{"id":"W2517051411","doi":"10.1038/nmeth.3963","title":"Impact of outdated gene annotations on pathway enrichment analysis","year":2016,"lang":"en","type":"letter","venue":"Nature Methods","topic":"Bioinformatics and Genomic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":"codex-gemma-dda1882f352a","candidate_categories":["research_integrity"],"consensus_categories":[],"category_scores_codex":[0.0005867486,0.0003477253,0.0005285935,0.0002803855,0.00004762318,0.0000200732,0.0003582967,0.002379176,0.00008060478],"category_scores_gemma":[0.00009125252,0.0002307891,0.0008278701,0.0003560316,0.00005752584,0.000001916856,0.00009830838,0.001120322,0.000006518025],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005349208,"about_ca_system_score_gemma":0.0001447893,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000008289851,"about_ca_topic_score_gemma":0.000002106949,"domain_scores_codex":[0.9983011,0.0003083158,0.000440291,0.0004026917,0.0002078846,0.0003396804],"domain_scores_gemma":[0.9982958,0.00009710466,0.0004326618,0.0009038292,0.0002099082,0.00006070168],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00006765725,0.00003769821,0.0001839746,0.00003753326,0.005441001,0.000008967125,0.00003718253,0.00031267,0.06373353,0.00002657663,0.8855619,0.04455134],"study_design_scores_gemma":[0.0004193687,0.0004799925,0.001294672,0.00002571715,0.0007108097,0.000005169944,0.000002500415,0.0001796267,0.03167424,0.000277989,0.9644411,0.0004888695],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"commentary","genre_scores_codex":[0.01797299,0.01279876,0.8161896,0.1185461,0.004131672,0.002076622,0.00913057,0.00009823523,0.01905544],"genre_scores_gemma":[0.05177297,0.001184594,0.4087467,0.4746332,0.01629691,0.0001377349,0.03128694,0.0002818472,0.0156591],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.4074429,"threshold_uncertainty_score":0.998916,"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."}}