{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003336273,0.00006459959,0.00008814701,0.0001138703,0.00006703398,0.00001381144,0.0001590488,0.0001069238,0.00004103069],"category_scores_gemma":[0.00005622074,0.00006555498,0.0000682484,0.0001530582,0.0001415871,0.000005154259,0.00005140056,0.00009271312,0.00001030441],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004217021,"about_ca_system_score_gemma":0.00009036258,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002063042,"about_ca_topic_score_gemma":0.00001985153,"domain_scores_codex":[0.9990754,0.00004269747,0.0002451008,0.0001853255,0.0002886772,0.0001627577],"domain_scores_gemma":[0.9994314,0.000009648956,0.00007333926,0.000222085,0.0002228773,0.0000406549],"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":[0.00005182966,0.00006083425,0.001422089,0.00005656126,0.00002553411,2.009429e-7,0.0001498655,0.0006563123,0.9965238,0.0002966066,0.00007349518,0.0006828943],"study_design_scores_gemma":[0.0006042014,0.0002706104,0.02750294,0.00001972299,0.000006584654,0.000003596777,0.0004223227,0.0006852522,0.9696198,0.0004166959,0.0003576393,0.00009064109],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9963052,0.0000951717,0.002992987,0.00009460807,0.0000647674,0.0001265745,0.00006271382,0.000003600722,0.0002543462],"genre_scores_gemma":[0.998998,0.00009771888,0.0003844319,0.000005653899,0.00005164744,0.000006305445,0.000157184,0.00001407149,0.0002849779],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02690398,"threshold_uncertainty_score":0.2673255,"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."}}