{"id":"W4415806188","doi":"10.1038/s44319-025-00612-4","title":"Early-stage lung adenocarcinoma affects DNA methylation and gene expression in adjacent tissues","year":2025,"lang":"en","type":"article","venue":"EMBO Reports","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"National Key Research and Development Program of China; Fundamental Research Funds for the Central Universities; Chinese Society of Clinical Oncology; Fundo para o Desenvolvimento das Ciências e da Tecnologia; Beijing Health Promotion Association","keywords":"DNA methylation; Methylation; CpG site; Adenocarcinoma; Gene expression; Gene; Regulation of gene expression; Gene expression profiling; Lung cancer","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003215411,0.0001252599,0.0001386187,0.00009163824,0.00005460619,0.00002947968,0.00004192196,0.0001527217,0.000009895989],"category_scores_gemma":[0.00009980179,0.0001238422,0.00003550383,0.0001018186,0.00002471512,0.000006082529,0.0001026033,0.00006586274,5.39551e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001963426,"about_ca_system_score_gemma":0.00004000001,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000392591,"about_ca_topic_score_gemma":0.00003354209,"domain_scores_codex":[0.9990043,0.00007737898,0.0002479191,0.0003956704,0.0001127962,0.0001619311],"domain_scores_gemma":[0.999464,0.00001415457,0.0001197827,0.0003125168,0.00003835852,0.00005117024],"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":[0.00001697661,0.00002151674,0.2325708,0.00002867751,0.000009811168,0.0000429464,0.0000664364,0.0001035444,0.76502,0.00001456587,0.0001112985,0.001993478],"study_design_scores_gemma":[0.0001598425,0.00004874646,0.3025689,0.0000318649,0.000008543903,0.000003088743,0.00001298986,0.00006703154,0.693817,0.0001477157,0.003040793,0.00009349202],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9809514,0.01501315,0.002139996,0.00005588761,0.0002147644,0.0002688257,0.000001948695,0.00001137052,0.001342615],"genre_scores_gemma":[0.9968212,0.0005460574,0.001007879,0.00002869414,0.0000684288,0.00002408347,0.00006259829,0.00001289935,0.001428118],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.07120298,"threshold_uncertainty_score":0.5050139,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008118898540272972,"score_gpt":0.2708895293808543,"score_spread":0.2627706308405813,"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."}}