{"id":"W2478983638","doi":"10.1093/nar/gkw691","title":"Evaluating the impact of single nucleotide variants on transcription factor binding","year":2016,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":43,"is_retracted":false,"has_abstract":true,"ca_institutions":"Child and Family Research Institute; University of British Columbia","funders":"National Institute of General Medical Sciences; Natural Sciences and Engineering Research Council of Canada; Child and Family Research Institute; Genome British Columbia; BC Children's Hospital; National Institutes of Health; Children's Hospital Foundation; Genome Canada","keywords":"Biology; Genetics; Transcription factor; Allele; Computational biology; ENCODE; Binding site; Sequence motif; Phenotype; DNA binding site; Single-nucleotide polymorphism; DNA; Gene; Promoter; Gene expression; Genotype","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":[0.003548029,0.001073061,0.001043084,0.001834521,0.0004695817,0.001410777,0.0004726339,0.0008396199,0.001539675],"category_scores_gemma":[0.007606196,0.0002861453,0.001433415,0.001401711,0.0005032197,0.0007096366,0.0005141518,0.001170798,0.0006935846],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004451565,"about_ca_system_score_gemma":0.0004767228,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00403835,"about_ca_topic_score_gemma":0.005156579,"domain_scores_codex":[0.9979835,0.0006203813,0.0001626776,0.0007596674,0.0003339188,0.0001398639],"domain_scores_gemma":[0.9909504,0.007393468,0.0005746932,0.0005470926,0.0002831547,0.0002512225],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0011001,0.0001996829,0.8334907,0.000259087,0.001478091,0.0004018662,0.0001057932,0.05475621,0.04724569,0.0003172565,0.0008269944,0.05981852],"study_design_scores_gemma":[0.00002695737,0.0004510942,0.5496231,0.00004858211,0.0006824928,0.0007335761,0.0001644705,0.4216841,0.02205152,0.002457328,0.001987964,0.00008875336],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9676178,0.001370255,0.02569582,0.0001585095,0.00004573902,0.00003866362,0.003782576,0.0003926184,0.0008980175],"genre_scores_gemma":[0.9898705,0.0002285888,0.006008679,0.00004066047,0.00001335559,0.00001427725,0.003592795,0.00004653355,0.0001846236],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.00403835,"threshold_uncertainty_score":0.01876396,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.09192144813052619,"score_gpt":0.3900441126592064,"score_spread":0.2981226645286802,"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."}}