{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001332201,0.0001160418,0.0001869367,0.00008281256,0.00007421281,0.000037563,0.0002072467,0.000118058,0.00002301326],"category_scores_gemma":[0.00005018475,0.0001082506,0.00008247306,0.00008397875,0.00009598606,0.000003748925,0.0001599834,0.00003347034,0.000001604973],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00000863052,"about_ca_system_score_gemma":0.00003150469,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002056094,"about_ca_topic_score_gemma":0.0005596266,"domain_scores_codex":[0.9992778,0.00002886823,0.0002141318,0.000270723,0.00006679032,0.0001416664],"domain_scores_gemma":[0.9991385,0.000003882959,0.0001980167,0.00056844,0.00004339176,0.00004775083],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00009489248,0.00008417189,0.1672903,0.00008435681,0.0001156437,0.000003994609,0.00004400308,0.00002246954,0.830215,0.00000971209,0.00008382633,0.00195163],"study_design_scores_gemma":[0.001986824,0.0002754458,0.4987678,0.00001892898,0.00008727229,0.000003604981,0.0000239114,0.00316763,0.4883671,0.00006102736,0.006935386,0.0003050315],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9107147,0.00000265135,0.00005340903,0.00004638773,0.00001236558,0.08882096,0.000024614,0.000005350113,0.0003195862],"genre_scores_gemma":[0.8076741,0.000002069747,0.001289544,0.0000267647,0.00003428062,0.1907123,0.00002161172,0.0000135774,0.000225796],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3418479,"threshold_uncertainty_score":0.4414331,"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."}}