Fig. 4

RNA-seq identifies multiple pathways that are altered across HD astrocyte differentiation. Top ten KEGG pathways reported from GO analyses of DE genes at the PSC (a), NPC (b), day 3 (c), and astrocyte (d) stages. Pathways are ranked by −log10(q value), determined by Benjamini–Hochberg procedures, with threshold set to q < 0.05. Line graphs show the ratio of DE genes in each KEGG pathway. e DE genes at any stage show overlap with the KEGG Huntington’s Disease pathway. f Huntington’s disease pathway showing DE genes (in purple) in HD cells at any stage of astrocyte differentiation. g Bar plot depicting the enrichment scores of the top 9 most enriched gene sets, which comprise 6 functional categories. Negative enrichment scores (left; blue) reflect HD-depleted gene sets, and positive enrichment scores (right; red) represent HD-enriched gene sets. NPC GSEA results are shown in purple and astrocyte GSEA results are shown in orange