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Outcomes meeting neither criterion are pre-registered as 'mixed' (overlap present but not specific, or explained by annotation depth)." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "GO annotations reflect what has been studied: genes are annotated to learning or memory largely because they were knocked out and tested behaviourally, which happens mostly to genes already well studied in development. Annotation-depth stratification addresses this only approximately." }, { "@value": "Mouse only and experimental evidence only. TAME frames the prediction across animals; other species or inclusion of inferred annotations could differ." }, { "@value": "Only the first half of the claim is tested. Whether memory genes appear in cancer, regeneration and embryogenesis screens is not addressed." }, { "@value": "Size-matched control terms include developmental processes adjacent to morphogenesis (axon, limb, cardiac chamber, neural tube development) with very high odds ratios, which raises the 75th-percentile bar; the depth-stratified result does not depend on this choice." }, { "@value": "The GO release is 'current' at retrieval time and is not versioned in the URL; re-running later will fetch a newer release, so exact numbers will drift. The SHA-256 above identifies the files used." }, { "@value": "The crude overlap is real: 69 genes against 34 expected (odds ratio 2.66, p = 1.1e-9), and removing channel, gap-junction and neurotransmission genes barely changes it (2.64 before exclusion). It does not survive control for annotation depth: learning-or-memory genes sit almost entirely in the most-annotated strata, and within the top decile (13-167 BP terms) 43 of 63 of them (68%) are morphogenesis genes against 621 of 961 other genes (65%). The pre-registered fail rule is met by the Mantel-Haenszel odds ratio (0.94 <= 1.2). The control comparison (64.5th percentile) fails pass criterion (c) but does not by itself meet the fail rule, since 2.66 is above the control median of 1.87." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "Pre-registered: after exclusions, (a) the one-sided Fisher exact test of overlap between the learning-or-memory set (GO:0007611 and is_a/part_of descendants) and the morphogenesis set (GO:0009653 and descendants) gives odds ratio > 1.5 and p < 0.001; (b) the Mantel-Haenszel odds ratio stratified by deciles of each gene's number of experimental BP annotations is > 1.5; (c) the unstratified odds ratio is above the 75th percentile of odds ratios between the morphogenesis set and every control BP term whose post-exclusion gene count is within a factor of 1.5 of the learning-or-memory set's and which is neither an ancestor nor a descendant of GO:0007611 or GO:0009653." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Pre-registered: unstratified odds ratio <= 1.2 or p >= 0.05, or Mantel-Haenszel odds ratio <= 1.2, or the odds ratio at or below the median of the size-matched control terms. Outcomes meeting neither criterion are pre-registered as 'mixed' (overlap present but not specific, or explained by annotation depth)." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.7", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/levin-2022-tame-19--claim-test--dataset-1" }, { "@id": "https://w3id.org/delphi/resource/evidence/levin-2022-tame-19--claim-test--dataset-2" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "refutes" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "Among mouse genes with experimental Gene Ontology biological-process annotations, genes annotated to learning or memory are over-represented among genes annotated to anatomical structure morphogenesis, even after removing ion channels, gap-junction channels and neurotransmission genes, and this overlap is larger than the overlap of morphogenesis with other biological-process terms of similar size." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "fetch.py downloads go-basic.obo and the MGI GAF. analysis.py drops NOT-qualified and obsolete-term lines, builds each gene's set of experimental BP terms and their is_a/part_of ancestors, removes 612 genes annotated to ion channel, gap junction or neurotransmission terms, and tests overlap of GO:0007611 and GO:0009653 in the remaining 10,243 genes with a one-sided Fisher exact test. 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