{"id":"W1997930876","doi":"10.1186/1471-2229-13-42","title":"Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas","year":2013,"lang":"en","type":"article","venue":"BMC Plant Biology","topic":"Plant Gene Expression Analysis","field":"Biochemistry, Genetics and Molecular Biology","cited_by":22,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; University of Guelph","funders":"Norges Teknisk-Naturvitenskapelige Universitet","keywords":"Biology; In silico; Computational biology; Genome; Gene; Motif (music); Cis-regulatory module; Genetics; Transcription factor","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":[0.002575851,0.002845826,0.002068484,0.003985897,0.001372983,0.002431581,0.002917882,0.001183931,0.01932576],"category_scores_gemma":[0.003411911,0.001861735,0.003454697,0.00195245,0.0005049321,0.001917077,0.002830781,0.002098854,0.008234388],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001131211,"about_ca_system_score_gemma":0.002269789,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002758845,"about_ca_topic_score_gemma":0.005252312,"domain_scores_codex":[0.9990849,0.0001023144,0.00006634857,0.0003621587,0.0002695163,0.000114698],"domain_scores_gemma":[0.999343,0.0002944923,0.0001118903,0.00008581689,0.00007752088,0.00008725056],"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":[0.007582603,0.0005081851,0.02134405,0.008108799,0.002676427,0.002781847,0.002182331,0.01807818,0.360015,0.01603332,0.2249182,0.3357711],"study_design_scores_gemma":[0.002090097,0.001230268,0.02759115,0.0005882403,0.0009919723,0.003169659,0.0005779111,0.2348219,0.2409341,0.02665529,0.4605581,0.0007912669],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.0405247,0.00238167,0.4519057,0.0004276878,0.000219872,0.0009646874,0.0951947,0.4026741,0.005706971],"genre_scores_gemma":[0.06791122,0.001325267,0.7510923,0.000381606,0.00004739935,0.002356315,0.1429985,0.02871617,0.005171149],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.01932576,"threshold_uncertainty_score":0.06465113,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01468351929796333,"score_gpt":0.2266106541951616,"score_spread":0.2119271348971982,"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."}}