{"id":"W3027341723","doi":"10.1101/gr.250704.119","title":"Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle","year":2020,"lang":"en","type":"article","venue":"Genome Research","topic":"Genetic and phenotypic traits in livestock","field":"Biochemistry, Genetics and Molecular Biology","cited_by":232,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Biotechnology and Biological Sciences Research Council; Agricultural Research Service; Oak Ridge Institute for Science and Education; National Institute of Food and Agriculture; Medical Research Council Canada; U.S. Department of Agriculture; United States - Israel Binational Agricultural Research and Development Fund; Medical Research Council; Directorate for Biological Sciences; U.S. Department of Energy","keywords":"Biology; Transcriptome; Gene; Genetics; Epigenomics; Computational biology; Genome; DNA methylation; Quantitative trait locus; RNA-Seq; Genome-wide association study; Somatic cell; Evolutionary biology; Gene expression; Single-nucleotide polymorphism","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001077242,0.00009506709,0.000187405,0.00006490507,0.00005218105,0.0000101334,0.0001994449,0.00008480025,0.00002999867],"category_scores_gemma":[0.00008803934,0.00008592875,0.00005368033,0.0001804989,0.0003075651,0.00000172971,0.00007010715,0.0001007336,0.000002416779],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005340466,"about_ca_system_score_gemma":0.00005898111,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001804684,"about_ca_topic_score_gemma":0.00001173096,"domain_scores_codex":[0.9989556,0.0001361236,0.0002189266,0.0003267005,0.0001111514,0.0002514693],"domain_scores_gemma":[0.9995203,0.00009230103,0.00002828598,0.0001112695,0.0001498528,0.00009797133],"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":[0.0001437028,0.00004463456,0.0009202241,0.00009652525,0.00004115947,2.566586e-7,0.0008280402,0.0005401096,0.9933382,0.0001696299,0.0001410974,0.003736431],"study_design_scores_gemma":[0.0008657667,0.002140739,0.9206942,0.0000147578,0.00001423949,0.000003858212,0.001040936,0.000243881,0.06449194,0.001243445,0.00903873,0.0002074548],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9631671,0.004331597,0.03135795,0.0004095959,0.00001281363,0.0004268122,0.0001102429,0.000003865759,0.0001799825],"genre_scores_gemma":[0.9739327,0.0002106025,0.02551909,0.0001180586,0.00006158523,0.00005412086,0.00006018029,0.00001010322,0.000033525],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9288462,"threshold_uncertainty_score":0.3504073,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.2122884698811956,"score_gpt":0.4252405037112863,"score_spread":0.2129520338300907,"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."}}