Hello, I would like to post a question about an analysis that I need to do for my project. In my project we are studying the deregulation of transposable elements and genes with RNA-seq. We have obtained deregulated genes and transposable elements under various conditions. We are currently interested in analyzing whether the deregulation of transposable elements could alter the expression of nearby genes. It seems that a widely used tool to obtain the genes close to a transposable element is bedtools closest tool, but I cannot find a consistent methodology to analyze whether the relationship between the deregulation of these elements is statistically significant. Do you know of studies in which similar analyzes have been made? Can you give me any advice on how to perform this analysis? Thanks to everyone who can help.