Fig. 3

Enrichment summary for the difference in ranks. A Pipeline for gene set enrichment analysis with GSEAPY preranked. Only genes with sufficient reads in the human-chimpanzee cortical organoid dataset and a sufficient number of samples in GTEx were included (see the “ Methods” section), leaving approximately 10,000 genes in the list used for enrichment analysis. B Summary of GO molecular function enrichments across all time points with false discovery rate (FDR) < 0.05. REVIGO in conjunction with a custom python script was used to generate the plot [33]. The axes are derived from multidimensional scaling and measure semantic similarity, enabling the removal of redundant GO terms and visualization of the similarity between GO categories. Each circle represents a GO term and circles near each other contain similar genes in the corresponding gene set. Labeled gene sets are generally those with the lowest FDR in a cluster of terms on the plot or those highlighted in the text. The size of the circles indicates the number of genes that are driving the enrichment for that category. C Summary of GO cellular component enrichments across all time points with FDR < 0.05