I am doing a job of post-GWAS analysis, and i have obtained an important gene set containing about 200 genes.
i want to give some detailed analysis to explain the relationship between genes and disease from pathway level.
traditianal analysis always use gene enrichment to look those important genes overlaped in KEGG database, then elucidate the importance of these enriched pathways. (Because i am not very good at pathway level analysis, i think it is too superficial to deal with the gene set i collected. Maybe there is any other better or deeper method to deal with these genes from pathway level? (not to construct a method.)
- could you offer me some suggestions? or some related references to deal with?
- And beside pathway level analysis, any ideas for dealing with this gene set in order to connect genes to disease? it will be very appreciate of you for offering the ideas!
And another question is i get some pathways from enrichment is KEGG. But i do not know whether the pathways i get is really harmful to the disease. So how can i confirm or validate the primary results? my idea is to look at pubmed using those pathway names as critical words?
Thank you !@@