{"id":"W4200349790","doi":"10.1038/s41467-021-27055-4","title":"A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer","year":2021,"lang":"en","type":"article","venue":"Nature Communications","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":48,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill Genome Centre; McGill University; McGill University Health Centre","funders":"Fonds de Recherche du Québec - Santé; Cancer Research Society; Canadian Institutes of Health Research; Fondation de l'Hôpital Général de Montréal; National Natural Science Foundation of China; McGill University","keywords":"Enhancer; SOX2; Biology; Chromatin; Activator (genetics); Cancer research; Transcription factor; Oncogene; CRISPR; Cell biology; Molecular biology; Cancer; Genetics; Gene; Cell cycle","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":[0.0001012995,0.00009128624,0.00009118124,0.00001535944,0.0001853642,0.00002598915,0.0003365293,0.000163986,0.000007137276],"category_scores_gemma":[0.00003852713,0.00006456935,0.00003064998,0.00008110108,0.00006439468,0.000002326231,0.0002164491,0.0001986801,4.031693e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001967279,"about_ca_system_score_gemma":0.0001461712,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000007085219,"about_ca_topic_score_gemma":0.001630279,"domain_scores_codex":[0.9994534,0.00005119737,0.000113627,0.0001970892,0.00006030729,0.0001243776],"domain_scores_gemma":[0.9989184,0.00006047348,0.00006801389,0.0007863303,0.0001383898,0.00002843199],"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":[0.00005780499,0.0001365144,0.0006639067,0.0000240167,0.00002305396,4.975158e-7,0.000539235,0.0001447022,0.9936467,0.0003582588,0.003857816,0.0005474462],"study_design_scores_gemma":[0.001207625,0.0001109869,0.003942606,0.00006329767,0.00004128509,0.00001513901,0.0009675194,0.003455041,0.843755,0.00004204017,0.1461546,0.0002448661],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9561031,0.03794422,0.0005280519,0.004418195,0.00003773826,0.0003458353,0.0001825762,0.000004163966,0.0004361644],"genre_scores_gemma":[0.9929987,0.003138602,0.002398076,0.0006106638,0.00002999297,0.0002348217,0.0002501906,0.00001455828,0.0003244518],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1498918,"threshold_uncertainty_score":0.2633062,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0125978908024423,"score_gpt":0.3053365178321263,"score_spread":0.292738627029684,"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."}}