{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.003556862,0.001180993,0.001611103,0.005001159,0.0004842563,0.001118485,0.001035932,0.001727603,0.001157075],"category_scores_gemma":[0.01405858,0.0006464833,0.001363278,0.002308941,0.0004197039,0.001415617,0.001250018,0.001482135,0.0004907289],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005626882,"about_ca_system_score_gemma":0.0009364238,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006497362,"about_ca_topic_score_gemma":0.01017796,"domain_scores_codex":[0.9984895,0.0005361321,0.0001276673,0.0003643988,0.0003607884,0.0001214769],"domain_scores_gemma":[0.9900448,0.008236147,0.0005013133,0.0003361447,0.0007138954,0.0001675771],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001498009,0.0004823279,0.2062347,0.0004208779,0.001353243,0.0007942144,0.0001604561,0.4403471,0.01343757,0.001442201,0.002257647,0.3315717],"study_design_scores_gemma":[0.00004850263,0.00005778046,0.01411606,0.00002503172,0.0001567314,0.0001579593,0.00002785131,0.9782977,0.003820531,0.002944393,0.0003176156,0.0000298724],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.5069604,0.001978071,0.4862436,0.0004736976,0.00003239728,0.00009548855,0.001715463,0.001616892,0.0008839609],"genre_scores_gemma":[0.8639062,0.0003442234,0.1321228,0.0001175043,0.00004884836,0.0000808561,0.002681813,0.00008559316,0.0006121331],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006497362,"threshold_uncertainty_score":0.01881069,"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."}}