{"id":"W3169426933","doi":"10.3390/ijms22126295","title":"Separating the Wheat from the Chaff: The Use of Upstream Regulator Analysis to Identify True Differential Expression of Single Genes within Transcriptomic Datasets","year":2021,"lang":"en","type":"article","venue":"International Journal of Molecular Sciences","topic":"RNA modifications and cancer","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Children's Hospital of Eastern Ontario; University of Ottawa","funders":"Ontario Genomics Institute; Universidad de Granada; Fundación Ramón Areces","keywords":"Regulator; Transcriptome; Upstream (networking); Chaff; Gene; Biology; Computational biology; Gene expression; Genetics; Expression (computer science); Differential (mechanical device); Computer science; Botany; Engineering; Telecommunications","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":[0.01267356,0.001438184,0.00192835,0.003884947,0.001275745,0.003073848,0.001154006,0.001424408,0.0008793335],"category_scores_gemma":[0.01993985,0.000678383,0.002419482,0.003718799,0.002470791,0.0021807,0.002976364,0.004604993,0.0008632463],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007356461,"about_ca_system_score_gemma":0.001329097,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001086578,"about_ca_topic_score_gemma":0.001948982,"domain_scores_codex":[0.9932916,0.002355252,0.0005040643,0.002326034,0.001278094,0.0002449513],"domain_scores_gemma":[0.9855204,0.009482144,0.001267151,0.002606733,0.0008572623,0.000266256],"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":[0.001649369,0.0003672749,0.05225649,0.002630359,0.002019188,0.001016904,0.002551601,0.01247087,0.5178902,0.02030345,0.004687688,0.3821566],"study_design_scores_gemma":[0.0002856336,0.001354411,0.1638005,0.0005866262,0.001108207,0.001706746,0.001823677,0.363994,0.1687506,0.2362325,0.05978749,0.0005696789],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.07912786,0.00218468,0.9107795,0.001109714,0.000212133,0.0002222853,0.002979144,0.001800109,0.001584555],"genre_scores_gemma":[0.3616064,0.001416971,0.6250252,0.002020607,0.0003114918,0.0008123707,0.006721307,0.001147425,0.0009382187],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01267356,"threshold_uncertainty_score":0.06702495,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04028098177161388,"score_gpt":0.3254135214430627,"score_spread":0.2851325396714489,"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."}}