Analysis Proposal
Analysis Question
Can we validate the co-discussed relationship between ANGPT1 and PDGFRB in neurodegeneration contexts?
Datasets
Brainspan developmental transcriptome (Allen Brain Atlas)Mayo Clinic LOAD RNA-seq dataset (syn2589203)Accelerating Medicines Partnership Alzheimer's Disease AMP-AD knowledge portal
Methods
Pearson correlation of normalized RNA-seq expression in prefrontal cortex and hippocampus across LOAD cases vs. controlsSTRING-db protein-protein interaction score extraction with confidence threshold ≥0.7Gene Set Enrichment Analysis (GSEA) against KEGG vascular smooth muscle contraction and PI3K-Akt signaling pathways
Expected Outputs
- Significant positive correlation (r > 0.3, p < 0.05) in disease-relevant brain regions would support biological relevance of co-discussion
- Physical interaction evidence ( STRING confidence ≥0.7 ) or shared pathway membership would provide mechanistic plausibility
- Absence of correlation across independent cohorts would refute the relationship and flag the edge as spurious literature co-occurrence