{"id":"W4386520053","doi":"10.1016/j.mcpro.2023.100644","title":"Pulse-SILAC and Interactomics Reveal Distinct DDB1-CUL4–Associated Factors, Cellular Functions, and Protein Substrates","year":2023,"lang":"en","type":"article","venue":"Molecular & Cellular Proteomics","topic":"Ubiquitin and proteasome pathways","field":"Biochemistry, Genetics and Molecular Biology","cited_by":11,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Sherbrooke","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"DDB1; Stable isotope labeling by amino acids in cell culture; Ubiquitin; Cullin; Ubiquitin-Protein Ligases; Ubiquitin ligase; F-box protein; Biochemistry; Cell division control protein 4; Proteasome; Protein degradation; Chemistry; Ubiquitin-conjugating enzyme; Cell biology; Biology; Proteomics","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":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0006514129,0.0005332242,0.0004382411,0.0001573882,0.0003045751,0.0001724537,0.0002677958,0.0004746103,0.00001993146],"category_scores_gemma":[0.0004768347,0.0005334484,0.0001735432,0.0003404206,0.0002606759,0.00002143747,0.0004024271,0.0004067885,0.0000350461],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005498934,"about_ca_system_score_gemma":0.0001088544,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004307819,"about_ca_topic_score_gemma":0.00002217894,"domain_scores_codex":[0.9973188,0.0002923827,0.0005066959,0.0009350491,0.000271848,0.0006751954],"domain_scores_gemma":[0.998697,0.00003161945,0.0002456204,0.0005694968,0.0001686288,0.0002875837],"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":[0.00008841225,0.00005945626,0.002553983,0.0001444306,0.0001688399,0.00008173168,0.0001458148,0.00001246801,0.9957958,0.0001406431,0.0002436673,0.0005646785],"study_design_scores_gemma":[0.0007646251,0.0003089554,0.000634448,0.00009302652,0.00006848147,0.00001946299,0.0002969048,0.0004937658,0.9936218,0.0007434441,0.002338566,0.000616473],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9942137,0.002308017,0.001107087,0.0002076308,0.0001692752,0.001465216,0.0001595401,0.0001371227,0.0002323883],"genre_scores_gemma":[0.9948369,0.0001742503,0.0005695107,0.00008575519,0.0001308329,0.000222607,0.001842498,0.0001236008,0.002014023],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002174027,"threshold_uncertainty_score":0.9997117,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01183512832779534,"score_gpt":0.2181980030361695,"score_spread":0.2063628747083741,"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."}}