{"id":"W4416179711","doi":"10.1016/j.immuni.2025.10.020","title":"FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry","year":2025,"lang":"en","type":"article","venue":"Immunity","topic":"T-cell and B-cell Immunology","field":"Immunology and Microbiology","cited_by":6,"is_retracted":false,"has_abstract":false,"ca_institutions":"","funders":"European Research Council; JDRF; Horizon 2020 Framework Programme; University of California, San Francisco; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; Rheumatology Research Foundation; National Research Foundation; Arthritis National Research Foundation; Juvenile Diabetes Research Foundation Canada; Lotte und Adolf Hotz-Sprenger Stiftung; European Commission; Childhood Arthritis and Rheumatology Research Alliance; Innovative Genomics Institute; James B. Pendleton Charitable Trust; Parker Institute for Cancer Immunotherapy; NOMIS Stiftung; Gilead Sciences; Arc Institute; Stanford Maternal and Child Health Research Institute; GlaxoSmithKline; National Institutes of Health; Pew Charitable Trusts; Lupus Foundation of America; Gladstone Institutes; Simons Foundation; Lupus Research Alliance; National Science Foundation; Cancer Research Institute; AstraZeneca; Larry L. Hillblom Foundation; Howard Hughes Medical Institute","keywords":"FOXP3; Transcription factor; Gene silencing; Cell; Mutagenesis; CRISPR; Regulation of gene expression; Transcription (linguistics); Transcriptional regulation","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow","insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0002105252,0.0002877622,0.0003342947,0.0002272874,0.0005548654,0.00002674184,0.0003414803,0.0004958463,0.001036973],"category_scores_gemma":[0.00001896511,0.0002625157,0.00009775775,0.0001796302,0.0002599815,0.000117251,0.0001267369,0.0007608247,0.0003293908],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007199877,"about_ca_system_score_gemma":0.00005425523,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00007108431,"about_ca_topic_score_gemma":0.00001146889,"domain_scores_codex":[0.9983101,0.0004275543,0.0003946907,0.0003884798,0.0000501235,0.0004289939],"domain_scores_gemma":[0.9990202,0.0001372118,0.0001144601,0.0006326602,0.0000691062,0.00002635628],"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":[0.0003961123,0.000402747,0.001478191,0.00003466268,0.00007944587,0.000002811545,0.00036202,6.850574e-7,0.9799832,0.0003689087,0.002793223,0.01409807],"study_design_scores_gemma":[0.002322657,0.000290247,0.02409967,0.00007334483,0.0000294723,0.000008071685,0.0003893943,6.670265e-7,0.9064513,0.0003139649,0.0657801,0.0002410423],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9825839,0.009190224,0.0001225156,0.00007932316,0.002028289,0.0002591621,0.00003144025,0.0001263104,0.005578769],"genre_scores_gemma":[0.9909867,0.0006258481,0.00002744334,0.0001955506,0.00001949573,0.00001742558,0.0001625825,0.00001961697,0.007945335],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.07353176,"threshold_uncertainty_score":0.9999827,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0186679207336558,"score_gpt":0.238211640668609,"score_spread":0.2195437199349532,"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."}}