{"id":"W2077026063","doi":"10.1101/gr.096305.109","title":"Integrating multiple evidence sources to predict transcription factor binding in the human genome","year":2010,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":100,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; National Institute of General Medical Sciences; Joint Genome Institute; Broad Institute; U.S. Department of Energy; National Institutes of Health; National Science Foundation","keywords":"Motif (music); Transcription factor; DNA binding site; Biology; Computational biology; Binding site; Sequence motif; Genome; Genetics; Sp3 transcription factor; Human genome; Bioinformatics; Promoter; Gene; Enhancer; Gene expression","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":[0.001695302,0.0001329196,0.0001138864,0.0001784457,0.0003321679,0.0001521532,0.0007723122,0.0001430388,0.00004307207],"category_scores_gemma":[0.0003475855,0.000103377,0.00006424681,0.0002901285,0.0001001483,0.000007561854,0.0001713943,0.0005762925,0.00003338741],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004042559,"about_ca_system_score_gemma":0.0000798641,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001678609,"about_ca_topic_score_gemma":0.001681571,"domain_scores_codex":[0.9983155,0.0001951274,0.0002426472,0.0003926086,0.0003507793,0.0005033796],"domain_scores_gemma":[0.9991796,0.00007832891,0.00003658261,0.0004856372,0.0001171412,0.0001027044],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00001438804,0.00003340012,0.009047962,0.0000227074,0.000008300989,0.000002619507,0.001771398,0.00007601189,0.9884078,0.00005329329,0.00001551347,0.0005466359],"study_design_scores_gemma":[0.001367269,0.002013857,0.7618814,0.0001523469,0.00001751032,0.00005924009,0.01040399,0.001999581,0.1753942,0.0004397145,0.04519825,0.001072617],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.998147,0.0002379166,0.0003807465,0.0002917173,0.00006440314,0.0005302131,0.00004132557,0.00000808745,0.0002985992],"genre_scores_gemma":[0.9983665,0.00007536638,0.0007866333,0.00004762932,0.0002800601,0.00008805478,0.00008035419,0.00002367194,0.0002516721],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8130136,"threshold_uncertainty_score":0.4215591,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06485114656262207,"score_gpt":0.3483433381821673,"score_spread":0.2834921916195453,"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."}}