{"id":"W2904871025","doi":"10.1093/bioinformatics/bty992","title":"Gene expression models based on transcription factor binding events confer insight into functional <i>cis</i> -regulatory variants","year":2018,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":14,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Children's Hospital; University of British Columbia","funders":"National Institute of General Medical Sciences; Natural Sciences and Engineering Research Council of Canada; Genome British Columbia; BC Children’s Hospital Foundation; BC Children's Hospital; National Institutes of Health; Children's Hospital Foundation; Canadian Institutes of Health Research; China Scholarship Council; Genome Canada","keywords":"CTCF; Computational biology; Transcription factor; Gene; Biology; Genetics; DNA binding site; Regulation of gene expression; Regulatory sequence; Gene expression; Enhancer; 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":[0.0001179927,0.000212279,0.0001400275,0.00008775735,0.0001964423,0.00003776513,0.0001695414,0.0002320743,0.00005653491],"category_scores_gemma":[0.00001351653,0.0001913694,0.00009591298,0.00006866796,0.0000620668,0.00002357711,0.0000535437,0.00008237507,0.00005714156],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005019182,"about_ca_system_score_gemma":0.0001197036,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000002465368,"about_ca_topic_score_gemma":0.00000440985,"domain_scores_codex":[0.9989177,0.00002643717,0.0003575008,0.0002045945,0.0002618025,0.000231971],"domain_scores_gemma":[0.9992273,0.00000744345,0.0001467992,0.0003877146,0.0001220943,0.0001086803],"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":[0.0001683581,0.0001040778,0.0001491788,0.00005618641,0.00003301024,4.496117e-7,0.0004765019,0.003335216,0.9931445,0.0001079869,0.001031674,0.001392904],"study_design_scores_gemma":[0.001490991,0.0005309437,0.001667317,0.0000690515,0.00002199909,0.000006349411,0.00008198684,0.4150087,0.5765468,0.0002511204,0.003891094,0.0004336141],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7648156,0.00002550113,0.232437,0.00003098802,0.0005500481,0.0002092903,0.0001017114,0.00002423422,0.001805554],"genre_scores_gemma":[0.9844337,0.0000242229,0.01398011,0.000497071,0.0002245845,0.00001283443,0.0006265776,0.00002725779,0.0001736054],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4165976,"threshold_uncertainty_score":0.7803817,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01584725336999276,"score_gpt":0.2141445878260201,"score_spread":0.1982973344560273,"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."}}