I am looking for links to similar studies that I can learn from, for questions that I should consider answering, and bioinformatic analysis I should / could conduct in order to help answer a question. I realize these kinds of posts are looked down upon by this community because it might look like I want you guys to solve my problem, but I have limited access to bioinformatic mentors at my institute and as the only computational biologist in my lab, I am only one view, and I have hit a wall on how to continue moving forward on my project.
The details:
I have ChIP data on a transcription factor that I identified to be found in intergenic regions. After overlaying this TF with a broad range of histone markers, I learned that a large subset of these intergenic TF peaks correlated nicely with known enhancer markers. I annotated these enhancer regions to their nearest gene (side question: Is there a more sophisticated method for associating enhancers to genes?).
I obtained some GRO-seq data from another lab in my cell line, and I am now interested in determining whether there is any relationship / correlation between eRNA activity in my enhancer regions and their associated gene transcription activity.
Preliminary analysis shows me that the majority of the associated genes are active, and only a small subset of enhancer regions show transcriptional activity (which I am assuming are eRNA's). I don't visually see any higher amounts of expression at genes that are associated with enhancers that show transcriptional activity.
What other analysis could I run to determine whether their is a relationship here, or not? What other wet lab studies should be conducted to identify if my TF actually has an effect on the associated gene and to what affect (RNA-seq, ChIP-seq of KO's of my TF?). I am more interested in papers that attempt to associated enhancers with associated genes.
Any and all help is appreciated.
PS: If this post is not allowed, please feel free to close.
