{"id":"W2130687223","doi":"10.1186/gb-2013-14-8-r86","title":"Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization","year":2013,"lang":"en","type":"article","venue":"Genome biology","topic":"Developmental Biology and Gene Regulation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":51,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"Fonds Wetenschappelijk Onderzoek; Agence Nationale de la Recherche; Science Foundation Ireland","keywords":"Enhancer; Biology; Effector; Transcription factor; Gene; Computational biology; Genome; Genetics; Cis-regulatory module; Regulation of gene expression; Cell biology","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001241423,0.0001599035,0.0002788255,0.00007925639,0.00005225715,0.00000402869,0.0002010335,0.0002683625,0.0003977573],"category_scores_gemma":[0.0001028989,0.0001341928,0.00007104062,0.0001811502,0.0001972833,0.000004867268,0.0001285266,0.00004212838,0.00002377517],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001343038,"about_ca_system_score_gemma":0.00005545378,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003672607,"about_ca_topic_score_gemma":0.00001113019,"domain_scores_codex":[0.998953,0.0001039611,0.0003698615,0.0003160452,0.00004980854,0.0002073029],"domain_scores_gemma":[0.9991726,0.00002054413,0.0002568161,0.0002562822,0.0002478411,0.00004596561],"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":[0.00002037553,0.00002994989,0.1290907,0.00002236948,0.0001165156,1.417967e-7,0.00003033021,0.00002775443,0.8696647,0.00002415094,0.0001110948,0.000861918],"study_design_scores_gemma":[0.0001120575,0.0001145058,0.4948313,0.000002243072,0.00001251112,0.000003098026,0.00001641301,5.324968e-7,0.5028312,0.0002599798,0.001721745,0.00009437343],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.992694,0.004298113,0.002061917,0.00007161377,0.0001053532,0.0002221076,0.00005821632,0.00000842952,0.0004802503],"genre_scores_gemma":[0.9944538,0.0003522624,0.002014706,0.00007278043,0.0001071021,0.00001707269,0.002253201,0.00001521329,0.0007138376],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3668335,"threshold_uncertainty_score":0.5472224,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009853837315367443,"score_gpt":0.2613650253746267,"score_spread":0.2515111880592593,"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."}}