{"artifact":{"id":"analysis_proposal-f1d5e63e-3207-48cd-ad5c-1d3f0896b153","artifact_type":"analysis_proposal","entity_ids":"[\"CHR2\", \"BDNF\"]","title":"Analysis Proposal: CHR2 -> BDNF [co_discussed, interacts_with]","quality_score":0.5,"created_by":"analysis_proposal_generator","provenance_chain":"[]","content_hash":"6b3c82a199bbdfc91223e4fadcf0570e3b4e5e39dc9224e5a0c57045571726cb","metadata":{"_origin":{"url":null,"type":"internal","tracked_at":"2026-04-28T07:05:26.779422"},"methods":["Automated literature mining extracting co-mention frequency and experimental context from PubMed; scoring by sentence-level proximity and MeSH term co-occurrence.","Cross-reference CHR2-BDNF interaction confidence in STRING database, filtering for physical interaction evidence from experimental assays (experimental_score ≥0.400).","Conduct Pearson correlation analysis of CHR2 and BDNF mRNA expression across brain regions and disease states using bulk and single-cell RNA-seq datasets.","Perform enrichment analysis to determine whether CHR2 and BDNF share significant pathway membership (e.g., neurotrophin signaling, synaptic plasticity) relevant to neurodegeneration."],"datasets":["PubMed abstracts via PubTator/Europe PMC API","STRING protein interaction database (confidence cutoff ≥0.400)","RNA-seq expression data from neurodegeneration cohorts (e.g., ROSMAP, Knight-ADNI)","Gene Ontology and KEGG pathway enrichment resources"],"edge_count":2,"source_entity":"CHR2","target_entity":"BDNF","edge_signature":"[\"CHR2|BDNF|co_discussed\", \"CHR2|BDNF|interacts_with\"]","_schema_version":1,"confidence_range":[0.4,0.434],"expected_outputs":["Frequency matrix of CHR2-BDNF co-mentions by publication year, tissue type, and experimental method (optogenetics, qPCR, ELISA); evidence supporting or refuting biological context for co_discussed.","Interaction confidence score from STRING with evidence type breakdown (experimental, database, text-mining); confirmation of physical BDNF-CHR2 binding or absence thereof.","Scatter plots and correlation coefficients (r, p-value) for CHR2 vs. BDNF expression; differential expression profiles in neurodegenerative vs. control tissue.","Pathway overlap statistics (Fisher's exact test p-value, overlap ratio) and shared GO term annotations; validation that CHR2 and BDNF converge on mechanistically relevant neurodegeneration pathways."],"source_relations":["co_discussed","interacts_with"],"analysis_question":"Can we validate the co-discussion and protein interaction relationships between CHR2 (channelrhodopsin-2) and BDNF in neurodegeneration contexts?","generation_method":"llm"},"created_at":"2026-04-28T00:05:26.779538-07:00","updated_at":"2026-04-28T00:05:26.779538-07:00","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":"3f980f78-321d-49a6-b0c9-3f22ee417bcd","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-8be62d73db60","link_type":"derives_from","strength":0.4,"evidence":"Proposal clusters 2 low-confidence edges"},{"target_artifact_id":"kg_edge-02e1363c6aaf","link_type":"derives_from","strength":0.434,"evidence":"Proposal clusters 2 low-confidence edges"},{"target_artifact_id":"wiki-proteins-bdnf","link_type":"cites","strength":0.5,"evidence":"Proposal cites relevant entity wiki page"}],"incoming_links":[],"current_artifact_id":"analysis_proposal-f1d5e63e-3207-48cd-ad5c-1d3f0896b153","is_canonical":true,"supersede_chain":["analysis_proposal-f1d5e63e-3207-48cd-ad5c-1d3f0896b153"]}