{"id":"W2172186301","doi":"10.1093/nar/gkh387","title":"MSCAN: identification of functional clusters of transcription factor binding sites","year":2004,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":65,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Children's Hospital; University of British Columbia","funders":"Canadian Institutes of Health Research; European Commission; University of Oxford","keywords":"Biology; Transcription factor; DNA binding site; Identification (biology); Computational biology; Genetics; Binding site; DNA-binding protein; Evolutionary biology; Gene; Promoter; Gene expression; Ecology","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":[0.0007726755,0.0008913586,0.0007622114,0.002464322,0.0009376272,0.0009904801,0.001223152,0.0005452784,0.009089198],"category_scores_gemma":[0.002121383,0.000480139,0.000693664,0.00109061,0.0004266857,0.0008281482,0.00116245,0.0006708164,0.004016669],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007140335,"about_ca_system_score_gemma":0.0009170194,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002373474,"about_ca_topic_score_gemma":0.004511624,"domain_scores_codex":[0.9995271,0.00007046218,0.00002056836,0.0001452529,0.000193398,0.00004325725],"domain_scores_gemma":[0.9993196,0.0002540395,0.00008765048,0.0001171107,0.0001399134,0.00008176221],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.002282573,0.0004524608,0.02188033,0.001101718,0.0002538189,0.0005544569,0.0005905586,0.05292439,0.2289719,0.02685364,0.1036844,0.5604498],"study_design_scores_gemma":[0.0001517969,0.0001724917,0.01572357,0.0000415508,0.00005914758,0.000702481,0.0001293552,0.8148578,0.09988307,0.01882377,0.04936251,0.00009236101],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1500332,0.0005754192,0.7542418,0.0004001221,0.0001424954,0.000410069,0.01914791,0.06605534,0.008993721],"genre_scores_gemma":[0.2493893,0.0002598404,0.7102305,0.000138552,0.00006744756,0.000538711,0.03007468,0.002132026,0.007169018],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.009089198,"threshold_uncertainty_score":0.03040642,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0384560784536434,"score_gpt":0.3033136281112737,"score_spread":0.2648575496576303,"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."}}