Fig. 3
MA-plot of genome-wide gene expression data. MA-plot (Bland-Altman plot) for visual representation of both absolute expression intensity of each gene and differences in expression of each gene between somatic and reproductive cells. Each point in this two-dimensional plot shows the relationship between two sets of data: M-values (Y-axis) represent the log2 fold difference in expression intensity of a given gene between the two cell types (somatic versus reproductive cells), and A-values (X-axis) represent the absolute intensity of expression (mean of normalized counts) of the same gene in logarithmic scale. Genes with positive M-values show higher expression in somatic cells compared to the other cell type (yellow arrow) and genes with negative M-values show higher expression in reproductive cells compared to the other cell type (green arrow). The test for differential expression was based on DEseq calculations [54] and Benjamini–Hochberg multiple testing adjustment [145]. The false discovery rate value was set to q = 0.1. Points in red color refer to genes with significant differential expression (fold difference in expression ≥ 2 and P adjusted ≤ 0.05), whereas black points refer to genes without significance regarding differential expression. An average baseMean expression value greater than 12.5 was sufficient for robust expression analysis (cutoff at 12.5). Blue lines indicate, for each cell type, both the top 100 most overexpressed genes compared to the other cell type and genes with a more than 30-fold difference in expression intensity compared to the other cell type. Blue, dotted circles indicate accumulations of functionally related genes