{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000363816,0.0002649222,0.0003872315,0.0007896255,0.0004285605,0.0006724467,0.0001372126,0.0002216356,0.00133861],"category_scores_gemma":[0.000384044,0.0001587577,0.000395371,0.001085632,0.0002263115,0.0002975119,0.0005157917,0.0003168713,0.0004259644],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002614778,"about_ca_system_score_gemma":0.0004002692,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002175604,"about_ca_topic_score_gemma":0.005896027,"domain_scores_codex":[0.9997211,0.00003508668,0.00001588202,0.0001125522,0.00006004458,0.00005533127],"domain_scores_gemma":[0.9997609,0.0000753379,0.00005537988,0.00003207126,0.00004789764,0.00002832504],"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":[0.0002155644,0.00001754796,0.04715221,0.0002403446,0.0001533201,0.0001154916,0.0002828643,0.001748596,0.9262738,0.0005674936,0.000561793,0.02267085],"study_design_scores_gemma":[0.00001878289,0.000135429,0.8849851,0.00005689857,0.0003471865,0.0005433902,0.0006404674,0.01206472,0.07989465,0.002188829,0.01906993,0.00005466854],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.952574,0.002151765,0.02705024,0.00009341894,0.00002294714,0.00002471579,0.01503929,0.0003011508,0.002742438],"genre_scores_gemma":[0.9461629,0.001516529,0.02542239,0.0001686113,0.00003746461,0.0001113235,0.0236966,0.0002467468,0.002637431],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002175604,"threshold_uncertainty_score":0.004478037,"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."}}