{"id":"W2112717966","doi":"10.1101/gr.4140006","title":"Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques","year":2006,"lang":"en","type":"review","venue":"Genome Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":219,"is_retracted":false,"has_abstract":true,"ca_institutions":"Genome British Columbia","funders":"National Institute of Diabetes and Digestive and Kidney Diseases; National Cancer Institute; National Human Genome Research Institute; National Institutes of Health; Michael Smith Health Research BC","keywords":"Biology; In silico; Computational biology; Transcription factor; DNA binding site; Genomics; Genome; Genetics; Gene; Gene expression; Promoter","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":[0.0008329118,0.000212881,0.0004709441,0.0002249069,0.0001171982,0.00005286834,0.0002447224,0.0002839143,0.00001384663],"category_scores_gemma":[0.00003414837,0.0002065717,0.0001147504,0.0002206368,0.0001536813,0.000002687913,0.0001705243,0.0002237731,0.000004051257],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007906332,"about_ca_system_score_gemma":0.0002453262,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001485667,"about_ca_topic_score_gemma":0.00004798729,"domain_scores_codex":[0.9982463,0.0003517536,0.0004335082,0.0004094141,0.0002621717,0.0002968631],"domain_scores_gemma":[0.9993063,0.00005397515,0.0001503307,0.0002311742,0.0001919798,0.0000662918],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00007704116,0.0005837463,0.000584832,0.03318805,0.0005093669,0.00001547989,0.0003897347,0.0001195062,0.371568,0.0001110253,0.0004801896,0.592373],"study_design_scores_gemma":[0.001305788,0.002940132,0.003466069,0.004206365,0.0002058048,0.0002250082,0.0004622077,0.000671092,0.02236111,0.0002032502,0.9610283,0.002924858],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.04453095,0.9535053,0.0004241336,0.000001787348,0.00001955912,0.0005815941,0.0007207355,0.000007273378,0.0002086129],"genre_scores_gemma":[0.07304052,0.9157242,0.002910062,0.000002449022,0.0001229527,0.0000917728,0.007561477,0.00008116181,0.00046547],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.9605481,"threshold_uncertainty_score":0.842375,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1207800905195266,"score_gpt":0.405242222909531,"score_spread":0.2844621323900045,"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."}}