{"id":"W2923747712","doi":"10.1016/j.ymeth.2019.03.017","title":"RNA-Seq analysis of the T3SA regulon in Shigella flexneri reveals two new chromosomal genes upregulated in the on-state","year":2019,"lang":"en","type":"article","venue":"Methods","topic":"Escherichia coli research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":17,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Ottawa","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Regulon; Biology; Pseudogene; Shigella flexneri; Gene; Genetics; RNA; Plasmid; Operon; Gene expression; Computational biology; Escherichia coli; Genome","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00009628835,0.0003292782,0.000307697,0.0002413807,0.0002805959,0.0004722038,0.0001703173,0.0003066048,0.001791951],"category_scores_gemma":[0.0001402241,0.000167197,0.0004760961,0.0002163558,0.0002770857,0.0001437802,0.0002025211,0.000539061,0.0004751823],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003395422,"about_ca_system_score_gemma":0.0003363049,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002660109,"about_ca_topic_score_gemma":0.006154295,"domain_scores_codex":[0.9999032,0.00000529416,0.000003880514,0.00003083896,0.00003060043,0.00002607418],"domain_scores_gemma":[0.9998727,0.00003896581,0.00002063536,0.00001201995,0.00002665092,0.00002900079],"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":[0.00007873543,0.00001050606,0.0004682419,0.00002103759,0.000002852842,0.00001547043,0.00001713041,0.00003809278,0.9987742,0.00003486541,0.00005894009,0.0004799136],"study_design_scores_gemma":[0.00001152231,0.0001213125,0.08639023,0.0000140902,0.00002445261,0.00009967462,0.0002300735,0.002573615,0.9084746,0.0001712511,0.001874098,0.00001515872],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9872698,0.0003301968,0.005198612,0.0001840007,0.00006402584,0.00002370799,0.00474858,0.0001918065,0.00198938],"genre_scores_gemma":[0.9794206,0.0003103243,0.006375481,0.000358045,0.00002571074,0.00005867694,0.00710902,0.0002161118,0.0061261],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002660109,"threshold_uncertainty_score":0.005994678,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02674383942965716,"score_gpt":0.3846680483035932,"score_spread":0.3579242088739361,"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."}}