User Wayne N. Frankel's email:
Can you implement a way to analyze pathways (e.g. GO) that pits one gene set against another and/or allows you to select the ‘up’ (or ‘down’) genes separately? It can be very useful to test one treatment of ‘up’ genes (which typically represent unique sets of pathways or GO terms) against a different treatment of ‘up’ genes (or down vs. down). MGI has had a tool (listed under their “Prototype tools” but it has been available for a long time) called VLAD that does this with a nice visual. It can be very powerful for teasing out meaningful differences especially in pathway/GO sets.
User Wayne N. Frankel's email:
Can you implement a way to analyze pathways (e.g. GO) that pits one gene set against another and/or allows you to select the ‘up’ (or ‘down’) genes separately? It can be very useful to test one treatment of ‘up’ genes (which typically represent unique sets of pathways or GO terms) against a different treatment of ‘up’ genes (or down vs. down). MGI has had a tool (listed under their “Prototype tools” but it has been available for a long time) called VLAD that does this with a nice visual. It can be very powerful for teasing out meaningful differences especially in pathway/GO sets.