{"id":"W2137531873","doi":"10.1038/nprot.2007.324","title":"Integration of biological networks and gene expression data using Cytoscape","year":2007,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2574,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Toronto","funders":"National Institute of General Medical Sciences","keywords":"Computational biology; Biological network; Gene regulatory network; Gene ontology; Functional genomics; Gene expression profiling; Computer science; Interaction network; Systems biology; Genomics; Context (archaeology); Bioinformatics; Gene expression; Biology; Gene; Data mining; Genome; Genetics","routes":{"ca_aff":true,"ca_fund":false,"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":[0.002560448,0.00131697,0.001336426,0.003406986,0.001095346,0.002358122,0.002169862,0.0009112018,0.01516839],"category_scores_gemma":[0.007629653,0.001172518,0.001391011,0.003095386,0.0004244601,0.001895304,0.001668348,0.003556664,0.004041513],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005678431,"about_ca_system_score_gemma":0.001814998,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004192532,"about_ca_topic_score_gemma":0.006133392,"domain_scores_codex":[0.9990461,0.0001788594,0.0001180673,0.0002152503,0.0003794863,0.00006230163],"domain_scores_gemma":[0.9965544,0.001947875,0.0001994058,0.0007515223,0.0003411472,0.0002056315],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.002125281,0.0007817224,0.006578697,0.008031537,0.003915856,0.001514438,0.001945608,0.06096717,0.2203903,0.07244914,0.2193019,0.4019984],"study_design_scores_gemma":[0.0004078764,0.000148838,0.006532314,0.0004310236,0.0008179773,0.001036756,0.0002327807,0.3215811,0.1767325,0.1509882,0.3406394,0.0004512505],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.01474647,0.0005499051,0.7098837,0.000759211,0.0006339091,0.0004923484,0.05224066,0.212331,0.008362855],"genre_scores_gemma":[0.1107597,0.001408877,0.7596877,0.0005626252,0.000210872,0.002355652,0.09921424,0.01871834,0.007082069],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01516839,"threshold_uncertainty_score":0.05074334,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04112985887454766,"score_gpt":0.3468823061421621,"score_spread":0.3057524472676144,"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."}}