To see if specific biological pathways were implicated in PTSD, gene-based test statistics were used to perform a competitive set-based analysis of 10,894 pre-defined curated gene sets and GO terms obtained from MsigDB using MAGMA. Significance of pathways was set at a Bonferroni-corrected threshold of P = 0.05/10,894 = 4.6 × 10−6. To test if tissue-specific gene expression was associated with PTSD, gene-set-based analysis was also used with expression data from GTEx v7 RNA-seq and BrainSpan RNA-seq, where the expression of genes within specific tissues were used to define the gene properties used in the gene-set analysis model.
