Question: Pathway enrichment in bacteria metagenomes
gravatar for francesca.defilippis
3.9 years ago by
European Union
francesca.defilippis40 wrote:


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?



ADD COMMENTlink modified 3.9 years ago by Luo Weijun1.4k • written 3.9 years ago by francesca.defilippis40
gravatar for Luo Weijun
3.9 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:

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:

ADD COMMENTlink written 3.9 years ago by Luo Weijun1.4k

Hi! Thanks for your reply! I didn't understand one thing: how to deal with KO  belonging to different pathways? I mean, of course each KO can belong to different pathways and metabolisms. How do I need to treat them? For example, if I want to do a heatplot at different kegg hierarchy levels , how do I deal with KO belonging both to carbohydrates or protein metabolisms?

ADD REPLYlink written 3.9 years ago by francesca.defilippis40
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