{"id":"W4406699052","doi":"10.1038/s41467-025-56187-0","title":"Motif distribution and DNA methylation underlie distinct Cdx2 binding during development and homeostasis","year":2025,"lang":"en","type":"article","venue":"Nature Communications","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of Diabetes and Digestive and Kidney Diseases; Canadian Institutes of Health Research; U.S. Department of Health and Human Services; National Institutes of Health; California Institute of Regenerative Medicine; Donald E. and Delia B. Baxter Foundation; Eunice Kennedy Shriver National Institute of Child Health and Human Development; California Institute for Regenerative Medicine","keywords":"Enhancer; DNA methylation; Biology; Transcription factor; Chromatin; Epigenetics; Epigenetics of physical exercise; CpG site; CDX2; Epigenomics; Cell biology; CTCF; Genetics; Gene; Gene expression; Homeobox","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":[0.0001086984,0.0001207947,0.0001186781,0.0001781975,0.0001543337,0.0002653838,0.0001402105,0.0001858086,0.001409348],"category_scores_gemma":[0.0001319085,0.0001371612,0.0000765385,0.00008810727,0.0001791031,0.0001848267,0.0002640409,0.0001823423,0.0002257293],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000236933,"about_ca_system_score_gemma":0.0001147004,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008019571,"about_ca_topic_score_gemma":0.002075402,"domain_scores_codex":[0.9998667,0.00001329513,0.000007131287,0.00005693928,0.00002915602,0.00002663796],"domain_scores_gemma":[0.9999436,0.000009337663,0.00001490482,0.000006725461,0.000008832127,0.00001659151],"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":[0.0000482365,0.000002777627,0.002129607,0.00001198518,0.000002552777,0.00002029352,0.00002237612,0.00003494625,0.9960039,0.0001629745,0.0000144217,0.001545837],"study_design_scores_gemma":[0.00001067596,0.00008929417,0.1352706,0.000008483677,0.00001482155,0.0005785856,0.0001045384,0.00200246,0.8580118,0.0003447632,0.003556239,0.000007809167],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9934976,0.001185069,0.003761406,0.00004360964,0.000006275253,0.000006416113,0.0001416733,0.00003562235,0.001322282],"genre_scores_gemma":[0.9962623,0.0002971925,0.001126099,0.00001510762,0.000003443937,0.000008314794,0.0001633891,0.000008783923,0.00211535],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001409348,"threshold_uncertainty_score":0.004714727,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01505831356007753,"score_gpt":0.2932182348357695,"score_spread":0.2781599212756919,"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."}}