{"id":"W4411951820","doi":"10.1101/2025.06.27.661997","title":"Confidence: A Web App for Cross-Platform Differential Gene Expression Analysis, Gene Scoring, and Enrichment Analysis","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Gene expression and cancer classification","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Queen's University","funders":"Canadian Institutes of Health Research; Mitacs; Queen's University","keywords":"Gene; Gene expression; Computational biology; Differential (mechanical device); Genetics; Biology; Computer science; Engineering","routes":{"ca_aff":true,"ca_fund":true,"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":[0.003361117,0.003002291,0.001686181,0.003408884,0.0005943519,0.001954411,0.003407311,0.001663999,0.07609338],"category_scores_gemma":[0.005420971,0.001670187,0.001445887,0.001335952,0.0004672394,0.001849839,0.00333352,0.002284437,0.03877236],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006170389,"about_ca_system_score_gemma":0.0009722419,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001097317,"about_ca_topic_score_gemma":0.001769328,"domain_scores_codex":[0.9984383,0.0002240363,0.0001416175,0.0002900019,0.000769227,0.0001368319],"domain_scores_gemma":[0.9964309,0.002156349,0.0002672814,0.0003190875,0.0005556415,0.0002707063],"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":[0.002324887,0.0005355531,0.004619027,0.002515025,0.0005756324,0.001476194,0.0003099517,0.003945296,0.03448972,0.004373098,0.7663902,0.1784454],"study_design_scores_gemma":[0.002872011,0.0007251887,0.02794673,0.001458926,0.0004541358,0.003041762,0.0002356398,0.2217818,0.1020766,0.02838629,0.6097243,0.001296613],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.005471188,0.0006400957,0.1953818,0.0003997631,0.0003294709,0.0008790155,0.04421224,0.7463447,0.006341758],"genre_scores_gemma":[0.07458537,0.001510953,0.5758684,0.004241741,0.0005759235,0.01074698,0.121676,0.1755399,0.03525466],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.07609338,"threshold_uncertainty_score":0.2545577,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0135401586137089,"score_gpt":0.2691177869479683,"score_spread":0.2555776283342594,"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."}}