{"id":"W4300003394","doi":"10.1101/2022.10.02.508492","title":"Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics","year":2022,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":16,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Cancer Institute; National Human Genome Research Institute; Azrieli Foundation; Klarman Cell Observatory, Broad Institute; Deutsche Forschungsgemeinschaft; Ludwig Center at Harvard; National Institutes of Health; Israel Science Foundation; Hebrew University of Jerusalem; National Institute of Allergy and Infectious Diseases; Howard Hughes Medical Institute; North Carolina State University; Stand Up To Cancer; U.S. Department of Defense","keywords":"Transcriptome; Biology; Computational biology; Multicellular organism; Cell; Human disease; Cell type; Cancer; Genomics; Gene expression; Genetics; Gene; Genome","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":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003135221,0.000651464,0.0006026333,0.0001881648,0.0001839425,0.0001256966,0.0004328795,0.0007432321,0.0001627985],"category_scores_gemma":[0.0001058739,0.0007950397,0.000150161,0.0002996374,0.0001518036,0.00001219548,0.0003704166,0.0008507021,0.000003755612],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002349792,"about_ca_system_score_gemma":0.0009292837,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003966698,"about_ca_topic_score_gemma":0.001165395,"domain_scores_codex":[0.9968556,0.0002552327,0.000645571,0.001339414,0.0003559537,0.0005482544],"domain_scores_gemma":[0.9985327,0.00005025479,0.0003107081,0.000582121,0.0002855976,0.0002386696],"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":[0.0005672898,0.0003493721,0.04375501,0.0001688211,0.000125232,0.00003715577,0.00003050885,0.001012242,0.9538625,0.000007183075,0.00007357659,0.00001114542],"study_design_scores_gemma":[0.002700762,0.0002419322,0.08683129,0.000116793,0.0001651123,3.092897e-8,0.000009019011,0.002313248,0.9013217,0.000002005543,0.005238408,0.001059694],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9879676,0.0036374,0.003802968,0.00008989712,0.001972952,0.0007312117,0.00171155,0.00007354908,0.00001288283],"genre_scores_gemma":[0.9957493,0.0008632056,0.001994028,0.0002236481,0.0006721399,0.0002676456,0.00004336192,0.0001707831,0.00001590255],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.05254076,"threshold_uncertainty_score":0.99945,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01737572527715694,"score_gpt":0.1982421605158723,"score_spread":0.1808664352387154,"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."}}