{"id":"W2517051411","doi":"10.1038/nmeth.3963","title":"Impact of outdated gene annotations on pathway enrichment analysis","year":2016,"lang":"en","type":"letter","venue":"Nature Methods","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":154,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Toronto; Ontario Institute for Cancer Research","funders":"National Human Genome Research Institute","keywords":"Annotation; Gene; Gene Annotation; Computational biology; Pathway analysis; Genome; Biology; Vocabulary; Genetics; Bioinformatics; Gene expression; Linguistics","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":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.02342089,0.0005933538,0.001041092,0.001222031,0.001044867,0.002490925,0.001743336,0.002043446,0.002391909],"category_scores_gemma":[0.1054467,0.0003586836,0.001198151,0.001814663,0.001310996,0.001761368,0.001906706,0.005194713,0.001486327],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001289037,"about_ca_system_score_gemma":0.001353592,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002219366,"about_ca_topic_score_gemma":0.006067021,"domain_scores_codex":[0.9865946,0.00651975,0.001054713,0.001375133,0.003969891,0.000486007],"domain_scores_gemma":[0.8909169,0.08491456,0.001774835,0.009610818,0.0114472,0.001335807],"domain_codex":null,"domain_gemma":"methods","domain_candidate":"methods","domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.004105835,0.0003643015,0.07150871,0.001417683,0.001725552,0.003385621,0.0007953904,0.005755784,0.03572134,0.01815426,0.1946426,0.662423],"study_design_scores_gemma":[0.0007639886,0.0007816218,0.08240151,0.001908362,0.003172702,0.01900147,0.001083807,0.1386756,0.08733875,0.3170185,0.3473381,0.0005154917],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"commentary","genre_gemma":"empirical","genre_scores_codex":[0.2704885,0.03781389,0.2251979,0.383124,0.04844947,0.0002786965,0.009559478,0.004294205,0.02079389],"genre_scores_gemma":[0.6689205,0.01050844,0.1538178,0.1361093,0.01854824,0.0002676317,0.004090982,0.001878538,0.005858531],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.9765791,"threshold_uncertainty_score":0.123863,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01140573330550317,"score_gpt":0.3556122688996559,"score_spread":0.3442065355941527,"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."}}