Analysis Proposal
Analysis Question
Can we validate the proposed associated_with and interacts_with relationships between microglia involvement in neurodegeneration and the microglial receptor TREM2?
Datasets
PubMed/MEDLINE literature corpus for semantic co-occurrence analysisGEO/ArrayExpress transcriptomic datasets from microglial cells under neurodegeneration conditionsSTRING/BioGRID protein-protein interaction databases for TREM2 network analysis
Methods
Named entity recognition and semantic relation extraction from abstracts to quantify co-occurrence frequency of microglia, neurodegeneration, and TREM2Differential expression analysis of TREM2 in microglial cells across neurodegeneration models versus controlsProtein interaction network construction from curated databases to identify direct and indirect connectivity pathsCross-validation using pathway enrichment tools (KEGG, Reactome) for microglial-neurodegeneration pathways containing TREM2
Expected Outputs
- Co-occurrence frequency metrics (TF-IDF scores, PMI values) quantifying literature evidence strength
- Differential expression fold-change and p-values for TREM2 in microglial neurodegeneration datasets
- Network graph showing interaction confidence scores and shortest paths between microglia markers and TREM2
- Quantitative confidence scores for each relation type (associated_with: pathway enrichment p-value; interacts_with: interaction database evidence score)