How to compare the differentially expressed genes between two species?

Question

[mgab]

For instance, I would like to compare pathway and functional enrichment studies from differentially expressed genes in humans and drosophila. Drosophila and Humans have different gene names. Thanks.

[Jean-Karim Heriche]

If I understand correctly, your problem is to map human and Drosophila genes to each other. If so, the proper way to do this is to look at orthology relationships. This is available for example from EnsEMBL.