{"id":"W4400533732","doi":"10.1186/s12864-024-10602-w","title":"Genome-wide analysis of histone modifications can contribute to the identification of candidate cis-regulatory regions in the threespine stickleback fish","year":2024,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":8,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Core Research for Evolutional Science and Technology; Institute of Genetics; Japan Society for the Promotion of Science","keywords":"Biology; H3K4me3; Chromatin; Genetics; Histone; Epigenetics; Epigenomics; Regulatory sequence; Gene; Stickleback; Enhancer; Computational biology; Indel; Genome; Regulation of gene expression; Promoter; Gene expression; Single-nucleotide polymorphism; DNA methylation","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000209532,0.0002630083,0.0001675835,0.0005572668,0.0001825404,0.000221949,0.0001490193,0.0002394548,0.001619939],"category_scores_gemma":[0.0001935799,0.0001034904,0.000271661,0.0004228008,0.0001267306,0.00009528107,0.0002062187,0.0002138474,0.0002435791],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002034766,"about_ca_system_score_gemma":0.0001302945,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002615195,"about_ca_topic_score_gemma":0.006119155,"domain_scores_codex":[0.9999269,0.000005133923,0.000004726254,0.00003706354,0.00001712504,0.000008880238],"domain_scores_gemma":[0.9998215,0.00004972558,0.00006920529,0.00001570085,0.00002169159,0.00002216087],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001433693,0.00002069963,0.05421476,0.0001332616,0.00009383669,0.0000882293,0.00006482562,0.0002987353,0.9381586,0.00005599137,0.00008982261,0.00663784],"study_design_scores_gemma":[0.000008794569,0.00009700981,0.9510038,0.00001376287,0.0001210153,0.0001871462,0.00009212083,0.001322476,0.04567248,0.0001424798,0.001328507,0.00001026868],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9930732,0.000597171,0.003573698,0.00003138324,0.000006994198,0.00001518445,0.001995831,0.00007966776,0.0006269824],"genre_scores_gemma":[0.9913128,0.0002268631,0.004771581,0.00006551201,0.00000610453,0.00002695174,0.003043215,0.00002183352,0.0005250293],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002615195,"threshold_uncertainty_score":0.005419195,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01160291108716706,"score_gpt":0.2601319942140595,"score_spread":0.2485290831268925,"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."}}