Fig. 3
Expression and statistical analysis of TEs predicted both by SQuIRE and TEcandidates. A. Heatmap of log2(normalized counts) of selected TEs. At the top of the heatmap, the housekeeping gene β-actin is shown as a reference. The heatmap was divided into genic TEs (overlapping genes) and intergenic TEs (not overlapping genes). B. Class distribution of genic TEs and intergenic TEs that explain changes in gene expression with statistical significance (p ≤ 0.05). C. Two plot examples of Gene vs TE log2(normalized counts), sorted by stage (i.e., from left to right, each point shows the gene and the TE normalized count at E14.5, E16.5, and so on). Each plot shows the R coefficient of correlation, and its corresponding p-value, and in blue, the regression line. The left plot shows an example of a positive correlation, and the right plot an example of a negative correlation