Suggestions for Pathway Level Analysis of Alternatively Spliced and Differentially Expressed Genes.

Question

[Sai Prasada]

Hi,

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.

1. 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.

2. 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.

Answer 1

[KoppesEA]

For Part 1 that sounds like a fit for IPA pathway analysis or just a literature search if just a few candidates.

For part 2: If you are looking for motifs that are enriched in the promoters of your DEGs, I really like the Enrichr tool (https://maayanlab.cloud/Enrichr/), its easy to use just plug in your list as gene symbols and it will give you both gene ontology and transcription factor binding site enrichment based on different databases like JASPAR and ENCODE. Then look at how your genes and potential regulatory TFs cluster. There are other ways using MEME suite DREME (https://meme-suite.org/meme/) that can also give you a more unbiased or discovery type approach.