{"id":"W4411168095","doi":"10.1101/gr.280320.124","title":"Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts","year":2025,"lang":"en","type":"article","venue":"Genome Research","topic":"Estrogen and related hormone effects","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Canadian Institutes of Health Research; KWF Kankerbestrijding; Oncode Institute; Türkiye Bilimler Akademisi; Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi; Ministerie van Volksgezondheid, Welzijn en Sport","keywords":"Epigenomics; Biology; Enhancer; Computational biology; Breast cancer; Annotation; Bioinformatics; Cancer; Genetics; DNA methylation; Gene; Transcription factor","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000303024,0.0002654147,0.0003514487,0.0008486523,0.000230786,0.0004372646,0.0002219325,0.0002130102,0.001663668],"category_scores_gemma":[0.0003232457,0.0001797431,0.0005536138,0.0007122912,0.0001357553,0.0002078333,0.0003992257,0.0003406597,0.0009229207],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002058894,"about_ca_system_score_gemma":0.0003914023,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001060694,"about_ca_topic_score_gemma":0.002870802,"domain_scores_codex":[0.9998006,0.00002012084,0.00001255631,0.00008849896,0.00005253496,0.00002575206],"domain_scores_gemma":[0.9998382,0.00004805361,0.00004200089,0.00002366662,0.00002877656,0.00001937931],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0003002408,0.00004093367,0.01687602,0.0004836068,0.00006566269,0.0001821699,0.0001970387,0.002502514,0.9449065,0.0009033388,0.0007736133,0.03276836],"study_design_scores_gemma":[0.00005230387,0.0003232544,0.3893548,0.0001815055,0.0003663748,0.001370436,0.0004129651,0.0447625,0.5096335,0.003035273,0.05041591,0.0000911772],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9096678,0.004311447,0.05428695,0.0001476662,0.00003531377,0.00005079022,0.02656853,0.001702429,0.003229065],"genre_scores_gemma":[0.9191502,0.00113577,0.04158299,0.00006617347,0.00001613433,0.0000603197,0.03509661,0.0002632082,0.002628649],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001663668,"threshold_uncertainty_score":0.005565464,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01936885332434775,"score_gpt":0.3330747292865416,"score_spread":0.3137058759621939,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}