{"id":"W3111845758","doi":"10.1016/j.stemcr.2020.11.005","title":"TINC— A Method to Dissect Regulatory Complexes at Single-Locus Resolution— Reveals an Extensive Protein Complex at the Nanog Promoter","year":2020,"lang":"en","type":"article","venue":"Stem Cell Reports","topic":"CRISPR and Genetic Engineering","field":"Biochemistry, Genetics and Molecular Biology","cited_by":15,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Manitoba; Research Institute in Oncology and Hematology; CancerCare Manitoba","funders":"Australian Research Council; Medical Research Council; National Health and Medical Research Council; State Government of Victoria; Australian Government; Stem Cells Australia; Howard Hughes Medical Institute","keywords":"Biology; Homeobox protein NANOG; Chromatin; Epigenome; Nanog Homeobox Protein; Embryonic stem cell; Gene; Promoter; Transcription factor; Computational biology; Genetics; Psychological repression; Regulation of gene expression; Epigenetics; Transcriptional regulation; Cell biology; Gene expression; DNA methylation; Induced pluripotent stem cell","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":[0.0003667163,0.0002461954,0.0002519057,0.00002270616,0.0002088951,0.00003266241,0.0001608265,0.0001142163,0.00005325058],"category_scores_gemma":[0.00004109935,0.000195305,0.0001223069,0.0001121105,0.00005604128,0.000003788366,0.0003917243,0.00008274941,0.00001455528],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005436518,"about_ca_system_score_gemma":0.00004180993,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001262474,"about_ca_topic_score_gemma":0.00003398601,"domain_scores_codex":[0.9981015,0.0001622292,0.0004361612,0.000708883,0.000244631,0.000346543],"domain_scores_gemma":[0.998641,0.00001465779,0.0001809174,0.0007822713,0.0001263103,0.0002548915],"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":[0.00007796774,0.0000288363,0.0002274177,0.00006274887,0.00002384076,0.000103915,0.0003536069,0.0007614266,0.9918829,0.000004065972,0.005484668,0.0009886513],"study_design_scores_gemma":[0.000137444,0.0004171207,0.001593718,0.00002338207,0.00002422586,0.0003290782,0.00009728344,0.0001188125,0.928421,0.00001562228,0.06854703,0.0002753062],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9862208,0.0007537236,0.009891738,0.0005854788,0.00009240983,0.001072501,0.000019382,0.00004642426,0.001317549],"genre_scores_gemma":[0.9894508,0.000002561741,0.004978236,0.0004661675,0.0002351675,0.00007491474,0.0001067874,0.00005166077,0.004633732],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06346188,"threshold_uncertainty_score":0.7964308,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02509391573438511,"score_gpt":0.2939416247603897,"score_spread":0.2688477090260045,"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."}}