Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Kelley D., Rinn J., Genome Biology, 2012.
There are a lot of papers on the subject. It is widely accepted now that TEs play a significant role in modifying gene expression and regulatory networks. One of the best examples (in plants) is from rice (Naito et al. 2009, Nature):
There are some quantitative estimates of expression change due to insertion in that paper, and those analyses may give you some ideas. The specific mechanisms will vary by taxa though, so keep that in mind. For example, retrotransposons are ubiquitous in human genes but plant genomes seem to be less tolerant of large insertions into genes. I suggest you start with a review and see where that takes you. Here are a couple that may be helpful: