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Fig. 4 | Biology of Sex Differences

Fig. 4

From: Sex differences in the transcriptome of extracellular vesicles secreted by fetal neural stem cells and effects of chronic alcohol exposure

Fig. 4

WCGNA-based Comparisons of the RNA Content of EVs Relative to Parental NSCs. WGCNA of RNA transcripts expressed in all 36 samples, shows that EVs contain a distinct set of gene networks compared to and their parent NSCs. Correlations with the trait of ‘Location’ (EV vs. cell) contributed to the majority of the difference between clusters. Other traits including ‘Pregnancy’ (NSCs derived from three separate pregnancies) and ‘Sex’ (female or male fetal sex) were smaller, but also significant contributors to the overall composition of identified networks. A Topological overlap matrix (TOM) plot for visualizing the weighted gene co-expression network, where the topological overlap considers each pair of genes’ similarity in relation to all other genes in the network. Modules are defined by hierarchical clustering, visualized by dendrograms and module color notation. Each row or column corresponds to a single gene, where lighter red denotes low topological overlap and darker red denotes high topological overlap. The grey module represents residual genes that could not be associated with networks. B Multidimensional Scaling (MDS) plot where each point represents a gene transcript. The distances between any two pair of points is a measure of the dissimilarity between those two genes. As visualized, blue and tan and brown module transcripts (enriched in cells) segregate from each other, and also from all other modules (EV-enriched modules). C Module eigengene (ME) dendrogram as a measurement of dissimilarity between MEs (1st principal component), showing that ME brown, ME blue, and ME tan are separated from the rest of the MEs. D Relationship between WGCNA modules and external sample traits of ‘Location’, ‘Pregnancy’ and ‘Sex’. Each row depicts a module eigengene (ME), identified by a unique module color identity, with sample traits arranged across columns. Numbers in the table correspond to the correlation coefficients between the ME and the specific trait, with p-value in parentheses. The strength and direction of the correlation is illustrated by the color legend, with red depicting positive and blue depicting negative correlation with a numerically encoded trait. The color intensity indicates the strength of the correlation. This analysis shows that ‘Location’ (EV vs. cell) is the most important determinant of module identity, with the brown, blue, and tan modules identifying cells, and the majority of the other modules identifying EVs. However, some modules also exhibit moderate but statistically significant correlations with the traits of ‘Pregnancy’ and ‘Sex’. E Bar plot of ‘Location’ (EV vs. cell) trait-based module significance (average gene significance in a module) across modules. Gene Significance (GS) is a measure biologically significant a given gene is to a sample trait, and module significance is calculated from the average gene significance of all genes in a module in relation to a phenotypic trait of ‘Location’

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