pathways differential expression analysis with KO

[Francy87]

Hello!
I assigne K0 onthology to my genes from bacteria metatranscriptome. Now I'd like to carry out a differential expression analysis. Obviously, the same K0 can be involved in multiple pathways and metabolisms.
How do you deal with this in pathway analysis? I mean, if I want to test if I have enrichment of certain pathways or metabolisms, how should I consider each gene (belonging to which pathway or metabolism)?
sorry for the basic question, but I'm really newbie!

Thanks

[bigmw]

You can use gage to do the pathway analysis and visualize the results using pathview. Both packages work with KO (KEGG Orthology) and 3000 KEGG species. For example, you may generate KO pathway gene sets using kegg.gsets function from gage. Please check out the documentation for more details:

http://bioconductor.org/packages/release/bioc/html/gage.html

http://bioconductor.org/packages/release/bioc/html/pathview.html