RNA-seq DEGs downstream analysis and reporting in literature

Question

[Ankur B. Sharma]

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently taking one gene at a time and googling if someone has shown its role for something similar to my research topic. My question is, how do I filter important genes from unimportant ones (like olfactory receptors, immunology related, and predicted genes)? How do you guys do it? Please give valuable suggestions.

Answer 1

[i.sudbery]

If you are just hypothesis generating - that is looking for genes important in your disease/condition/developmental stage etc, then there isn't really a better approach than what you are doing. That kind of work either takes a deep knowledge of the systems you are working with, or a long time reading.

The alternative is to define some more directed questions that just looking for important genes, devising tests of those hypotheses, and applying the data to test those hypotheses (or designing further experiments to do so).