{"id":"W2883298629","doi":"10.1038/sdata.2018.141","title":"MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations","year":2018,"lang":"en","type":"article","venue":"Scientific Data","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":19,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Children's Hospital; University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; Norges Forskningsråd; Universitetet i Oslo; European Molecular Biology Laboratory; Western Canada Research Grid; Weston Brain Institute; BC Children's Hospital; Children's Hospital Foundation; Compute Canada; Canadian Institutes of Health Research; Genome Canada","keywords":"DNA binding site; Genome; Binding site; Biology; Transcription factor; 1000 Genomes Project; Computational biology; Genetics; Database; Single-nucleotide polymorphism; Computer science; Gene; Promoter; Gene expression; Genotype","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":[0.0003772765,0.0000554178,0.00007683662,0.00005203872,0.0002299527,0.00004535848,0.000734659,0.00002614025,0.00003099074],"category_scores_gemma":[0.00004682983,0.00003443608,0.00007781528,0.0003262474,0.0002440904,0.000008638519,0.0002694083,0.00002198102,0.000002366168],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000003530972,"about_ca_system_score_gemma":0.00004076715,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002166861,"about_ca_topic_score_gemma":0.00100956,"domain_scores_codex":[0.9993287,0.00002087867,0.0001771072,0.0002735452,0.0001033723,0.00009644245],"domain_scores_gemma":[0.998123,0.00001195385,0.0001182277,0.001629289,0.0001006142,0.00001692441],"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":[0.000008005094,0.0000231773,0.0003450823,0.00001085952,0.0001741821,1.568085e-8,0.0001045804,0.00008283225,0.99323,0.0001014829,0.005422575,0.0004971754],"study_design_scores_gemma":[0.0004799967,0.00006885178,0.009749421,0.00002283295,0.001439866,0.000001506916,0.0003364942,0.2549517,0.5871673,0.00005533491,0.1455091,0.0002176146],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9300339,0.00008322205,0.02186672,0.0001023687,0.0004646137,0.0001708688,0.04725822,0.000001508505,0.00001858648],"genre_scores_gemma":[0.9804984,0.00002903397,0.001283989,0.0000210062,0.00004506221,0.000004037729,0.01776269,0.000005083587,0.0003506359],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4060627,"threshold_uncertainty_score":0.1768633,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03316037739362557,"score_gpt":0.2848577802092167,"score_spread":0.2516974028155911,"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."}}