{"id":"W2089528193","doi":"10.1371/journal.pcbi.1002256","title":"Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers","year":2011,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"Child and Family Research Institute; University of British Columbia","funders":"National Institute of General Medical Sciences; Canadian Institutes of Health Research; Michael Smith Health Research BC","keywords":"MyoD; C2C12; Computational biology; Biology; Enhancer; Myogenesis; Regulatory sequence; Functional genomics; Conserved sequence; Sequence (biology); Genetics; Gene; Regulation of gene expression; Genomics; Genome; Gene expression; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002156518,0.0004101299,0.0004957382,0.0005609096,0.0002497916,0.000436549,0.000550162,0.0002829635,0.001105557],"category_scores_gemma":[0.004335531,0.0002228983,0.0004633883,0.0004521939,0.0002915918,0.0002622563,0.0003623033,0.0003772763,0.0003542279],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002063715,"about_ca_system_score_gemma":0.0005578394,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001153457,"about_ca_topic_score_gemma":0.002004151,"domain_scores_codex":[0.9995056,0.0001663506,0.00002654874,0.0001582217,0.00009990422,0.00004337219],"domain_scores_gemma":[0.9975387,0.001951275,0.0001249517,0.0001338731,0.000187923,0.00006328724],"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":[0.003610952,0.0004261869,0.1705254,0.0006347172,0.0005066416,0.0006272923,0.000325974,0.3364876,0.3668115,0.002104886,0.001087471,0.1168515],"study_design_scores_gemma":[0.0001170724,0.0004060989,0.03575576,0.00002787689,0.0001510428,0.0002284894,0.0000684668,0.8649439,0.09640858,0.001169904,0.0006943019,0.00002852175],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9787003,0.00009900272,0.01928277,0.00003557988,0.000003757653,0.00002443411,0.00063995,0.0006161784,0.0005980138],"genre_scores_gemma":[0.9760556,0.00004044231,0.02167006,0.00003322705,0.000002945656,0.00002752214,0.001898912,0.0001023282,0.0001691137],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002156518,"threshold_uncertainty_score":0.01140487,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0246268502432785,"score_gpt":0.2295387458150918,"score_spread":0.2049118955718133,"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."}}