{"id":"W2051033712","doi":"10.1371/journal.pone.0050562","title":"Genome Context as a Predictive Tool for Identifying Regulatory Targets of the TetR Family Transcriptional Regulators","year":2012,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Bacterial Genetics and Biotechnology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":75,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University","funders":"Canadian Institutes of Health Research","keywords":"TetR; Biology; Genetics; Repressor; Gene; Context (archaeology); Protein family; Gene family; Transcriptional regulation; Computational biology; Genome; Gene expression","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0001672104,0.0001245281,0.0001728624,0.00003194857,0.00008040608,0.000008106587,0.0002209937,0.0002556578,0.00001685447],"category_scores_gemma":[0.00006739725,0.0001014849,0.0001282679,0.00006251199,0.00016419,0.000005222038,0.00008541332,0.00007528238,0.000003225612],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001691015,"about_ca_system_score_gemma":0.0000569991,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004217049,"about_ca_topic_score_gemma":0.000003149661,"domain_scores_codex":[0.9991115,0.00003378556,0.0002266802,0.0002080202,0.0001652459,0.0002547557],"domain_scores_gemma":[0.9993749,0.000008545409,0.0001122055,0.0003320379,0.0001250015,0.00004731214],"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":[0.0001558056,0.0003186763,0.001905972,0.00005026206,0.0002610674,5.258865e-8,0.00006455076,0.000001223929,0.9963324,0.0006840964,0.00005352524,0.0001723637],"study_design_scores_gemma":[0.0004324925,0.000281453,0.1079422,0.00002861477,0.00009763028,0.000001964882,0.00006583252,0.00000625357,0.8866813,0.0002330783,0.004105958,0.0001232127],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9959265,0.00265529,0.0003080606,0.0001562303,0.0001994486,0.0005030981,0.0001462823,0.00001121151,0.00009386384],"genre_scores_gemma":[0.9978922,0.00009330719,0.0009137307,0.0001571905,0.0003448684,0.00006264662,0.00006350171,0.00002221206,0.0004503654],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1096511,"threshold_uncertainty_score":0.4138436,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02744244280185239,"score_gpt":0.223150481680491,"score_spread":0.1957080388786386,"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."}}