Hello!

i'm analysing gut metagenome samples. 

I used DeSeq2 to obtain a list of differentially expressed genes. I'd like to explore if an enrichment in specific pathways is present. I have both KO and eggNog IDs of the genes. Is there a tool to get the pathway they belonging to and explore for up or downregulation of specific pathways?

thanks

francesca

You can use gage to do the pathway analysis and visualize the results using pathview. Particularly, both packages work with KO (KEGG Orthology) and all 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