{"id":"W3080928337","doi":"10.1186/s13059-020-02110-3","title":"Cis and trans effects differentially contribute to the evolution of promoters and enhancers","year":2020,"lang":"en","type":"article","venue":"Genome biology","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":74,"is_retracted":false,"has_abstract":true,"ca_institutions":"SickKids Foundation; University of Toronto","funders":"Life Sciences Research Foundation; Ministerio de Ciencia, Innovación y Universidades; Howard Hughes Medical Institute","keywords":"Enhancer; Biology; Promoter; Genetics; Gene; Regulation of gene expression; Regulatory sequence; Trans-acting; Gene expression; Mutant","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":[0.00006242054,0.00008749571,0.000131631,0.0000129241,0.00004047007,0.000006139657,0.00009844822,0.00008438149,0.000002374073],"category_scores_gemma":[0.00002731027,0.00006517176,0.00002868571,0.00003618727,0.00008192637,7.433744e-7,0.00008372626,0.00003634443,8.201133e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000009453914,"about_ca_system_score_gemma":0.00002430199,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001913422,"about_ca_topic_score_gemma":0.00004026026,"domain_scores_codex":[0.9994698,0.00004481059,0.0001135814,0.0002137728,0.00002272906,0.0001353278],"domain_scores_gemma":[0.9997463,0.00001046836,0.00004287653,0.00010703,0.00002385805,0.00006950515],"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":[0.00006265972,0.000006243916,0.0007930204,0.00003418657,0.00004578493,2.426737e-7,0.0002484135,0.00001447446,0.9966377,0.0001532263,0.00001839042,0.001985644],"study_design_scores_gemma":[0.006483064,0.01534134,0.2945395,0.00005032879,0.0003700013,0.00005850699,0.0008432151,0.003046833,0.6129145,0.001740495,0.06317295,0.001439263],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9606498,0.001472521,0.03629024,0.001157332,0.00005504001,0.0002629051,0.00008013054,0.000003539974,0.00002844366],"genre_scores_gemma":[0.9990314,0.0002283998,0.0002826021,0.0002953085,0.0000738042,0.00001203349,0.00005754561,0.00000716494,0.00001172599],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3837232,"threshold_uncertainty_score":0.2657627,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.003298030067420566,"score_gpt":0.1936216491295338,"score_spread":0.1903236190621132,"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."}}