I just finished the first phase of my project where I characterized alternatively spliced and differentially expressed genes in two different populations of people with a certain disease*. Now, there are two main avenues of exploration that I would like to go through.
I want to perform an analysis to see whether a gene that is alternatively spliced at the gene level can cause differential expression of other genes that are involved in the same pathway as that gene.
I also want to analyze the differentially expressed genes to see if they have any common motifs in their regulatory regions that are highly expressed (mainly want to understand if there is a transcription factor or a set of transcription factors that are common among these genes).
Any tips or pointers in the right direction on how to go about solving this problem will be greatly appreciated :)
*It is well-established that this disease affects one group more than the other, so I am trying to understand why that is the case.