{"id":"W2791552580","doi":"10.1093/gbe/evy016","title":"Pervasive Correlated Evolution in Gene Expression Shapes Cell and Tissue Type Transcriptomes","year":2018,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":68,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"John Templeton Foundation; National Science Foundation","keywords":"Biology; Transcriptome; Phylogenetic tree; Gene; Evolutionary biology; Phylogenetics; Lineage (genetic); Genetics; Computational biology; Gene regulatory network; Hierarchical clustering; RNA-Seq; Gene expression profiling; Gene expression; Cluster analysis","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":[0.0004551983,0.0001346862,0.0003101974,0.0007174662,0.0002946022,0.0005474939,0.0001716095,0.0002740201,0.000477577],"category_scores_gemma":[0.0009744211,0.0002064242,0.0003465843,0.0007274924,0.0004654907,0.00032988,0.0003979605,0.000368127,0.0002009011],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002658817,"about_ca_system_score_gemma":0.0001785317,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005878208,"about_ca_topic_score_gemma":0.001336233,"domain_scores_codex":[0.9995384,0.00008431385,0.00002083196,0.0002262738,0.00007700158,0.00005322823],"domain_scores_gemma":[0.9991502,0.0003355261,0.0002051591,0.0001350817,0.0001154215,0.00005865577],"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":[0.0001573183,0.00003019429,0.1100538,0.00007586371,0.0001067143,0.0001031077,0.0003087344,0.002295712,0.8749934,0.0006821509,0.0001212197,0.01107184],"study_design_scores_gemma":[0.000005060631,0.00006554014,0.9558963,0.00001051415,0.00005657267,0.0002486678,0.0001863898,0.01308225,0.02830368,0.001025929,0.001096597,0.00002251456],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9918858,0.0002206895,0.006523386,0.00002391306,0.000004145192,0.000008235353,0.0005750083,0.00004440499,0.0007143678],"genre_scores_gemma":[0.9943208,0.0001177306,0.004218664,0.00005737567,0.000005159871,0.0000230321,0.0009202735,0.00003295624,0.0003039352],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0007174662,"threshold_uncertainty_score":0.002407372,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007376209515875694,"score_gpt":0.2277539628779052,"score_spread":0.2203777533620295,"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."}}