Hi everyone,
I have run CAFE and got a list of gene families that got rapidly evolved (expanded & contracted) during evolution, and the next step is to interpret their function. I think I could perform a GO enrichment analysis on the genes from the families that got a rapid expansion but I'm not sure what to be the background for the enrichment. The problem got worse when checking those families that got contracted since genes in the families may go extinct.
Could I infer the ancestral genes based on the CAFE's result, then perform the analysis based on ancestral genes? Or I shouldn't perform GO enrichment here, and if so, what should I do to make a summary of these families since there are hundreds of genes from dozens of families?
Best, Yang
I am also interested in this issue and I would like to ask how you solved it ? My idea is to reconstruct the ancestral coding genes and then use this as a background gene set for GO enrichment analysis. Do you have any suggestions?
Yawen