Analysis Proposal
Analysis Question
Can we validate the co-discussed relationship between APOE and LDLR in neurodegeneration contexts?
Datasets
GTEx Brain Tissue Transcriptomics (v8)Alzheimer's Disease Neuroimaging Initiative (ADNI) gene expressionSTRING Protein-Protein Interaction Database v12
Methods
Spearman correlation of APOE and LDLR expression in human brain tissue samplesColocalization analysis (eCAVIAR) of APOE and LDLR brain eQTLs with AD GWAS signalsProtein-protein interaction confidence scoring using STRING physical interaction evidence
Expected Outputs
- Correlation coefficient r > 0.3 with p < 0.05 in ≥ 3 brain regions supporting transcriptional co-regulation
- Colocalization posterior probability > 0.7 indicating shared causal variant with AD risk loci
- STRING physical interaction confidence score > 0.7 (combined score) confirming direct protein interaction