{"id":"W2061478525","doi":"10.1371/journal.pgen.0030159","title":"In Vivo Validation of a Computationally Predicted Conserved Ath5 Target Gene Set","year":2007,"lang":"en","type":"article","venue":"PLoS Genetics","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":56,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; University of Tokyo; Deutsche Forschungsgemeinschaft; European Commission","keywords":"Biology; In silico; Genome; Chromatin immunoprecipitation; DNA binding site; Conserved sequence; Transcription factor; Genetics; Computational biology; Promoter; Binding site; Gene; Phylogenetic tree; Regulatory sequence; Gene expression; Peptide sequence","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001866421,0.0001170923,0.0001370166,0.00006185519,0.00002366395,0.000008534395,0.0001495841,0.0001350783,0.00002901615],"category_scores_gemma":[0.00003881383,0.000133121,0.00004598065,0.0001034542,0.00005185138,0.000001846382,0.00007321337,0.00005143565,0.000001850048],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001756794,"about_ca_system_score_gemma":0.00009064381,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000003955625,"about_ca_topic_score_gemma":0.00002909849,"domain_scores_codex":[0.9990493,0.00003184431,0.00037108,0.0002072661,0.0001537559,0.0001867215],"domain_scores_gemma":[0.9994122,0.00002048544,0.00014015,0.0002123714,0.000158353,0.00005637682],"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":[0.0000435382,0.0001224465,0.01720005,0.00003065564,0.00004504786,0.000003535639,0.00009683054,0.008403611,0.9736868,0.00003118219,0.0003106704,0.00002565271],"study_design_scores_gemma":[0.0006108846,0.0001595035,0.00483834,0.000009272851,0.00001538568,0.000007080113,0.00003622833,0.01987049,0.9733335,0.0002868705,0.0006942866,0.000138136],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9938904,0.0001765211,0.005152381,0.00004088655,0.0000775656,0.000192767,0.0001893288,0.000006353126,0.00027378],"genre_scores_gemma":[0.9832779,0.00006625681,0.01584489,0.0001390307,0.0000880366,0.000005194546,0.0004842644,0.00002136517,0.00007312373],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01236171,"threshold_uncertainty_score":0.5428518,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01081786774687725,"score_gpt":0.233906606685314,"score_spread":0.2230887389384368,"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."}}