{"id":"W2071042066","doi":"10.1371/journal.pone.0016432","title":"An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq","year":2011,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":48,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; BC Cancer Agency; Université Laval; Montreal Clinical Research Institute","funders":"British Columbia Knowledge Development Fund; National Institutes of Health; BC Cancer Foundation; Vancouver Foundation; Genome British Columbia; National Human Genome Research Institute; Michael Smith Health Research BC; National Institute of Environmental Health Sciences; Genome Canada; Heart and Stroke Foundation of Canada","keywords":"Bioconductor; Computer science; Computational biology; Pipeline (software); Genome browser; CTCF; Chip; Visualization; Genome; DNA binding site; Transcription factor; Data mining; Biology; Genetics; Genomics; Gene; Enhancer; Gene expression; Operating system","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":[0.005690694,0.004200409,0.002749082,0.003776445,0.001650302,0.002325768,0.005479519,0.001341348,0.02655212],"category_scores_gemma":[0.00657603,0.002657186,0.003031754,0.002982204,0.0007367557,0.001594752,0.003699531,0.004535163,0.02571293],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001555313,"about_ca_system_score_gemma":0.004297716,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00553972,"about_ca_topic_score_gemma":0.007873309,"domain_scores_codex":[0.9971411,0.0003875169,0.0003578375,0.001005718,0.0008072568,0.0003006623],"domain_scores_gemma":[0.9975709,0.0006518087,0.0002011972,0.0005570045,0.0007730675,0.0002459015],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.002047848,0.0005265153,0.005782516,0.003243994,0.001251467,0.0008178466,0.0008159628,0.01405179,0.226586,0.007270614,0.4090853,0.3285202],"study_design_scores_gemma":[0.001549427,0.0006786133,0.0332561,0.0004624149,0.0009829139,0.001965613,0.0002175751,0.2158169,0.2188556,0.03551592,0.4894481,0.001250745],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.003982166,0.0003605826,0.7342937,0.0003135351,0.0002468025,0.001126308,0.06080748,0.1964017,0.002467689],"genre_scores_gemma":[0.01199314,0.0003134673,0.8445553,0.0003811084,0.00007052378,0.004275512,0.1189036,0.01619337,0.003313886],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.02655212,"threshold_uncertainty_score":0.08882564,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0429347746975812,"score_gpt":0.224433465548659,"score_spread":0.1814986908510778,"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."}}