{"id":"W2136499960","doi":"10.1094/mpmi-19-1167","title":"Whole-Genome Expression Profiling Defines the HrpL Regulon of <i>Pseudomonas syringae</i> pv. <i>tomato</i> DC3000, Allows de novo Reconstruction of the Hrp <i>cis</i> Element, and Identifies Novel Coregulated Genes","year":2006,"lang":"en","type":"article","venue":"Molecular Plant-Microbe Interactions","topic":"Plant Pathogenic Bacteria Studies","field":"Agricultural and Biological Sciences","cited_by":119,"is_retracted":false,"has_abstract":true,"ca_institutions":"Wilfrid Laurier University","funders":"Agricultural Research Service; U.S. Department of Agriculture; National Science Foundation","keywords":"Pseudomonas syringae; Regulon; Biology; Effector; Genetics; Gene; Promoter; Type three secretion system; Sigma factor; Computational biology; Virulence; Regulation of gene expression; 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":[0.0002022933,0.0002361664,0.0002836189,0.0000318384,0.0003997428,0.00006945107,0.000326024,0.00009280266,0.00002228985],"category_scores_gemma":[0.00003646404,0.00009745661,0.0001674022,0.0002632056,0.0002222435,0.0001560644,0.0002436175,0.0001732371,0.000002889639],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003300303,"about_ca_system_score_gemma":0.0000181132,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003425791,"about_ca_topic_score_gemma":0.001012661,"domain_scores_codex":[0.9985055,0.0001299234,0.0005504233,0.0003338983,0.0001899405,0.000290254],"domain_scores_gemma":[0.9989979,0.0001935025,0.0004772703,0.0001680205,0.0001281564,0.00003514996],"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":[0.0000598728,0.00008900206,0.002869552,0.00002891348,0.00005505451,0.000004143882,0.00006435277,0.0001037815,0.9960674,0.00008637959,0.0002500494,0.0003214888],"study_design_scores_gemma":[0.000215777,0.00003574319,0.01634297,0.0002210211,0.00008346829,0.0009805986,0.0003135988,0.0000645644,0.9781429,0.0001247431,0.003297992,0.000176642],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.996087,0.0005725588,0.0001571569,0.0006770903,0.0003404565,0.0003960097,0.00157442,0.00004438039,0.0001509515],"genre_scores_gemma":[0.9985914,0.0001141158,0.0005740685,0.00009108189,0.00008130485,0.00003560726,0.0003139959,0.00000466302,0.0001938157],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01792452,"threshold_uncertainty_score":0.3974165,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009593143436747654,"score_gpt":0.1925159100655514,"score_spread":0.1829227666288037,"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."}}