Fig. 3
Differential Gene Expression and Pathway Overrepresentation Analysis. A Principal component analysis was performed on the 500 most variant RNA transcripts from 18 NSC parental cell samples and their corresponding 18 EV samples. This analysis shows that the samples could be segregated with the 1st principal component, by the sample trait of ‘Location’ (whether the RNA transcripts were from EV or cell sample). B Volcano plot of log2 fold change and − log10 p-value of all genes differentially expressed in EV samples vs. their parental cell samples (EV, n = 18; Cell n = 18). C Dot plot depicting pathway overrepresentation (based on ReactomePA) for significantly altered genes (adjusted p < 0.05) enriched in EV samples relative to their parental cell samples. D Dot plot depicting pathways related to significantly altered genes (adjusted p < 0.05) enriched in cell samples relative to their derived EV samples. Each plot presents overrepresented pathways, ordered by gene ratio, i.e., the proportion of differentially expressed genes/transcripts within an ontology term. The size of each dot denotes the number of genes/transcripts in a pathway that were contained within this dataset, while the color of each dot encodes the Benjamini and Hochberg-adjusted p-value for significance of pathway overrepresentation. n = 18 EV samples, 18 cell samples. E, F Graphical representation of the relationship between enriched pathways and their associated genes/transcripts. Significantly altered genes (adjusted p < 0.05) were selected for this analysis. Pathways that reached a Benjamini–Hochberg false discovery rate-adjusted p value criterion of < 0.05 were selected. The size of each filled central circle represents the number of transcripts in a pathway that were overexpressed in EVs (E) or in cells (F). The color of each dot associated with that pathway denotes the fold change for that transcript in EVs relative to parental cells