{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001137874,0.0001337352,0.0001354058,0.00005112976,0.0001453612,0.000006299209,0.00005979877,0.0002368035,0.00001047363],"category_scores_gemma":[0.00001765673,0.0001230423,0.00001796379,0.00007681673,0.0002298986,0.000001922419,0.00007444803,0.00006097325,0.000008221659],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000208277,"about_ca_system_score_gemma":0.00003016948,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006033728,"about_ca_topic_score_gemma":0.00006649299,"domain_scores_codex":[0.9991962,0.00006379055,0.0001497754,0.0003487143,0.00002716871,0.0002143097],"domain_scores_gemma":[0.9997281,0.000007652795,0.0000467929,0.00009885177,0.00007095753,0.00004760606],"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":[0.0001177539,0.00001962356,0.06671137,0.000008674431,0.00001301093,4.42061e-7,0.0002021395,0.000007659968,0.9325489,0.00008167921,0.00003504746,0.0002537426],"study_design_scores_gemma":[0.0008371613,0.001222089,0.8729106,0.000009763577,0.00002468663,0.00002218003,0.0002246197,0.00008634567,0.1178748,0.001126193,0.005398967,0.0002626285],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9749841,0.02323869,0.001111879,0.00004879827,0.0001998014,0.0001498345,0.00002108147,0.00000460805,0.0002411741],"genre_scores_gemma":[0.9972069,0.001815343,0.00049508,0.00004421655,0.00020441,0.000009882796,0.00005605359,0.000009300023,0.0001588414],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8146741,"threshold_uncertainty_score":0.501752,"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."}}