{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0008701416,0.0001147461,0.0001127167,0.00007801264,0.0001816879,0.00003589547,0.0003641927,0.0001119892,0.0001495592],"category_scores_gemma":[0.0003034205,0.00006253146,0.0001332806,0.0001408951,0.0001644086,0.000005412868,0.0001000008,0.000128341,0.00004510748],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009065135,"about_ca_system_score_gemma":0.0001356277,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004300517,"about_ca_topic_score_gemma":0.000007405028,"domain_scores_codex":[0.9985496,0.0002314315,0.0002022954,0.0002713078,0.0003804428,0.0003649428],"domain_scores_gemma":[0.9991226,0.00008262818,0.00006418362,0.0004591363,0.0002022065,0.00006920028],"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":[0.0001313886,0.0000809372,0.001305945,0.00000741958,0.00004642228,6.078532e-7,0.0001086563,0.00004190973,0.9795285,0.0000727936,0.0002463104,0.01842907],"study_design_scores_gemma":[0.002366797,0.01067923,0.09956124,0.0001983648,0.00001876008,0.00001545938,0.0003704294,0.003859605,0.8803312,0.001144503,0.001018142,0.0004362284],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9978964,0.00004332511,0.0001738911,0.0002004254,0.00006916865,0.000217081,0.000076289,0.000006298711,0.001317078],"genre_scores_gemma":[0.9989232,0.00007239045,0.0001976749,0.00001101236,0.0001344475,0.000009076298,0.00001218719,0.00003033927,0.0006096982],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0991973,"threshold_uncertainty_score":0.2549959,"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."}}