{"id":"W4290973443","doi":"10.1371/journal.pcbi.1010348","title":"Nine quick tips for pathway enrichment analysis","year":2022,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":79,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"","keywords":"Relevance (law); Computer science; Data science; Simple (philosophy); Software; Computational biology; Biology; Programming language","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":[0.01649503,0.00481866,0.002061311,0.006542072,0.002078817,0.004981754,0.00475822,0.004279869,0.05562745],"category_scores_gemma":[0.1307079,0.002665149,0.003084669,0.004457812,0.001927664,0.006496494,0.005800846,0.007799721,0.0461035],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001730082,"about_ca_system_score_gemma":0.004269675,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001267121,"about_ca_topic_score_gemma":0.004379826,"domain_scores_codex":[0.9846814,0.006812191,0.002822671,0.001079793,0.003975912,0.000628039],"domain_scores_gemma":[0.8813782,0.06348196,0.004220351,0.007212719,0.03934294,0.004363837],"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":[0.000413098,0.0001714228,0.001738491,0.004238921,0.0001708837,0.0009935256,0.0008894689,0.002014842,0.004686345,0.01287692,0.6763924,0.2954137],"study_design_scores_gemma":[0.00029924,0.0003133044,0.002557998,0.004472839,0.0001727553,0.002164087,0.0008226484,0.009216353,0.008729747,0.07851218,0.8923895,0.00034926],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.003242203,0.006129623,0.8710378,0.01708918,0.006587276,0.00205574,0.008372247,0.07181591,0.01367005],"genre_scores_gemma":[0.006183086,0.002791345,0.9582844,0.006364629,0.000954059,0.001881295,0.004823337,0.009289835,0.009428001],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.05562745,"threshold_uncertainty_score":0.1860924,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01256881737139967,"score_gpt":0.2415497012157091,"score_spread":0.2289808838443094,"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."}}