https://w3id.org/np/RALBS2evldaVNTa3ZAjgKk6hSD6qATRdWyeeFJ6mh2niQ/Head https://w3id.org/np/RALBS2evldaVNTa3ZAjgKk6hSD6qATRdWyeeFJ6mh2niQ http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RALBS2evldaVNTa3ZAjgKk6hSD6qATRdWyeeFJ6mh2niQ/assertion https://w3id.org/np/RALBS2evldaVNTa3ZAjgKk6hSD6qATRdWyeeFJ6mh2niQ http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RALBS2evldaVNTa3ZAjgKk6hSD6qATRdWyeeFJ6mh2niQ/provenance https://w3id.org/np/RALBS2evldaVNTa3ZAjgKk6hSD6qATRdWyeeFJ6mh2niQ http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RALBS2evldaVNTa3ZAjgKk6hSD6qATRdWyeeFJ6mh2niQ/pubinfo https://w3id.org/np/RALBS2evldaVNTa3ZAjgKk6hSD6qATRdWyeeFJ6mh2niQ http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RALBS2evldaVNTa3ZAjgKk6hSD6qATRdWyeeFJ6mh2niQ/assertion https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test http://purl.org/dc/terms/description fetch.py downloads the four files; analysis.py reuses the first-half test's GO parsing and memory-set definition. The universe is the 9,325 genes with both an MP annotation in MGI_GenePheno.rpt and an experimental GO BP annotation. For each outcome set (MP:0002006 neoplasm; MP:0001672 or MP:0008762 for embryogenesis; the 33 MP terms whose label contains 'regenerat'), it computes the unstratified odds ratio and Fisher test, and the Mantel-Haenszel odds ratio with a one-sided continuity-corrected CMH test over deciles of genes ranked by number of distinct MP terms. Secondary runs exclude channel/synaptic genes, stratify by GO depth instead, or define memory genes by MP:0002063. https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/Assessment https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 0.7349 Mantel-Haenszel odds ratio (phenotyping-depth deciles), GO learning-or-memory genes vs MP embryogenesis phenotype genes; cancer and regeneration in extra (n = 9325, one-sided CMH p = 9.696e-01). Interpretation: 'Genetic studies of cancer, regeneration and embryogenesis' are operationalised as mouse mutant phenotypes curated by MGI (MGI_GenePheno.rpt: genotypes with a mutation in one marker), mapped to genes by MGI marker ID. Outcome sets, each with all MP is_a descendants: cancer = MP:0002006 neoplasm; embryogenesis = MP:0001672 abnormal embryo development or MP:0008762 embryonic lethality; regeneration = every MP term whose label contains 'regenerat' (MP has no single regeneration parent; this includes e.g. MP:0002658 abnormal liver regeneration, MP:0000750 abnormal muscle regeneration, MP:0004858 abnormal nervous system regeneration). 'Memory genes' are defined as in the first-half test (test-data/claim-tests/levin-papers/levin-2022-tame-19): GO:0007611 learning or memory and descendants, experimental evidence codes only, so the memory set is defined independently of the MP outcome annotations. The universe is genes with at least one MP annotation in MGI_GenePheno.rpt and at least one experimental GO BP annotation. The claim's second half has no 'beyond ion channels' qualifier, so the primary analysis does not exclude channel or synaptic genes; the first-half exclusion is repeated as a secondary analysis. Secondary analyses also report the same test with the memory set defined genetically by MP:0002063 abnormal learning/memory/conditioning, and stratified by GO experimental BP depth instead of MP depth. Secondary analyses do not change the verdict. https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of levin-2022-tame-19-screens: refutes, confidence 0.65 https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/levin-papers/levin-2022-tame-19-screens/result.json https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5 https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Planned datasets: go-basic-obo, mgi-gaf, mp-obo, mgi-genepheno https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Pre-registered: the claim is refuted if the stratified odds ratio is <= 1.2 or p >= 0.05 in at least two of the three categories. Any other outcome (for example one or two categories pass) is 'mixed'. Unstratified odds ratios and raw counts ('memory genes appear at all') are reported but are not decisive, because almost any well-studied gene set 'appears' in large phenotype catalogues. https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/evidenceAgainst MGI phenotype curation is literature-driven: which phenotypes were looked for depends on each lab's interest, so 'not annotated' is not 'tested and normal'. Depth stratification controls only partly for this. A systematic screen such as IMPC, which runs every knockout through the same pipeline, would be a stronger test for viability, though IMPC barely assays learning or tumours. https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/evidenceAgainst MP has no single regeneration parent term; the regeneration set is the union of 33 label-matched terms and is small (95 genes), so that comparison is underpowered (3 overlapping genes). https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Memory genes do 'appear' in all three kinds of study (15 cancer, 45 embryogenesis and 3 regeneration genes in the primary set), as they would for nearly any gene set this size. The pre-registered test asks whether they appear more than expected; they appear slightly less than expected in all three categories once phenotyping depth is controlled, and no primary or GO-defined secondary analysis reaches significance in the claim's direction. https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Mouse only. TAME's 'genetic studies' could equally mean planarian RNAi regeneration screens, zebrafish fin-regeneration mutants or human cancer driver lists; those are not tested here. https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The one positive signal is secondary: with memory genes defined by mutant phenotype (MP:0002063, 1,248 genes) the regeneration odds ratio is 1.97 (CMH p = 0.007, 21 observed vs 12.5 expected), spread across nervous-system, liver and muscle regeneration terms. It does not meet the pre-registered p < 0.001 and is the kind of result an extension should test properly. https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Viability bias: a mouse that dies as an embryo cannot be tested for learning, which would push the embryogenesis overlap down. The effect looks modest here (11.7% of