Gene sets databases

[hnsaghire]

Hello Jesse, 

Many of the gene sets are overlapping between different databases like cell cycle can be found in GO and Reactome. But certain databases contain certain gene sets that are not in the others. My question is: it is necessary to limit our analysis to one database or we can use more than one? 

Kind regards

Hussein

[hnsaghire]

Hi Hussain,

Great question - that's exactly the value of EGAN.  Instead of just looking at tables and p-values of gene set enrichment, EGAN shows how different gene sets from different databases overlap and relate with respect to different genes from your significant set.  Knowing how different databases represent biomolecular concepts/pathways with different sets of genes is very important.

Can I ask a favor from you?  Can you post your question to the Google Group?  I'd like it (and the answer) to be available for other people to read publicly.  It's asked quite often.

Best,

Jesse

[ucsf egan]

For example, what genes are in the WNT Pathway?

http://akt.ucsf.edu/EGAN/images/screenshots/EGAN_screenshot_gene_set_ambiguity.png