{"id":"W2290481676","doi":"10.1093/molbev/msw030","title":"Decreased Transcription Factor Binding Levels Nearby Primate Pseudogenes Suggest Regulatory Degeneration","year":2016,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"SickKids Foundation; University of Toronto","funders":"","keywords":"Biology; Pseudogene; Nonsynonymous substitution; Genetics; Transcription factor; Frameshift mutation; Gene; Lineage (genetic); Regulatory sequence; DNA binding site; Coding region; Evolutionary biology; Mutation; Promoter; Gene expression; Genome","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0001419588,0.0002493604,0.0002698998,0.0005282931,0.0002579452,0.000254378,0.0002691502,0.0004018582,0.003284753],"category_scores_gemma":[0.0005001645,0.0001935847,0.0001999284,0.0002967471,0.0004360186,0.0002115466,0.0002176056,0.0003627071,0.0004790924],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001489031,"about_ca_system_score_gemma":0.0001111123,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005952709,"about_ca_topic_score_gemma":0.0008116288,"domain_scores_codex":[0.9998486,0.00002082594,0.00001010348,0.00006603239,0.00003728216,0.00001708126],"domain_scores_gemma":[0.9995096,0.0001512056,0.0001537027,0.00005858914,0.00005267949,0.00007420395],"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":[0.00008900194,0.000004774485,0.007701687,0.0000321158,0.000009039942,0.00007153049,0.0000581455,0.00008846678,0.9910052,0.0001164671,0.00001077191,0.0008128473],"study_design_scores_gemma":[0.00001500797,0.0003688337,0.559709,0.00001664184,0.00005656221,0.002612974,0.0003017792,0.002438435,0.4302673,0.001232203,0.00295662,0.00002467203],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9957579,0.0003752199,0.002854196,0.00002669213,0.000004532079,0.000003255968,0.0002245222,0.00005731837,0.0006963874],"genre_scores_gemma":[0.996403,0.000138509,0.002256136,0.00004845222,0.000005072601,0.000009808236,0.0004910054,0.00001717699,0.0006308616],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003284753,"threshold_uncertainty_score":0.01098859,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009216506899146201,"score_gpt":0.2398911400766655,"score_spread":0.2306746331775193,"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."}}