{"id":"W4411158875","doi":"10.1101/2025.06.08.653722","title":"RetiGene, a comprehensive gene atlas for inherited retinal diseases (IRDs)","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Montreal Children's Hospital; McGill Genome Centre; McGill University Health Centre","funders":"Instituto de Salud Carlos III; Fonds de Recherche du Québec - Santé; Vlaamse regering; Generalitat Valenciana; Fonds Wetenschappelijk Onderzoek; Fondazione Telethon; Bijzonder Onderzoeksfonds UGent; National Institutes of Health; Foundation Fighting Blindness; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; Leids Universitair Medisch Centrum; Universiteit Gent; European Regional Development Fund; Fondation de l'Hôpital de Montréal pour enfants; European Commission; Fight for Sight UK; Children's Hospital Foundation; Canadian Institutes of Health Research; National Science Foundation","keywords":"Computational biology; Gene; Biology; Candidate gene; Disease; Genetics; Medicine","routes":{"ca_aff":true,"ca_fund":true,"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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0001580416,0.0006839582,0.0006427199,0.0001568528,0.0002230063,0.0001483892,0.0006841226,0.0008507628,0.00001114397],"category_scores_gemma":[0.0002036356,0.0007742514,0.0004306149,0.0002368636,0.0001863046,0.000006312157,0.0004623672,0.0004047516,0.000007211448],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009284793,"about_ca_system_score_gemma":0.0008327639,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004425244,"about_ca_topic_score_gemma":0.000006339516,"domain_scores_codex":[0.9970558,0.0001315334,0.0005750524,0.001379531,0.0002470613,0.0006110514],"domain_scores_gemma":[0.9971644,0.00004724869,0.0003041869,0.001306997,0.0008930099,0.000284147],"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":[0.0004082239,0.0002030087,0.004204924,0.00068161,0.0003352659,0.00001415531,0.000004038187,0.0001160161,0.991721,0.0001066123,0.002200342,0.000004847023],"study_design_scores_gemma":[0.001336007,0.0002493278,0.02698237,0.0003519916,0.0003295677,3.055248e-8,0.000002618151,0.0004060683,0.8973188,0.000005339671,0.07192791,0.001089961],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9769306,0.0062506,0.01001309,0.0001803782,0.001763572,0.001396001,0.0032652,0.0001812846,0.00001924466],"genre_scores_gemma":[0.9859825,0.001239315,0.01011316,0.0006799286,0.001276154,0.0004684199,0.00003471119,0.0001416376,0.00006413244],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.09440215,"threshold_uncertainty_score":0.9994708,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01654046446744615,"score_gpt":0.2333744745929247,"score_spread":0.2168340101254785,"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."}}