Fig. 2: Enrichment analysis identifies subtype-specific disease pathways.
From: Molecular subtypes of ALS are associated with differences in patient prognosis
a Benjamini-Hochberg adjusted p-values, derived from a Fisher’s exact test, are presented on the –log10 scale. All presented pathways are significantly enriched in at least one subtype. Negative enrichment is encoded as the negative magnitude of the –log10(adjusted p-value). P, Fisher’s exact test, one-tailed, Benjamini-Hochberg method for multiple hypothesis test correction. b–d Gene sets enriched in each ALS subtype are presented along the Y-axis, with GSEA normalized enrichment score (NES) presented along the X-axis. e Heatmap of transposable element expression, with 426 unique TEs and 544 biologically independent transcriptomes. Patient samples were plotted by subgroup, with the thin black lines denoting sample separation by subtype. TE count values were subject to VST, followed by z-score normalization, with red indicating elevated expression. f–k Pathways enriched specifically for one or more subtypes were generated using GSEA rank metric scores. Genes comprising each functional pathway are included, with subtype-specific gene enrichment scores encoded on a red-blue scale. Source data are provided as a Source Data file.
