{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00008001886,0.0001051403,0.0001925871,0.00006245251,0.00005240512,0.00001277447,0.0002069634,0.00008848334,0.00009082825],"category_scores_gemma":[0.00003478975,0.00008017192,0.0001286457,0.0001349433,0.0000341881,0.00000318709,0.00001629827,0.00004554696,0.000001451121],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000009524783,"about_ca_system_score_gemma":0.00001789129,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001291268,"about_ca_topic_score_gemma":0.0005555914,"domain_scores_codex":[0.99937,0.00002349737,0.0002086138,0.0002009059,0.00007469918,0.0001222983],"domain_scores_gemma":[0.9994197,0.00002135229,0.0001037021,0.000314637,0.0001015108,0.00003909092],"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":[0.00006650394,0.000336669,0.01485866,0.00001200517,0.001423913,9.519024e-8,0.0003786813,0.00006136552,0.9825796,0.000006708202,0.000004537516,0.0002712797],"study_design_scores_gemma":[0.0003865844,0.0002604197,0.07665443,0.00001110014,0.002051066,6.711317e-8,0.0003639173,0.04624392,0.8736683,0.00007199022,0.00009732934,0.0001909519],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9766515,0.0002251305,0.02195692,0.00002163565,0.00001722582,0.0001835191,0.0009072022,0.000007893431,0.00002897787],"genre_scores_gemma":[0.9910458,0.0001694801,0.005969652,0.00004646167,0.000051212,0.00001772421,0.002598697,0.00001708984,0.00008385368],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1089114,"threshold_uncertainty_score":0.3269316,"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."}}