{"id":"W2734981423","doi":"10.1371/journal.pgen.1006883","title":"Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses","year":2017,"lang":"en","type":"article","venue":"PLoS Genetics","topic":"Chromosomal and Genetic Variations","field":"Agricultural and Biological Sciences","cited_by":192,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; Japan Society for the Promotion of Science","keywords":"Biology; DNA binding site; Transcription factor; Genetics; Long terminal repeat; Endogenous retrovirus; Computational biology; Regulatory sequence; GATA transcription factor; Gene; Genome; Promoter; Gene expression","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":[],"consensus_categories":[],"category_scores_codex":[0.00006954463,0.00007346462,0.0001447367,0.00000651288,0.0003677249,0.00008868905,0.0001934777,0.00004837834,0.00005777391],"category_scores_gemma":[0.00004514411,0.00003565585,0.00002674915,0.00002598866,0.00004952795,0.00005292568,0.00006864119,0.00002332788,0.000006586939],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008166096,"about_ca_system_score_gemma":0.000003569073,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002815175,"about_ca_topic_score_gemma":0.0000894245,"domain_scores_codex":[0.9992522,0.00004266807,0.0003113628,0.0001584038,0.0001506621,0.00008472051],"domain_scores_gemma":[0.9992947,0.00003002497,0.0004162429,0.000149981,0.00007073153,0.00003833926],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.000001519039,0.00004456858,0.03799799,0.0001112987,0.00002667017,2.595553e-7,0.0001015141,1.347327e-7,0.9613181,0.00003454679,4.497024e-7,0.0003628958],"study_design_scores_gemma":[0.00005711929,0.00003807905,0.5668871,0.0001066097,0.00004874452,4.879677e-7,0.00002520553,0.0001055231,0.4324224,0.0002493689,0.000005808967,0.00005352434],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9992989,0.0001109561,0.000002457753,0.00006341904,0.00005295382,0.0002761699,0.0001309996,0.0000135811,0.00005054621],"genre_scores_gemma":[0.9995924,0.00006116052,0.00005247543,0.00001440208,0.00009569606,0.00001684131,0.0001281178,0.000001025147,0.00003783505],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5288958,"threshold_uncertainty_score":0.282828,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05073707396468481,"score_gpt":0.2313981089769613,"score_spread":0.1806610350122764,"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."}}