{"id":"W2810899744","doi":"10.21769/bioprotoc.2181","title":"In silico Analysis and Site-directed Mutagenesis of Promoters","year":2017,"lang":"en","type":"article","venue":"BIO-PROTOCOL","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Sherbrooke","funders":"","keywords":"Promoter; In silico; Gene; Biology; Transcription factor; Reporter gene; Mutagenesis; Computational biology; Transcription (linguistics); Genetics; Response element; DNA binding site; Cis-regulatory module; Gene expression; Regulation of gene expression; Mutation","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":[0.00158536,0.001591212,0.001495342,0.001057848,0.000699974,0.0008455181,0.00135579,0.0008373936,0.005306517],"category_scores_gemma":[0.001200749,0.001013132,0.001414846,0.0007405998,0.0005804169,0.0003380592,0.0004927276,0.00257794,0.003830434],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000610762,"about_ca_system_score_gemma":0.001466381,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008854589,"about_ca_topic_score_gemma":0.002083027,"domain_scores_codex":[0.9989167,0.0003163546,0.0001221332,0.0002338161,0.0002768324,0.0001340725],"domain_scores_gemma":[0.9991339,0.000403047,0.00007822391,0.0001822281,0.0001292815,0.00007338162],"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":[0.0002492541,0.0001360261,0.000425186,0.0005669671,0.00004540021,0.000220366,0.00009441213,0.001670203,0.9897367,0.001424371,0.0007883785,0.004642743],"study_design_scores_gemma":[0.00004939141,0.0001766114,0.001123162,0.00003455687,0.0001244935,0.0003965217,0.00004781745,0.009863677,0.9668018,0.0006699567,0.02067876,0.00003313399],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.2571547,0.00126822,0.7059249,0.0006425229,0.0004193963,0.001963171,0.01793992,0.007643764,0.007043458],"genre_scores_gemma":[0.4097351,0.001980714,0.5488753,0.0003369214,0.00006447673,0.001538033,0.02793069,0.002261687,0.007277104],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.005306517,"threshold_uncertainty_score":0.01775205,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007911603717085224,"score_gpt":0.2842458910149819,"score_spread":0.2763342872978967,"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."}}