{"id":"W7116765966","doi":"10.64898/2025.12.18.695070","title":"Multi-omics analysis of TNBC organoids identifies phosphorylation of the membrane trafficking machinery as key event associated with FER-mediated invasion","year":2025,"lang":"","type":"article","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Skin and Cellular Biology Research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"KWF Kankerbestrijding","keywords":"Phosphorylation; Endosome; Organoid; Kinase; Focal adhesion; Cell membrane; Cell; Cell adhesion","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.001323687,0.0004627659,0.0008034775,0.0004974525,0.0002723889,0.00005944538,0.0007365788,0.0007666243,0.00005560124],"category_scores_gemma":[0.001555917,0.0003790589,0.0004263309,0.003749699,0.0005899384,0.00001720923,0.00035782,0.0004205256,0.000004048819],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001425658,"about_ca_system_score_gemma":0.001097771,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009332073,"about_ca_topic_score_gemma":0.0000861904,"domain_scores_codex":[0.996569,0.0006325786,0.0009283965,0.0008500453,0.0004857128,0.000534309],"domain_scores_gemma":[0.9966284,0.0001535284,0.0007994028,0.00117751,0.001109574,0.0001316057],"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":[0.0002828995,0.0005225507,0.112818,0.0001376083,0.003979331,0.00001092019,0.00002597235,0.0005932389,0.8815675,0.00003976578,0.00001801773,0.00000419424],"study_design_scores_gemma":[0.001210262,0.0001362867,0.2205294,0.0002366486,0.001354167,2.025349e-8,0.00002693095,0.003629881,0.7725053,1.527846e-7,0.00008521548,0.0002857816],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9944906,0.003286794,0.0008588216,0.0001206113,0.0003596548,0.0006264333,0.000222961,0.00002250399,0.00001161064],"genre_scores_gemma":[0.9984253,0.001148018,0.00013538,0.00008109464,0.00003578944,0.00002834062,0.00001489375,0.00005179387,0.0000793579],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1090622,"threshold_uncertainty_score":0.9998661,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00835777906057587,"score_gpt":0.2296941369064128,"score_spread":0.221336357845837,"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."}}