Fig. 2

DE statistics for case versus RHI comparisons. Early and late stage CTE versus RHI controls showed general concordance in direction of DE genes, but mixed agreement on the biological process level. A, B) Distribution of log2 fold change for DE genes with FDR < 0.1 for both CTE-H versus RHI and CTE-L versus RHI, respectively. C Log2 fold change values for DE genes with FDR < 0.1 in either CTE-H or CTE-L analyses. D Normalized Enrichment Scores (NES) from Gene Set Enrichment Analysis (GSEA) of GO terms from the c5 MSigDB curated GO annotation at FDR < 0.1. Gene sets significant in both analyses are highlighted and colored based on concordance (i.e. same or different direction of effect). E Hierarchically clustered heatmap of NES for enriched GO terms from D that have nominal p-value less than 0.05 in both CTE-H versus RHI and CTE-L versus RHI. Diamond and X markers correspond to GO terms significant at FDR < 0.1 in both from D. GO term names are colored red if the direction of effect is discordant between analyses. NS—GO namespace of corresponding term: BP—biological process, CC—cellular component, MF—molecular function