{"id":"W2113833510","doi":"10.1093/nar/gki624","title":"oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes","year":2005,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":378,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research","keywords":"Biology; Gene; DNA binding site; Genetics; Computational biology; Opossum; Transcription factor; False positive paradox; Promoter; Functional genomics; Gene expression profiling; Genomics; Genome; Gene expression; Computer science","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":[0.0007935204,0.0006056362,0.0006819691,0.001456802,0.0004045042,0.000615951,0.00052945,0.0003739669,0.001334714],"category_scores_gemma":[0.001329822,0.0003031803,0.0006275013,0.001025841,0.0005016169,0.0004393983,0.0009317891,0.0003744697,0.0002905772],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004907456,"about_ca_system_score_gemma":0.000526669,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003568052,"about_ca_topic_score_gemma":0.005596539,"domain_scores_codex":[0.9996112,0.00004877126,0.00001780846,0.0001634456,0.0001025626,0.00005620759],"domain_scores_gemma":[0.999517,0.0002273986,0.0001293534,0.00004932824,0.0000388056,0.00003807678],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.002634054,0.0001854399,0.08933106,0.0006938695,0.0004384912,0.001010523,0.0005511742,0.03649412,0.6164914,0.003714369,0.003566265,0.2448892],"study_design_scores_gemma":[0.0002748161,0.0005425593,0.1704764,0.00007537296,0.0004682925,0.002819578,0.000383805,0.5616114,0.2410701,0.009180446,0.01296719,0.000129975],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8097823,0.0006791633,0.1813882,0.0001395013,0.00002288255,0.00008746285,0.002157183,0.004690689,0.001052611],"genre_scores_gemma":[0.6924372,0.0003364747,0.2997438,0.00009299898,0.00001377924,0.0001357195,0.005638729,0.000443101,0.001158121],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003568052,"threshold_uncertainty_score":0.007094562,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04135626195073181,"score_gpt":0.3443882632611404,"score_spread":0.3030320013104086,"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."}}