MP-memory genes are also embryonic lethal against 14.6% of all phenotyped genes, presumably through heterozygous and conditional alleles), but it biases the embryogenesis comparison against the claim. https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/expectedObservation Pre-registered: for each of the three outcome categories (cancer, regeneration, embryogenesis), the Mantel-Haenszel odds ratio of the learning-or-memory set versus the outcome set, stratified by deciles of each gene's number of distinct MP phenotype terms, is > 1.5 with one-sided Cochran-Mantel-Haenszel p < 0.001. The claim is supported if all three pass. https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/failCriterion Pre-registered: the claim is refuted if the stratified odds ratio is <= 1.2 or p >= 0.05 in at least two of the three categories. Any other outcome (for example one or two categories pass) is 'mixed'. Unstratified odds ratios and raw counts ('memory genes appear at all') are reported but are not decisive, because almost any well-studied gene set 'appears' in large phenotype catalogues. https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.65 https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-3 https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-4 https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/hasVerdict refutes https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/hypothesis Second half of the claim: mouse learning-or-memory genes are over-represented among genes whose mutants show cancer, regeneration or embryogenesis phenotypes, beyond what their depth of phenotyping explains. https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/inferenceMethod fetch.py downloads the four files; analysis.py reuses the first-half test's GO parsing and memory-set definition. The universe is the 9,325 genes with both an MP annotation in MGI_GenePheno.rpt and an experimental GO BP annotation. For each outcome set (MP:0002006 neoplasm; MP:0001672 or MP:0008762 for embryogenesis; the 33 MP terms whose label contains 'regenerat'), it computes the unstratified odds ratio and Fisher test, and the Mantel-Haenszel odds ratio with a one-sided continuity-corrected CMH test over deciles of genes ranked by number of distinct MP terms. Secondary runs exclude channel/synaptic genes, stratify by GO depth instead, or define memory genes by MP:0002063. https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/passCriterion Pre-registered: for each of the three outcome categories (cancer, regeneration, embryogenesis), the Mantel-Haenszel odds ratio of the learning-or-memory set versus the outcome set, stratified by deciles of each gene's number of distinct MP phenotype terms, is > 1.5 with one-sided Cochran-Mantel-Haenszel p < 0.001. The claim is supported if all three pass. https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/levin-2022-tame-19-screens https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/levin-2022-tame-19-screens--claim-test https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-1 http://purl.org/dc/terms/description GO hierarchy for the learning-or-memory set and the channel/synaptic exclusions https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-1 http://purl.org/dc/terms/license CC BY 4.0 https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-1 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: Gene Ontology, basic edition (go-basic.obo) https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://purl.obolibrary.org/obo/go/go-basic.obo https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-1 http://www.w3.org/ns/prov#wasDerivedFrom https://geneontology.org/docs/download-ontology/ https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:b08d45b268b8c24ccb2513dbbbc7d4df9f6521c099b413f79eb31e06e0fa3bcc https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-2 http://purl.org/dc/terms/description experimental BP annotations defining the memory gene set and the GO side of the universe https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-2 http://purl.org/dc/terms/license CC BY 4.0 https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-2 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-2 http://www.w3.org/2000/01/rdf-schema#label Dataset: Mouse Genome Informatics GO annotations (GAF 2.2), via the GO Consortium https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-2 http://www.w3.org/ns/prov#atLocation https://current.geneontology.org/annotations/mgi.gaf.gz https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-2 http://www.w3.org/ns/prov#wasDerivedFrom https://current.geneontology.org/products/pages/downloads.html https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-2 https://w3id.org/delphi/ontology/hasChecksum sha256:9b7613f786f9f805531a8f6768f310220d28c82095f938e1212c86f39596ce30 https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-3 http://purl.org/dc/terms/description phenotype hierarchy for the cancer, embryogenesis and regeneration outcome sets and the MP memory set https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-3 http://purl.org/dc/terms/license CC BY 4.0 https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-3 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-3 http://www.w3.org/2000/01/rdf-schema#label Dataset: Mammalian Phenotype Ontology https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-3 http://www.w3.org/ns/prov#atLocation https://purl.obolibrary.org/obo/mp.obo https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-3 http://www.w3.org/ns/prov#wasDerivedFrom https://obofoundry.org/ontology/mp.html https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-3 https://w3id.org/delphi/ontology/hasChecksum sha256:93bacc7a9731aec917377cf8d8f95e22b12e61d7665d180ce2d2a17d195728d3 https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-4 http://purl.org/dc/terms/description mouse mutant phenotypes: the 'genetic studies' of cancer, regeneration and embryogenesis https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-4 http://purl.org/dc/terms/license MGI terms of use (free for research, cite MGI) https://w3id.org/delphi/resource/evidence/levin-2022-tame-19-screens--claim-test--dataset-4 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem 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