How to study transposable elements expression relationship with its closest gene?

Question

[fernandogs97]

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.

Answer 1

[kalavattam]

Hi fernandogs97,

Given your questions, it might be useful to take a look at this publication, e.g., Figure 1g (we assigned significance with Mann Whitney U tests). These are general analyses and don't look at specific TEs, but it could be a good start.

Regarding more specific analyses, I think the analyses performed with this program could be worth looking into (same with its associated publication). It uses an LR model to predict associations between expressed TEs and adjacent genes.

Best of luck with your project, Kris

[fernandogs97]

Thank you very much!!!

Answer 2

[fernandogs97]

Finally for me the best way of perfoming this analysis was to use the package RegineR (just if anyone see this some day)