{"id":"W4281736544","doi":"10.4049/jimmunol.2100717","title":"Characterization of Proteasome-Generated Spliced Peptides Detected by Mass Spectrometry","year":2022,"lang":"en","type":"article","venue":"The Journal of Immunology","topic":"vaccines and immunoinformatics approaches","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"Princess Margaret Cancer Centre; University of Toronto; University Health Network","funders":"Japan Society for the Promotion of Science; Ministry of Education, Culture, Sports, Science and Technology; Japan Agency for Medical Research and Development; Takeda Science Foundation","keywords":"Minigene; RNA splicing; Human leukocyte antigen; Alternative splicing; Proteasome; Biology; Computational biology; Antigen processing; Antigenicity; Peptide; CD8; Molecular biology; Chemistry; Genetics; Biochemistry; Antigen; Gene; MHC class I; Messenger RNA","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":[0.0004677303,0.0001003312,0.0001864079,0.00008546204,0.0001212262,0.000007852315,0.0003978468,0.00005706729,0.00006167127],"category_scores_gemma":[0.00005037327,0.00007234989,0.00007611499,0.0001925891,0.00005136176,0.000007927023,0.0001383724,0.0002249834,0.000001093259],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002207774,"about_ca_system_score_gemma":0.00007048713,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000005836401,"about_ca_topic_score_gemma":3.684731e-7,"domain_scores_codex":[0.9990265,0.0001948768,0.0004507086,0.00005929957,0.0001207139,0.0001479182],"domain_scores_gemma":[0.9989237,0.0000119906,0.0006835366,0.0002263505,0.0001377423,0.00001667448],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0004710679,0.00005530961,0.0001267829,0.000007486438,0.0002077243,4.226631e-7,0.0001249499,0.00004870854,0.9982303,0.00001169581,0.0001836781,0.0005318611],"study_design_scores_gemma":[0.0007027129,0.001394356,0.003539469,0.000004334119,0.00003364481,0.0002485432,0.0005246655,0.0001143846,0.9907855,0.00002357638,0.002543467,0.00008528971],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9950745,0.001213793,0.003189179,0.0001673068,0.0001349524,0.0001458664,0.00002347393,0.000002923752,0.00004808068],"genre_scores_gemma":[0.9986361,0.0004842047,0.0004437995,0.00005732901,0.00005277104,0.000007246255,0.00008707722,0.00001391835,0.0002175227],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.007444756,"threshold_uncertainty_score":0.2950343,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007063977529069372,"score_gpt":0.2002777321120184,"score_spread":0.193213754582949,"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."}}