Fig. 2

GSEA across irMyositis, Mi2 subtype, TIF1γ subtype, and NDC. A: Dot plot of significant enrichment scores for Reactome pathways, categorized by comparison (Benjamini–Hochberg correction – BH—5% FDR). Dot size refers to the number of genes belonging to the enrichment core, i.e., genes whose coordinated fold-change led to the significant gene set enrichment score (Count). Color depicts the GSEA enrichment score normalized by its expected value under the null hypothesis, given the pathway size (NES). B: Enrichment map of the significantly enriched pathways. Node sizes reflect the cardinalities of the union of unique genes belonging to enrichment cores of a pathway, while node sectors and their colors represent relative proportions of the respective enrichment core sizes in each comparison (GSEA). If the Jaccard similarity between unions of core enrichments for two distinct gene sets is higher than 0.2, an edge is drawn to represent a functional overlap between gene sets. C: Heatmap of 33 genes, selected based on belonging to at least one comparison-wise enrichment core (top blocks), and on showing a significant F-statistics at the same time (BH, 5% FDR). Correspondence between genes and enriched pathways is encoded by black rectangles. The genes are depicted and clustered column- and row-wise according to DGE (observed log2 fold-change). Discrete color codes for B and C, are annotated collectively (Comparison). To reduce the figure complexity, we have only depicted Reactome pathways listed within the top-nine absolute-value NES per comparison (A-B), and detailed annotation for the minimum set of enriched pathways that would include all selected genes (C).