{"id":"W4404259733","doi":"10.1101/2024.11.11.622123","title":"Extensive binding of nebulous human transcription factors to genomic dark matter","year":2024,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; Genome Canada","funders":"Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung","keywords":"Biology; Human genome; Genome; Enhancer; Transcription factor; Genetics; Chromatin; Promoter; Computational biology; Transposable element; Evolutionary biology; Gene; Gene expression","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0001463594,0.0002260254,0.0002218528,0.0003919639,0.0002808307,0.0003337264,0.0001418865,0.0002573424,0.002016847],"category_scores_gemma":[0.0003338302,0.0001617854,0.0001758119,0.0004190255,0.0003376746,0.0002467828,0.0004001456,0.0002339756,0.0006706505],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002407583,"about_ca_system_score_gemma":0.0002102214,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001152574,"about_ca_topic_score_gemma":0.001799278,"domain_scores_codex":[0.9997939,0.00002005026,0.000007606374,0.0001116277,0.00003683894,0.00002991531],"domain_scores_gemma":[0.9998536,0.00004143761,0.00002819054,0.00002879753,0.00001354045,0.00003431831],"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":[0.0003313976,0.00001196261,0.0157635,0.0001950263,0.00003723892,0.0002469417,0.00018886,0.0003169023,0.9682136,0.0008737158,0.0005580159,0.01326289],"study_design_scores_gemma":[0.00002920213,0.0001629553,0.2194852,0.00006139377,0.00007170399,0.002376667,0.00051033,0.001790105,0.7295999,0.00282585,0.04304567,0.00004106822],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9740314,0.01060217,0.009619089,0.0002833126,0.0000360569,0.000008997356,0.001633932,0.0001956274,0.00358932],"genre_scores_gemma":[0.9892644,0.001819255,0.00350101,0.0002130354,0.00002864416,0.000009890156,0.002489451,0.0000403507,0.00263392],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002016847,"threshold_uncertainty_score":0.006747007,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009520923522607347,"score_gpt":0.2166325616465931,"score_spread":0.2071116381239858,"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."}}