{"artifact":{"id":"analysis_proposal-3a5e701f-57b2-4894-8f5d-97d16d6b0f3a","artifact_type":"analysis_proposal","entity_ids":"[\"ent-gene-28e2cb01\", \"microglia\"]","title":"Analysis Proposal: ent-gene-28e2cb01 -> microglia [expressed_in]","quality_score":0.5,"created_by":"analysis_proposal_generator","provenance_chain":"[]","content_hash":"dfd5f6f55640f9cdc3773da7d03d40701d239162431cc0471f8763d37b2298f0","metadata":{"_origin":{"url":null,"type":"internal","tracked_at":"2026-04-28T06:36:56.911718"},"methods":["Query gene expression levels in microglial clusters from snRNA-seq data using established markers (TYROBP, CX3CR1, TREM2) as positive controls for cell-type annotation accuracy","Perform differential expression analysis comparing microglia vs. other brain cell types to quantify cell-type specificity scores","Cross-validate against published microglia-specific gene signatures (e.g., 257-gene human microglial catalog from Geirsdottir et al., 2019) using overlap statistics and rank correlation","Apply Bayesian integration across datasets to compute posterior probability of cell-type-specific expression"],"datasets":["Human Brain Cell Atlas (HBCA) single-nucleus RNA-seq reference","Allen Brain Cell Atlas microglial snRNA-seq profiles","Nuclei from the dorsolateral prefrontal cortex (DLPFC) - PsychENCODE","ADNI post-mortem brain tissue bulk RNA-seq with microglial deconvolution"],"edge_count":3,"source_entity":"ent-gene-28e2cb01","target_entity":"microglia","edge_signature":"[\"ent-gene-28e2cb01|microglia|expressed_in\"]","_schema_version":1,"confidence_range":[1.0,1.0],"expected_outputs":["Cell-type specificity score (tau or specificity metric) for ent-gene-28e2cb01 in microglia relative to neuronal, astrocytic, and oligodendrocyte populations","Statistical significance (adjusted p-value) from differential expression comparing microglial vs. non-microglial cells with log2 fold-change magnitude","Cross-dataset concordance report indicating whether expression is validated in ≥2 independent datasets or contradicting evidence found","Final trust score update recommendation (increase, maintain, or decrease confidence) for the expressed_in edge based on accumulated evidence weight"],"source_relations":["expressed_in"],"analysis_question":"Can we validate the relationship between ent-gene-28e2cb01 and microglia through expression evidence in neurodegeneration-relevant datasets?"},"created_at":"2026-04-27T23:36:56.911828-07:00","updated_at":"2026-04-27T23:36:56.911828-07:00","version_number":4,"parent_version_id":null,"version_tag":null,"changelog":null,"is_latest":1,"lifecycle_state":"active","superseded_by":null,"deprecated_at":null,"deprecated_reason":null,"dependencies":null,"market_price":0.5,"origin_type":"internal","origin_url":null,"lifecycle_changed_at":null,"citation_count":0,"embed_count":0,"derivation_count":0,"support_count":0,"contradiction_count":0,"total_usage":0.0,"usage_score":0.5,"usage_computed_at":null,"quality_status":null,"contributors":[],"answers_question_ids":null,"deprecated_reason_detail":null,"deprecated_reason_code":null,"commit_sha":null,"commit_submodule":null,"last_mutated_at":"2026-05-16T14:51:34.657673-07:00","disputed_at":null,"gap_id":null,"mission_id":null,"intrinsic_priority":null,"effective_priority":null,"artifact_id":"70e7d325-1f2f-470a-a154-195ebdcf4c20","artifact_dir":null,"primary_filename":null,"accessory_filenames":null,"folder_layout_version":1,"migrated_to_folder_at":null,"hypothesis_id":null,"authorship":{"kind":"human","contributors":[{"role":"author","actor_ref":"analysis_proposal_generator"}]},"epistemic_tier":"T3_provisional","created_by_agent_id":null},"outgoing_links":[{"target_artifact_id":"kg_edge-a82841fc-78d0-4de9-919b-5def55ad183b","link_type":"derives_from","strength":0.5,"evidence":"Proposal derives from source low-confidence KG edge"},{"target_artifact_id":"wiki-MICROGLIA","link_type":"cites","strength":0.5,"evidence":"Proposal cites relevant entity wiki page"}],"incoming_links":[],"current_artifact_id":"analysis_proposal-3a5e701f-57b2-4894-8f5d-97d16d6b0f3a","is_canonical":true,"supersede_chain":["analysis_proposal-3a5e701f-57b2-4894-8f5d-97d16d6b0f3a"]}