyond neural development, EFNA2 is induced by stiff extracellular matrix and acts as a mechanotransduction effector promoting proliferation, migration, EMT, and tumor growth in hypopharyngeal cancer [#9]. Its downstream signaling effectors beyond receptor activation remain largely uncharacterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 1994,\n      \"claim\": \"Established the molecular identity of EFNA2 as a GPI-anchored membrane ligand for Eph-family receptors, answering what class of molecule it is and how it is displayed.\",\n      \"evidence\": \"Receptor-AP fusion binding (RAP in situ), cDNA cloning, and PI-PLC sensitivity in cell surface assays\",\n      \"pmids\": [\"7522971\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream signaling consequences of receptor binding not addressed\", \"Physiological context of expression not yet defined\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Demonstrated that EFNA2 and its receptor Mek4 are expressed in reciprocal complementary gradients, providing the molecular basis for a positional-label system in topographic map formation.\",\n      \"evidence\": \"RNA in situ hybridization plus AP-fusion binding on retinotectal tissue sections\",\n      \"pmids\": [\"7634327\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Correlational gradient mapping does not prove functional guidance\", \"Mechanism of how graded binding translates to axon positioning unresolved\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Confirmed EFNA2 functionally activates a receptor (Cek7) by inducing autophosphorylation, establishing it as a bona fide receptor activator beyond mere binding.\",\n      \"evidence\": \"cDNA cloning, sequence analysis, and receptor autophosphorylation assay\",\n      \"pmids\": [\"7876076\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Downstream effectors of Cek7 activation not identified\", \"Single lab, limited orthogonal validation\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Provided direct in vitro and in vivo evidence that EFNA2 is a repellent guidance cue with nasal-temporal selectivity, settling whether the gradient is functionally instructive for retinotectal specificity.\",\n      \"evidence\": \"In vitro stripe/collapse assay and retroviral overexpression in vivo with axon mapping\",\n      \"pmids\": [\"8797822\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signaling pathway mediating repulsion not defined\", \"Basis of nasal vs temporal differential response unexplained at this stage\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Extended EFNA2's guidance role beyond the retinotectal system, showing it patterns hippocamposeptal projections via the Bsk receptor through graded, topographically selective neurite control.\",\n      \"evidence\": \"In situ hybridization, neurite outgrowth assay, receptor binding, and tyrosine kinase activation assay\",\n      \"pmids\": [\"8855326\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Intracellular signaling downstream of Bsk activation unresolved\", \"How selectivity between medial and lateral neurons is encoded not determined\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"Clarified the functional distinction between EFNA2 and related ephrins, linking its selective repellent activity to the strength of receptor interaction on RGC axons.\",\n      \"evidence\": \"Two independent in vitro assays (stripe and collapse) with receptor binding correlation\",\n      \"pmids\": [\"9135142\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of differential receptor affinity not structurally defined\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"Identified clustering/membrane presentation as a strict requirement for EFNA2 receptor activation, defining a key mechanistic constraint on its signaling, and extended its function to motoneuron axon growth.\",\n      \"evidence\": \"Receptor phosphorylation and neurite growth inhibition assays comparing clustered Fc-chimeric vs soluble forms\",\n      \"pmids\": [\"9232603\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and geometry of functional clusters not resolved\", \"Downstream growth-inhibitory effectors unidentified\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"Quantified high-affinity binding to the MDK1 receptor and detected a downstream phosphorylation event, advancing understanding of the proximal signaling output.\",\n      \"evidence\": \"Scatchard analysis, receptor autophosphorylation, phosphotyrosine western blotting, and PI-PLC treatment in Rat1 cells\",\n      \"pmids\": [\"9010230\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the 62 kDa phosphoprotein never established\", \"Functional consequence of MDK1 activation not characterized\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Defined the human EFNA2 genomic structure, showing conservation of the receptor-binding exon architecture across ephrin-A family members.\",\n      \"evidence\": \"Genomic cloning, intron/exon analysis, and sequence comparison\",\n      \"pmids\": [\"9465306\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional inference beyond structural conservation\", \"Single method, single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Implicated EFNA2 as a mechanotransduction effector in cancer, showing matrix stiffness induces its expression to drive proliferation, migration, and EMT, a role outside its developmental guidance functions.\",\n      \"evidence\": \"Hydrogel stiffness model, EFNA2 gene editing, colony/EDU/Transwell assays, EMT marker blotting, and xenografts in hypopharyngeal cancer cells\",\n      \"pmids\": [\"40091591\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Upstream pathway linking stiffness sensing to EFNA2 induction not resolved\", \"Whether Eph-receptor signaling mediates the pro-tumorigenic effect not tested\", \"Single lab\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Positioned EFNA2 as a downstream node of a circRNA-miRNA axis regulating osteogenic differentiation, implicating it in Wnt-dependent BMSC biology.\",\n      \"evidence\": \"RIP assay, luciferase reporter, overexpression/knockdown, and OVX mouse model\",\n      \"pmids\": [\"36764273\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"EFNA2 role established only indirectly as a downstream target; not independently validated as a protein effector\", \"Direct molecular link between EFNA2 and Wnt inactivation not demonstrated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The intracellular signaling effectors transducing EFNA2-driven Eph receptor activation and how its developmental guidance role connects to its cancer mechanotransduction function remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No defined downstream signaling cascade beyond receptor autophosphorylation\", \"62 kDa phosphoprotein and other effectors unidentified\", \"No structural model of ligand-receptor selectivity\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0048018\", \"supporting_discovery_ids\": [0, 3, 5, 7]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3, 6, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [1, 2, 5]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3, 6, 7]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"EPHA3\", \"EPHA4\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}