Analysis Proposal
Analysis Question
Can we validate the co-discussion and protein interaction relationships between PLA2G6 and PLA2G4A in neurodegeneration contexts?
Datasets
GTEx v8 gene expression data (brain tissue)AlzData neurodegeneration multi-omics databaseSTRING v12 protein-protein interaction databaseGWAS Catalog (neuroscience-related phenotype summary statistics)
Methods
Pearson/Spearman co-expression analysis across brain region RNA-seq cohortsBayesian network inference for shared regulatory pathwaysFunctional enrichment overlap analysis (GO, KEGG, Reactome)LDSC-based colocalization to assess shared genetic architecture
Expected Outputs
- Co-expression correlation coefficients with 95% CI and Benjamini-Hochberg adjusted p-values
- Mutual information scores and directionality indicators for regulatory relationships
- Enrichment odds ratios and FDR values for shared neuroinflammatory/oxidative stress pathways
- Colocalization posterior probabilities (PP4) indicating shared causal variants