{"id":"W2954268421","doi":"10.1101/681924","title":"RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions","year":2019,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":23,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; McGill University Health Centre","funders":"Medical Research Council; RIKEN; European Commission; Ministry of Education, Culture, Sports, Science and Technology; Wellcome Trust; Francis Crick Institute; Cancer Research UK","keywords":"Chromatin; Genome; ChIA-PET; ENCODE; Biology; Computational biology; RNA; Transcription (linguistics); Gene; Genetics; Chromosome conformation capture; Gene expression; Chromatin remodeling; Enhancer","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005115584,0.0003314792,0.0004368057,0.0005737749,0.0002759082,0.0007953084,0.0004390652,0.0004565922,0.002307919],"category_scores_gemma":[0.0004261868,0.0003180487,0.000384206,0.0003655897,0.0004070123,0.0003461836,0.00061452,0.0006128261,0.001226239],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002876551,"about_ca_system_score_gemma":0.0002802837,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007656139,"about_ca_topic_score_gemma":0.00226087,"domain_scores_codex":[0.999616,0.00003255016,0.00001290168,0.0002073962,0.00008504545,0.00004602381],"domain_scores_gemma":[0.9996943,0.00009838556,0.00005723977,0.00006259005,0.00005768348,0.00002978432],"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":[0.00006513517,0.00001098611,0.002803129,0.00007912679,0.00001586457,0.0000381344,0.00002716792,0.0005330766,0.9910632,0.0004005207,0.000355469,0.00460819],"study_design_scores_gemma":[0.00002435682,0.00009364888,0.04616566,0.00002564861,0.00004441956,0.0004498748,0.000115667,0.01823441,0.91732,0.001327326,0.01615111,0.00004794712],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.74138,0.003046522,0.2241271,0.0004663962,0.0001561392,0.0001261676,0.01164752,0.003923729,0.01512643],"genre_scores_gemma":[0.8978207,0.0007543152,0.07968747,0.000802529,0.00005720773,0.0001191508,0.0112876,0.0007596222,0.008711421],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002307919,"threshold_uncertainty_score":0.007720768,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01120096588875868,"score_gpt":0.208595073668758,"score_spread":0.1973941077799993,"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."}}