{"id":"W2128612482","doi":"10.1101/gr.104356.109","title":"Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver","year":2010,"lang":"en","type":"article","venue":"Genome Research","topic":"Pancreatic function and diabetes","field":"Medicine","cited_by":118,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre; Child and Family Research Institute; Sunny Hill Health Centre for Children; University of British Columbia; BC Children's Hospital; BC Cancer Agency","funders":"National Institutes of Health; Michael Smith Health Research BC; Genome British Columbia; Canadian Institutes of Health Research; Canada's Michael Smith Genome Sciences Centre; Genome Canada","keywords":"FOXA2; Enhancer; Biology; H3K4me3; Transcription factor; Nucleosome; DNA binding site; Promoter; Histone; PDX1; Binding site; Genetics; Gene expression; Gene; Cell biology","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":[],"consensus_categories":[],"category_scores_codex":[0.001611888,0.0001097857,0.0002478503,0.0002103208,0.0002284667,0.00005590956,0.00006194803,0.0001136357,0.0005225845],"category_scores_gemma":[0.0002899808,0.00007995314,0.00002696663,0.0002512901,0.0009051228,0.00008873174,0.0001104153,0.0005100567,0.00001627834],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003244613,"about_ca_system_score_gemma":0.0001004631,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004356307,"about_ca_topic_score_gemma":0.00004844648,"domain_scores_codex":[0.9985874,0.0001494511,0.0002229578,0.0003006581,0.0004186891,0.0003208843],"domain_scores_gemma":[0.9988652,0.0004129972,0.00004422314,0.0003006623,0.0001964455,0.000180477],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001019705,0.0002885323,0.5066833,0.0008434916,0.0001778786,0.00005668566,0.002108169,0.000001363293,0.4724582,0.005517925,0.0016407,0.009203984],"study_design_scores_gemma":[0.001412486,0.0002745019,0.9860755,0.00004761599,0.00002671255,0.00008382208,0.0002537031,0.000190226,0.002589931,0.001975277,0.006980191,0.00009004589],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9900452,0.002811946,0.000007197689,0.00139053,0.00003891226,0.0003871126,0.00002453588,0.00001279614,0.005281778],"genre_scores_gemma":[0.9975355,0.0006776737,0.0001143579,0.0001375456,0.0001075368,0.00001986751,0.00001943268,0.00001299907,0.001375104],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4793922,"threshold_uncertainty_score":0.5721933,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04309563251233253,"score_gpt":0.346445542826439,"score_spread":0.3033499103141064,"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."}}