{"id":"W2160953907","doi":"10.7554/elife.02626","title":"Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways","year":2014,"lang":"en","type":"article","venue":"eLife","topic":"RNA Research and Splicing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":107,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; SickKids Foundation","funders":"European Research Council; Natural Sciences and Engineering Research Council of Canada; EMBO; Canada Research Chairs; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; Institut National de la Santé et de la Recherche Médicale; Wellcome; European Molecular Biology Laboratory; Wellcome Trust; Consejo Nacional de Ciencia y Tecnología; Cancer Research UK; Sick Kids Foundation","keywords":"Biology; Transcription factor; Gene; DNA binding site; Conserved sequence; Genetics; Promoter; Genome; Cis-regulatory module; Human genome; Computational biology; DNA sequencing; Gene expression; Enhancer; Peptide sequence","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":[0.0002691804,0.0001701197,0.0002536386,0.00005795939,0.000104958,0.00002533696,0.0002252389,0.0002063551,0.00005623041],"category_scores_gemma":[0.000164846,0.000134159,0.000108258,0.00007059606,0.0001381673,0.000005001299,0.00004291354,0.0001143471,0.00004206308],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001671279,"about_ca_system_score_gemma":0.0000321732,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002339853,"about_ca_topic_score_gemma":0.00003637093,"domain_scores_codex":[0.9986311,0.0001699321,0.0002978625,0.0003556299,0.0001985523,0.0003469048],"domain_scores_gemma":[0.9992686,0.00004006548,0.00009394695,0.0003016491,0.0001397928,0.0001559374],"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":[0.0001147064,0.00009938268,0.005012982,0.00001288014,0.00002976409,0.000002660288,0.00002960718,0.000006383194,0.9932234,0.0002262667,0.0003188499,0.0009230686],"study_design_scores_gemma":[0.002158751,0.0005035198,0.02930559,0.00001615409,0.000003902358,0.000002917715,0.00003758917,0.0005573788,0.8749728,0.00000129075,0.0922655,0.0001746199],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9480051,0.0008031981,0.0504722,0.00009557747,0.0001578163,0.0002669485,0.0001007529,0.0000246263,0.00007377611],"genre_scores_gemma":[0.995742,0.00058654,0.002370507,0.00008733218,0.0001965113,0.0000179608,0.0001266415,0.00001754898,0.0008549913],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1182507,"threshold_uncertainty_score":0.5470844,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06486844271219598,"score_gpt":0.2769052932645588,"score_spread":0.2120368505523628,"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."}}