Genes were ranked according to fold change in NEAT1 ASO-treated cells versus control ASO-treated cells and used as input for a pre-ranked GSEA using gene sets from the KEGG and Gene Ontology Molecular Function collections. Significant gene sets were selected based on an FDR < 0.25, a cutoff commonly applied for gene set discovery. Significant channel gene sets (n = 3) were subsequently analyzed in KCl-stimulated versus unstimulated neurons. Significance of these gene sets was evaluated based on FDR < 0.05. Specific genes included in significant gene sets are shown in Supplementary Table 3. The x-axis (Fig. 3b,c) shows all genes that are expressed in the samples, ranked from positive to negative fold change (i.e. most up-regulated to most down-regulated). The color-coding along the x-axis corresponds to the value of the fold change (ranging from red, up-regulated, over white to blue, down-regulated). The vertical bars indicate the position of the genes from the respective channel gene sets in the ranked list of genes along the x-axis. Based on these positions, an enrichment score and FDR-value are calculated to evaluate whether the genes in the gene set are enriched among the up- or down-regulated genes.
